diff --git a/Bugs/BUGTRAX b/Bugs/BUGTRAX
index e664c9e7..5fad5845 100644
--- a/Bugs/BUGTRAX
+++ b/Bugs/BUGTRAX
@@ -1342,6 +1342,9 @@ an optimally accurate parsetree, if it's not a legal local begin
state, then don't allow a local begin.
//
+####
+#### 1.1.1 release: 23 July 2014
+####
ID i44
TITLE cmalign --mapstr allows broken basepairs
@@ -1374,3 +1377,6 @@ checks that both a broken non-pseudoknotted basepair and a
pseudoknotted broken basepair are both correctly removed.
//
+####
+#### 1.1.2 release: June 2014
+####
diff --git a/COPYRIGHT b/COPYRIGHT
deleted file mode 100644
index 5908a64b..00000000
--- a/COPYRIGHT
+++ /dev/null
@@ -1,46 +0,0 @@
-Infernal - inference of RNA secondary structural alignments
-@INFERNAL_COPYRIGHT@
-------------------------------------------------------------------
-
-Copyright (C) 2013 HHMI Janelia Farm Research Campus
-
- Portions Copyright (C) 1991-2013 Sean R. Eddy
- Portions Copyright (C) 2005-2013 Eric P. Nawrocki
- Portions Copyright (C) 2005-2011 Diana L. Kolbe
- Portions Copyright (C) 2004 Zasha Weinberg
- Portions Copyright (C) 1990 Don G. Gilbert
- Portions Copyright (C) 1995-2006 Washington University in St. Louis
- Portions Copyright (C) 1992-1995 Medical Research Council, UK
- Portions Copyright (C) 2004 University of Washington, Seattle
- Portions Copyright (C) 1986,1993,1995 University of Toronto
- Portions Copyright (C) 1989-2001 Free Software Foundation
- Portions Copyright (C) 1991 Massachusetts Institute of Technology
-
-Infernal includes the HMMER software package, which has its own license and
-copyright information. See hmmer/COPYRIGHT and hmmer/LICENSE.
-
-Infernal uses the Easel software library, which has its own license and
-copyright information. See easel/COPYRIGHT and easel/LICENSE.
-
-Infernal is distributed under the terms of the GNU General Public
-License version 3 (GPLv3). See the file LICENSE for details.
-
-This program is free software: you can redistribute it and/or modify
-it under the terms of the GNU General Public License as published by
-the Free Software Foundation, either version 3 of the License, or (at
-your option) any later version.
-
-This program is distributed in the hope that it will be useful,
-but WITHOUT ANY WARRANTY; without even the implied warranty of
-MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-GNU General Public License for more details.
-
-A copy of the GNU General Public License is in the file LICENSE. You
-may also obtain a copy from .
-
-------------------------------------------------------------------
-The Infernal development team
-HHMI Janelia Farm Research Campus
-http://infernal.janelia.org/
-
-
diff --git a/INSTALL b/INSTALL
index aa7bf5d6..2e2b6e10 100644
--- a/INSTALL
+++ b/INSTALL
@@ -30,20 +30,33 @@ instruction sets, you won’t be able to install and run Infernal 1.1 on
it.
-------------------------------------------------------------
-Starting from a Subversion (SVN) working copy:
+Starting from a Git Repo:
-If you have checked Infernal out from its Subversion repository, there's
+If you have cloned the Infernal Git repository, there's
some additional stuff you need to do one-time-only in your new working
-directory:
+directory.
+First you need to clone easel and hmmer too:
+ cd infernal
+ git clone https://github.com/EddyRivasLab/easel.git
+ git clone https://github.com/EddyRivasLab/hmmer.git
+
+And switch to the h3-master branch:
+ cd hmmer
+ git checkout h3-master
+
+You may want to switch to the 'develop' branch of infernal, the
+'h3-develop' branch of hmmer and the 'develop' branch of easel if you
+want the in-development code.
+
+And finally:
ln -s easel/aclocal.m4 aclocal.m4
- ln -s easel/aclocal.m4 hmmer/aclocal.m4
+ (cd hmmer; ln -s ../easel/aclocal.m4 aclocal.m4;)
autoconf
(cd easel; autoconf; cd ../hmmer; autoconf;)
-------------------------------------------------------------
The Infernal development team
-HHMI Janelia Farm Research Campus
-http://infernal.janelia.org/
-
+github.com/EddyRivasLab/infernal/
+http://eddylab.org/infernal
diff --git a/LICENSE b/LICENSE
index 9cc2a8cc..5f6b2993 100644
--- a/LICENSE
+++ b/LICENSE
@@ -1,6 +1,6 @@
Infernal - inference of RNA secondary structural alignments
@INFERNAL_COPYRIGHT@
-Copyright (C) 1991-2013 Sean R. Eddy
+Copyright (C) 1991-2016 Sean R. Eddy
Copyright (C) 2005-2016 Eric P. Nawrocki
Copyright (C) 2005-2011 Diana L. Kolbe
Copyright (C) 2004 Zasha Weinberg
diff --git a/README b/README
index c5a7522a..aebf22de 100644
--- a/README
+++ b/README
@@ -1,5 +1,6 @@
Infernal - inference of RNA secondary structure alignments
-http://infernal.janelia.org/
+http://eddylab.org/infernal/
+
Version @INFERNAL_VERSION@; @INFERNAL_DATE@
@INFERNAL_COPYRIGHT@
------------------------------------------------------------------
@@ -14,14 +15,13 @@ more homologs of your RNAs (the "cmsearch" program). You can also use
a CM of a representative alignment of your sequence family to create a
larger consensus alignment of any number of RNAs (the "cmalign"
program). Infernal is the software engine underlying the Rfam RNA
-database (http://rfam.janelia.org).
+database (http://rfam.xfam.org/).
Other files to read in the top-level source directory:
INSTALL Brief installation instructions.
Userguide.pdf The Infernal User's Guide.
- COPYRIGHT Copyright and license information.
- LICENSE The GNU General Public License (GPLv3).
+ LICENSE copyright and license information
To get started after installation, see the Tutorial section in the
Infernal User's Guide (Userguide.pdf).
@@ -29,8 +29,5 @@ Infernal User's Guide (Userguide.pdf).
-------------------------------------------------------------------
The Infernal development team
-HHMI Janelia Farm Research Campus
-http://infernal.janelia.org/
-
-
-
+github.com/EddyRivasLab/infernal/
+http://eddylab.org/infernal
diff --git a/configure.ac b/configure.ac
index 34e79da1..593bf42d 100644
--- a/configure.ac
+++ b/configure.ac
@@ -44,7 +44,7 @@
# Autoconf 2.61 has a bug in AC_FUNC_FSEEKO; don't use it.
AC_PREREQ(2.63)
-AC_INIT(Infernal, 1.1.1x, eric.nawrocki@nih.gov, infernal)
+AC_INIT(Infernal, 1.1.2, eric.nawrocki@nih.gov, infernal)
AC_MSG_NOTICE([Configuring Infernal for your system.])
# remember if the user is overriding CFLAGS
@@ -58,7 +58,7 @@ fi
# The four AC_INIT args set these output variables and preprocessor symbols:
# PACKAGE_NAME e.g. "Infernal"
# PACKAGE_VERSION e.g. "1.0"
-# PACKAGE_BUGREPORT e.g. "eddys@janelia.hhmi.org"
+# PACKAGE_BUGREPORT e.g. "eric.nawrocki@nih.gov"
# PACKAGE_TARNAME e.g. "infernal"
# From them, it derives one more:
# PACKAGE_STRING , e.g. "Infernal 1.0"
@@ -73,27 +73,27 @@ fi
#
################################################################
-INFERNAL_DATE="May 2016"
+INFERNAL_DATE="July 2016"
INFERNAL_COPYRIGHT="Copyright (C) 2016 Howard Hughes Medical Institute."
INFERNAL_LICENSE="Freely distributed under a BSD open source license."
INFERNAL_VERSION=$PACKAGE_VERSION
-INFERNAL_URL="http://infernal.janelia.org/"
+INFERNAL_URL="http://eddylab.org/infernal/"
INFERNAL_ESLDIR="easel"
INFERNAL_HMMERDIR="hmmer"
INFERNAL_SADIR="hmmer/libdivsufsort"
-HMMER_DATE="May 2016"
+HMMER_DATE="July 2016"
HMMER_COPYRIGHT="Copyright (C) 2016 Howard Hughes Medical Institute."
HMMER_LICENSE="Freely distributed under a BSD open source licence."
-HMMER_VERSION=i$PACKAGE_VERSION
+HMMER_VERSION="3.1b3"
HMMER_URL="http://hmmer.org/"
HMMER_ESLDIR="../easel"
HMMER_SADIR="libdivsufsort"
-EASEL_DATE="July 2014"
+EASEL_DATE="July 2016"
EASEL_COPYRIGHT="Copyright (C) 2016 Howard Hughes Medical Institute"
EASEL_LICENSE="Freely distributed under a BSD open source license."
-EASEL_VERSION="i$PACKAGE_VERSION"
+EASEL_VERSION="0.43"
EASEL_URL="http://bioeasel.org/"
# Output variables (AC_OUTPUT replaces @var@ in input files, such as Makefiles)
@@ -333,17 +333,17 @@ if test "$impl_choice" = "none"; then
fi
if test "$impl_choice" = "none"; then
- AC_MSG_WARN([Infernal 1.1.1 requires VMX or SSE capability for parallel instructions.])
+ AC_MSG_WARN([Infernal 1.1.2 requires VMX or SSE capability for parallel instructions.])
AC_MSG_ERROR([It appears your platform has neither and will not support Infernal.])
fi
if test "$impl_choice" = "sse" && test "$enable_sse" = "no"; then
- AC_MSG_WARN([Infernal 1.1.1 requires VMX or SSE capability for parallel instructions.])
+ AC_MSG_WARN([Infernal 1.1.2 requires VMX or SSE capability for parallel instructions.])
AC_MSG_WARN([Your platform supports only SSE, but you have disabled it.])
AC_MSG_ERROR([You must reconfigure without disabling SSE for Infernal to build.])
fi
if test "$impl_choice" = "vmx" && test "$enable_vmx" = "no"; then
- AC_MSG_WARN([Infernal 1.1.1 requires VMX or SSE capability for parallel instructions.])
+ AC_MSG_WARN([Infernal 1.1.2 requires VMX or SSE capability for parallel instructions.])
AC_MSG_WARN([Your platform supports only VMX, but you have disabled it.])
AC_MSG_ERROR([You must reconfigure without disabling VMX for Infernal to build.])
fi
@@ -555,7 +555,7 @@ vmx) AC_MSG_NOTICE([Activating Altivec/VMX optimized DP implementation])
INFERNAL_IMPLDIR=""
;;
-*) AC_MSG_WARN([Infernal 1.1.1 requires VMX or SSE capability for parallel instructions.])
+*) AC_MSG_WARN([Infernal 1.1.2 requires VMX or SSE capability for parallel instructions.])
AC_MSG_ERROR([Unable to use vector instructions (SSE or VMX).])
;;
esac
@@ -594,6 +594,10 @@ AC_SUBST(LIBGSL)
# anyway according to Sean. We still need to define LIBGSL though, because Easel
# has files with @LIBGSL@ in them.
+# Easel stopwatch high-res timer may try to use clock_gettime,
+# which may be in librt
+AC_SEARCH_LIBS(clock_gettime, [rt posix4])
+
# Checks for headers
# Defines HAVE_SYS_TYPES_H, HAVE_STDINT_H, etc.
AC_CHECK_HEADERS([ \
diff --git a/documentation/manpages/cmscan.man b/documentation/manpages/cmscan.man
index 66703709..cde06298 100644
--- a/documentation/manpages/cmscan.man
+++ b/documentation/manpages/cmscan.man
@@ -65,7 +65,11 @@ The output format is designed to be human-readable, but is often so
voluminous that reading it is impractical, and parsing it is a pain. The
.B --tblout
option saves output in a simple tabular format that is concise and
-easier to parse.
+easier to parse. The
+.BI --fmt " 2"
+option modifies the format of the tabular output by adding several
+fields, including markup of overlapping hits, as described in section
+6 of the Infernal user guide.
The
.B -o
option allows redirecting the main output, including throwing it away
@@ -172,7 +176,27 @@ instead of the default stdout.
.BI --tblout " "
Save a simple tabular (space-delimited) file summarizing the
hits found, with one data line per hit.
-The format of this file is described in the Infernal user guide.
+The format of this file is described in section 6 of the Infernal user guide.
+
+.TP
+.BI --fmt " "
+specify the format of the tabular output file specified with
+.BI --tblout " "
+be in format
+.I .
+Possible values for
+.I
+are 1 or 2. By default
+.I
+is 1 when
+.B --tblout
+is used without
+.B --fmt.
+With
+.BI --fmt " 2"
+nine additional fields are added to the tabular output file, most of
+which pertain to the annotation of overlapping hits.
+See section 6 the Infernal user guide for a description of both formats.
.TP
.B --acc
@@ -297,7 +321,7 @@ that is above all known false positives.
.SH OPTIONS CONTROLLING THE ACCELERATION PIPELINE
.PP
-Infernal 1.1 searches are accelerated in a six-stage
+Infernal searches are accelerated in a six-stage
filter pipeline. The first five stages use a profile HMM to define
envelopes that are passed to the stage six CM CYK filter. Any
envelopes that survive all filters are assigned final scores using the
@@ -561,14 +585,14 @@ megabytes. By default this size is 128 Mb.
This should be large enough for the vast majority of searches,
especially with smaller models.
If
-.B cmsearch
+.B cmscan
encounters an envelope in the CYK or Inside stage that requires a
larger matrix, the envelope will be discounted from
consideration. This behavior is like an additional filter that
prevents expensive (slow) CM DP calculations, but at a potential cost
to sensitivity.
Note that if
-.B cmsearch
+.B cmscan
is being run in
.I
multiple threads on a multicore machine then each thread may
@@ -688,6 +712,56 @@ must list valid names of models from
each separated by any whitespace character (e.g. a newline character).
.TP
+.BI --clanin " "
+Read clan information on the models in
+.I
+from file
+.I .
+Not all models in
+.I
+need to be a member of a clan.
+This option must be used in combination with
+.BI --fmt " 2"
+and
+.B --tblout
+because clan annotation is only output in format 2 of the tabular
+output file.
+See section 9 of the Infernal user guide for specifications on the format of the
+clan input file
+.I .
+
+.TP
+.B --oclan
+Only mark overlaps between models in the same clan.
+This option must be used in combination with
+.BI --fmt " 2"
+,
+.B --tblout
+and
+.B --clanin
+because clan annotation is only output in format 2 of the tabular
+output file, and clan information can only be input using the
+.B --clanin
+option.
+
+.TP
+.BI --oskip " "
+Omit any hit h from the tabular output file that satisifies the
+following: another hit h2 overlaps with h and the E-value of h2 is
+lower than that of h. Hit h will not appear in the tabular output
+file, although it will still exist in the standard output.
+This option must be used in combination with
+.BI --fmt " 2"
+.B --tblout
+because overlap annotation is only output in format 2 of the tabular
+output file.
+When used in combination with
+.B "--oclan"
+only hits h that satisfy the following are omitted:
+another hit h2 overlaps with h, the E-value of h2 is lower than that
+of h, and both h and h2 are hits to models that are in the same clan.
+
+.TP
.BI --cpu " "
Set the number of parallel worker threads to
.I .
diff --git a/documentation/manpages/cmsearch.man b/documentation/manpages/cmsearch.man
index 59b50629..04bfebae 100644
--- a/documentation/manpages/cmsearch.man
+++ b/documentation/manpages/cmsearch.man
@@ -167,7 +167,7 @@ to the file
.BI --tblout " "
Save a simple tabular (space-delimited) file summarizing the
hits found, with one data line per hit. The format of this file is
-described in the Infernal user guide.
+described in section 6 of the Infernal user guide.
.TP
.B --acc
diff --git a/documentation/userguide/Makefile.in b/documentation/userguide/Makefile.in
index 76001000..e26adf78 100644
--- a/documentation/userguide/Makefile.in
+++ b/documentation/userguide/Makefile.in
@@ -41,6 +41,7 @@ MANPAGES = \
TEXFILES =\
cmbuild.tex\
+ copyright.tex\
filter.tex\
format_prior.tex\
formats.tex\
@@ -57,7 +58,7 @@ TEXFILES =\
pdf: Userguide.pdf
-Userguide.pdf: symlinks.stamp titlepage.tex copyright.tex manpages.tex
+Userguide.pdf: symlinks.stamp titlepage.tex manpages.tex
@for prog in pdflatex bibtex; do \
command -v $$prog >/dev/null 2>&1 || { echo >&2 "The $$prog program is required to build the Userguide, but it's not installed. Aborting."; exit 1; } \
done
@@ -83,10 +84,6 @@ titlepage.tex: ${srcdir}/titlepage.tex.in
@cp -f ${srcdir}/titlepage.tex.in titlepage.tex
@${SEDITION} INFERNAL_VERSION ${INFERNAL_VERSION} INFERNAL_DATE ${INFERNAL_DATE} titlepage.tex
-copyright.tex: ${srcdir}/copyright.tex.in
- @cp -f ${srcdir}/copyright.tex.in copyright.tex
- @${SEDITION} INFERNAL_COPYRIGHT ${INFERNAL_COPYRIGHT} copyright.tex
-
# manpages: convert man pages to LaTeX chapter in User Guide.
# uses PolyglotMan 3.2 "rman", and rmanprocess.pl script in easel's devkit
manpages.tex: ${MANPAGES}
@@ -114,7 +111,7 @@ distclean: clean
done ;\
fi
-rm -f symlinks.stamp
- -rm -f titlepage.tex copyright.tex manpages.tex
+ -rm -f titlepage.tex manpages.tex
-rm -f Userguide.pdf
-rm -f Makefile
diff --git a/documentation/userguide/ack.tex b/documentation/userguide/ack.tex
index 3fde3a53..4a6cacb5 100644
--- a/documentation/userguide/ack.tex
+++ b/documentation/userguide/ack.tex
@@ -34,9 +34,8 @@ \section{Acknowledgements}
Infernal testing requires \emph{a lot} of compute power, and we are
extremely fortunate to have access to a highly reliable and
-state-of-the-art computing cluster, thanks to Goran Ceric, Rob Lines,
-Peter Bukowinski, Ken Carlile, Patrick Yeboah, and others here at
-Janelia.
+state-of-the-art computing cluster, thanks to Jesse Becker, Ron
+Patterson and others at NCBI.
Infernal is primarily developed on GNU/Linux and Apple Macintosh
machines, but is tested on a variety of hardware. Over the years,
diff --git a/documentation/userguide/cmbuild.tex b/documentation/userguide/cmbuild.tex
index af540187..a1cb86f6 100644
--- a/documentation/userguide/cmbuild.tex
+++ b/documentation/userguide/cmbuild.tex
@@ -524,9 +524,7 @@ \subsubsection{Architecture construction}
an insertion. Importantly though this frequency is determined using
the relative weights from the sequence weighting step, instead of
absolute gaps (e.g. a residue in a sequence with weight $0.8$ will count
-as $0.8$ residues)\footnote{This behavior is new in Infernal 1.1, in all
-previous versions of Infernal, absolute weights, not relative weights
-were used at this step.}.
+ as $0.8$ residues).
The threshold defaults to 0.5. It can be changed to another number
\otext{} (from 0 to 1.0) by the \prog{--symfrac } option. The
diff --git a/documentation/userguide/copyright.tex b/documentation/userguide/copyright.tex
new file mode 100644
index 00000000..e69de29b
diff --git a/documentation/userguide/copyright.tex.in b/documentation/userguide/copyright.tex.in
deleted file mode 100644
index fbeaa3e2..00000000
--- a/documentation/userguide/copyright.tex.in
+++ /dev/null
@@ -1,18 +0,0 @@
-\vspace*{\fill}
-\begin{flushleft}
-@INFERNAL_COPYRIGHT@\vspace{5mm}
-
-\vspace{5mm}
-Permission is granted to make and distribute verbatim copies of this
-manual provided the copyright notice and this permission notice are
-retained on all copies.\vspace{5mm}
-
-\vspace{5mm} Infernal is licensed and freely distributed under the GNU
-General Public License version 3 (GPLv3). For a copy of the License,
-see \url{http://www.gnu.org/licenses/}.
-
-\vspace{5mm}
-\end{flushleft}
-
-
-
diff --git a/documentation/userguide/formats.tex b/documentation/userguide/formats.tex
index d7fa16b4..cc57be46 100644
--- a/documentation/userguide/formats.tex
+++ b/documentation/userguide/formats.tex
@@ -129,9 +129,6 @@ \subsection{Infernal CM files}
The CM format is described in more detail below, followed by a
description of the HMMER3 HMM format for the CM's mandatory filter HMM
filter.
-%The HMM format is similar but is not described in detail here. See the
-%HMMER user guide for more information
-%(\url{http://hmmer.janelia.org}{http://hmmer.janelia.org}).
\subsubsection{CM header section}
@@ -1328,6 +1325,45 @@ \subsection{Null model file format}
fourth non-comment lines are interpreted as the background
probabilities of a ``C'', ``G'' and ``U'' respectively.
+\subsection{Clan input file format for cmscan}
+
+The \ccode{cmscan} program has a \ccode{--clanin } option that
+allows the user to supply an input file \ccode{} with information
+on clan membership for models in the CM file. This option must be used
+in combination with the \ccode{--tblout} and \ccode{--fmt 2}
+options. An example clan input file is included with the Infernal
+source distribution, \ccode{tutorial/Rfam.12.1.clanin}. This file
+specifies the clan membership for the 2474 models in the Rfam 12.1
+release, of which 311 models belong to 104 clans. This file should be
+used in combination with the Rfam.cm file for Rfam 12.1, available for
+download as a gzipped file here:
+\url{ftp://ftp.ebi.ac.uk/pub/databases/Rfam/12.1/Rfam.cm.gz}. Note that
+many of the Rfam models are not members of a clan; the clan input file does
+not need to specify clan membership for all models in the CM file.
+
+A clan input file contains one line per clan. Each line must contain
+at least two space-delimited tokens. The first token is the name of
+the clan (this name cannot contain spaces). Each token after the first
+is the name of a model that is a member of the clan named in the first
+token. These tokens must be valid names of models in the file CM file
+you are using with \ccode{cmscan}. These tokens cannot be the
+accessions of models. Valid model names cannot contain spaces
+(enforced by \prog{cmbuild} during model construction). To determine
+the names of models in a CM file, use \ccode{cmstat}.
+
+For example, in the file \ccode{tutorial/Rfam.12.1.clanin} the first token
+of the first line is ``CL00001'' and tokens two through five are
+``tRNA'', ``cyano\_tmRNA'', ``tRNA-Sec'', ``mt-tmRNA'', indicating
+that these four models are members of the CL00001 clan. \ccode{cmscan}
+will output the clan name of models in clans in its tabular output
+file specified with \ccode{--tblout} when the \ccode{--fmt 2} option
+is also used. Furthermore, you can specify
+that only overlapping hits between models of the same clan are
+annotated (as opposed to all overlapping hits) in the tabular output
+file by additionally using the \ccode{--oclan} option. Finally, you
+can specify that lower scoring overlaps within clans are not output by
+additionally using the \ccode{--oskip} and the \ccode{--oclan}
+options.
diff --git a/documentation/userguide/install.tex b/documentation/userguide/install.tex
index ed5cdeae..26a6ee76 100644
--- a/documentation/userguide/install.tex
+++ b/documentation/userguide/install.tex
@@ -4,14 +4,14 @@ \section{Installation}
\subsection{Quick installation instructions}
-Download \prog{infernal-1.1.1.tar.gz} from \url{http://infernal.janelia.org/}, or
-directly from
-\url{ftp://selab.janelia.org/pub/software/infernal/infernal-1.1.1.tar.gz};
+Download \prog{infernal-1.1.2.tar.gz} from \url{http://eddylab.org/infernal/}, or
+directly from \\
+\url{eddylab.org/infernal/infernal-1.1.2.tar.gz};
unpack it, configure, and make:
-\user{wget ftp://selab.janelia.org/pub/software/infernal/infernal-1.1.1.tar.gz}\\
-\user{tar xf infernal-1.1.1.tar.gz}\\
-\user{cd infernal-1.1.1}\\
+\user{wget eddylab.org/infernal/infernal-1.1.2.tar.gz}\\
+\user{tar xf infernal-1.1.2.tar.gz}\\
+\user{cd infernal-1.1.2}\\
\user{./configure}\\
\user{make}
@@ -77,9 +77,12 @@ \subsection{System requirements}
\paragraph{Compiler:} The source code is C conforming to POSIX and ANSI
C99 standards. It should compile with any ANSI C99 compliant compiler,
-including the GNU C compiler \prog{gcc}. We test the code using both
-the \prog{gcc} and \prog{icc} compilers. We find that \prog{icc}
-produces somewhat faster code at present.
+including the GNU C compiler \prog{gcc}.
+% as of 1.1.2, I don't test on icc anymore:
+We test the code using both
+the \prog{gcc} and \prog{icc} compilers.
+% We find that \prog{icc}
+%produces somewhat faster code at present.
\paragraph{Libraries and other installation requirements:} Infernal includes
two software libraries, HMMER and Easel, which it will automatically
@@ -134,8 +137,7 @@ \subsection{MPI parallelization for clusters is optional}
The \prog{cmalign}, \prog{cmcalibrate}, \prog{cmsearch} and
\prog{cmscan} programs also support MPI (Message Passing Interface)
parallelization on clusters. To use MPI, you first need to have an
-MPI library installed, such as OpenMPI (\url{www.open-mpi.org}). We
-use Intel MPI at Janelia.
+MPI library installed, such as OpenMPI (\url{www.open-mpi.org}).
MPI support is not enabled by default, and it is not compiled into the
precompiled binaries that we supply with Infernal. To enable MPI support
diff --git a/documentation/userguide/introduction.tex b/documentation/userguide/introduction.tex
index 2f90f850..2ebf62ce 100644
--- a/documentation/userguide/introduction.tex
+++ b/documentation/userguide/introduction.tex
@@ -8,7 +8,7 @@ \section{Introduction}
structurally annotated multiple sequence alignment of an RNA family
with a position-specific scoring system for substitutions, insertions,
and deletions. Positions in the profile that are basepaired in the
-consensus secondary structure of the alignment are modeled as
+ h consensus secondary structure of the alignment are modeled as
dependent on one another, allowing Infernal's scoring system to
consider the secondary structure, in addition to the primary sequence,
of the family being modeled. Infernal profiles are probabilistic
@@ -239,7 +239,7 @@ \subsection{How to learn more about CMs and profile HMMs}
book chapters \citep{Eddy06b,NawrockiEddy09}, and a few doctoral
theses \citep{Klein03,Nawrocki09b,Kolbe10} related to
CMs\footnote{Eddy lab publications are available from
-\url{http://selab.janelia.org/publications.html}}. The book
+\url{http://eddylab.org/publications.html}}. The book
\emph{Biological Sequence Analysis: Probabilistic Models of Proteins
and Nucleic Acids} \citep{Durbin98} has several chapters devoted to
HMMs and CMs. Profile HMM filtering for CMs was introduced by Weinberg
@@ -269,7 +269,7 @@ \subsection{How to learn more about CMs and profile HMMs}
searches, EP Nawrocki and SR Eddy. Bioinformatics, 29:2933-2935,
2013.) is the most appropriate paper to cite. If you’re writing for an
enlightened (url-friendly) journal, you may want to cite the webpage
-\url{infernal.janelia.org} because it is kept up-to-date.
+\url{http://eddylab.org/infernal/} because it is kept up-to-date.
\end{srefaq}
diff --git a/documentation/userguide/main.tex b/documentation/userguide/main.tex
index 7b765471..ef73a24a 100644
--- a/documentation/userguide/main.tex
+++ b/documentation/userguide/main.tex
@@ -47,8 +47,9 @@
\newpage
\input{tabular}
-\newpage
-\input{diffoptions}
+% Changes in options between 1.0 and 1.1 are omitted from the 1.1.2 user guide.
+%\newpage
+%\input{diffoptions}
\newpage
\input{more}
diff --git a/documentation/userguide/more.tex b/documentation/userguide/more.tex
index b359667f..2d88894a 100644
--- a/documentation/userguide/more.tex
+++ b/documentation/userguide/more.tex
@@ -12,10 +12,10 @@ \subsection{How do I cite Infernal?}
Bioinformatics, 29:2933-2935, 2013.
The most appropriate citation is to the web site,
-\url{infernal.janelia.org}. You should also cite what version of the
-software you used. We archive all old versions, so anyone should be
-able to obtain the version you used, when exact reproducibility of an
-analysis is an issue.
+\url{http://eddylab.org/infernal/}. You should also cite what version
+of the software you used. We archive all old versions, so anyone
+should be able to obtain the version you used, when exact
+reproducibility of an analysis is an issue.
The version number is in the header of most output files. To see it
quickly, do something like \prog{cmscan -h} to get a help page, and
@@ -23,17 +23,17 @@ \subsection{How do I cite Infernal?}
\begin{sreoutput}
# cmscan :: search sequence(s) against a CM database
-# INFERNAL 1.1.1 (July 2014)
-# Copyright (C) 2014 Howard Hughes Medical Institute.
-# Freely distributed under the GNU General Public License (GPLv3).
+# INFERNAL 1.1.2 (June 2016)
+# Copyright (C) 2016 Howard Hughes Medical Institute.
+# Freely distributed under a BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
\end{sreoutput}
-So (from the second line there) this is from Infernal 1.1.1.
+So (from the second line there) this is from Infernal 1.1.2.
\subsection{How do I report a bug?}
-Email us, at \url{infernal@janelia.hhmi.org}.
+Email us, at \url{sean@eddylab.org}.
Before we can see what needs fixing, we almost always need to
reproduce a bug on one of our machines. This means we want to have a
@@ -131,7 +131,7 @@ \subsubsection{Reading from a stdin pipe using - (dash) as a filename argument}
%note: can't use \user{} here because too many special characters
%(believe me I tried). Only difference between \user{} and the way
-%I've done it below ts that we're not bold, oh well.
+%I've done it below is that we're not bold, oh well.
\indent\indent\small\verb+> cmsearch --tblout tRNA5.mrum-genome.tbl tRNA5.cm mrum-genome.fa+ \\
\indent\indent\small\verb+> esl-sfetch --index mrum-genome.fa+ \\
\indent\indent\small\verb+> cat tRNA5.mrum-genome.tbl | grep -v ^# | grep ! \ + \\
diff --git a/documentation/userguide/tabular.tex b/documentation/userguide/tabular.tex
index 833b9847..ff7e99a3 100644
--- a/documentation/userguide/tabular.tex
+++ b/documentation/userguide/tabular.tex
@@ -2,18 +2,29 @@ \section{Tabular output formats}
\label{section:tabular}
\setcounter{footnote}{0}
-\subsection{The target hits table}
-
-The \ccode{--tblout} output option in \prog{cmscan} and
- \prog{cmsearch} produces the \emph{target hits table}. The target
- hits table consists of one line for each different query/target
- comparison that met the reporting thresholds, ranked by decreasing
- statistical significance (increasing E-value). Each line consists
- of \textbf{18 space-delimited fields} followed by a free text target
- sequence description, as follows:\footnote{The \ccode{tblout} format
- is deliberately space-delimited (rather than tab-delimited) and
- justified into aligned columns, so these files are suitable both for
- automated parsing and for human examination. Tab-delimited data
+\subsection{Target hits tables}
+
+The \ccode{--tblout} output option in \prog{cmsearch} and
+\prog{cmscan} produces \emph{target hits tables}. There are two
+different formats of target hits table, which are both described
+below. By default, both \prog{cmsearch} and \prog{cmscan} produce the
+target hits table in \emph{format 1}. Format 1 is the only format that
+was used by Infernal versions 1.1rc1 through 1.1.1. As of version 1.1.2,
+with \prog{cmscan}, the \ccode{--fmt 2} option can be used in
+combination with \ccode{--tblout} to produce a target hits table in
+the alternative \emph{format 2}. Both formats 1 and 2 target hits
+table consist of one line for each different query/target comparison
+that met the reporting thresholds, ranked by decreasing statistical
+significance (increasing E-value).
+
+\subsubsection{Target hits table format 1}
+
+In the format 1 table, each line
+consists of \textbf{18 space-delimited fields} followed by a free text
+target sequence description, as follows:\footnote{The \ccode{tblout}
+ format is deliberately space-delimited (rather than tab-delimited)
+ and justified into aligned columns, so these files are suitable both
+ for automated parsing and for human examination. Tab-delimited data
files are difficult for humans to examine and spot check. For this
reason, we think tab-delimited files are a minor evil in the
world. Although we occasionally receive shrieks of outrage about
@@ -120,7 +131,118 @@ \subsection{The target hits table}
The remainder of the line is the target's description line, as free text.
\end{description}
-This table is columnated neatly for human readability, but do not
+\subsubsection{Target hits table format 2}
+\label{tabular-format2}
+
+Format 2 includes all 18 of the fields from format 1 in the same order, plus 9
+additional fields that are interspersed between some of the 18 from
+format 1, as follows:
+
+\begin{description}
+
+\item[\emprog{(Before field 1 of format 1) idx:}]
+ The index of the hit in the list. The first hit has index '1', the
+ second has index '2', the Nth hit has index 'N'.
+
+\item[\emprog{(Before field 5 of format 1) clan name:}]
+ The name of the clan the model for this hit belongs to, or \ccode{-} if
+ the model does not belong to a clan. A clan is a group of related
+ models. For example, Rfam groups three LSU rRNA models
+ (LSU\_rRNA\_archaea, LSU\_rRNA\_bacteria, and LSU\_rRNA\_eukarya)
+ into the same clan. The value in this field will always be \ccode{-}
+ unless the \ccode{--clanin } option was used with
+ \ccode{cmscan} to specify clan/model relationships in the input file
+ \ccode{}. See section~\ref{section:formats} for a description of
+ the format of the input file used with \ccode{--clanin}.
+
+\end{description}
+
+The following seven fields all occur in format 2 between fields 17
+('inc:') and 18 ('description of target') from format 1.
+
+\begin{description}
+
+\item[\emprog{olp:}] A single character indicating the overlap status
+ of this hit. Here, two hits are deemed to \emph{overlap} if they
+ share at least one nucleotide on the same strand of the same
+ sequence. There are three possible values in this field: \ccode{*},
+ \ccode{\^} and \ccode{=}. \ccode{*} indicates this hit does not
+ overlap with any other reported hits. \ccode{\^} indicates that this
+ hit does overlap with at least one other hit, but none of the hits
+ that overlap with it have a higher score (occur above it in the hit
+ list). \ccode{=} indicates that this hit does overlap with at least
+ one other hit that has a higher score (occurs above it in the hit
+ list). If the \ccode{--oclan} option was enabled, the definition of
+ \emph{overlap} for the designations of the three characters
+ \ccode{*}, \ccode{\^} and \ccode{=} described above changes to: two
+ hits are deemed to \emph{overlap} if they share at least one
+ nucleotide on the same strand of the same sequence and they are to
+ models that are in the same clan. That is, only overlaps between
+ hits to models that are in the same clan are counted, all other
+ overlaps are ignored and not annotated. Infernal will never report
+ two overlapping hits to the same model.
+
+\item[\emprog{anyidx:}]
+For hits that have \ccode{=} in the ``olp'' field, this is the
+index of the best scoring hit that overlaps with this hit.
+For hits with either \ccode{*} or \ccode{\^} in the "olp" field,
+this field will always be \ccode{-}.
+
+\item[\emprog{anyfrct1:}]
+For hits that have \ccode{=} in the "olp" field, this is the
+fraction of the length of this hit that overlaps with the best scoring
+overlapping hit (the hit index given in the "anyidx" field), to
+4 significant digits.
+For hits with \ccode{-} in the "anyidx"
+field, this field will always be \ccode{-}.
+
+\item[\emprog{anyfrct2:}]
+For hits that have \ccode{=} in the "olp" field, this is the
+fraction of the length of the best scoring overlapping hit (the hit
+index given in the "anyidx" field) that overlaps with this hit,
+to 4 significant digits.
+For hits with \ccode{-} in the "anyidx"
+field, this field will always be \ccode{-}.
+
+\item[\emprog{winidx:}]
+For hits that have \ccode{=} in the "olp" field, this is either
+\ccode{"} or the index of the best scoring hit that overlaps with this
+hit that is marked as \ccode{\^} in the "olp" field. If the value
+is \ccode{"} it means that the best scoring hit that overlaps with
+this hit that is marked as \ccode{\^} in the "olp" field is
+already listed in the "anyidx" field, which is usually the case.
+For hits with either \ccode{*} or \ccode{\^} in the "olp" field,
+this field will always be \ccode{-}.
+
+\item[\emprog{winfrct1:}]
+For hits that have neither \ccode{-} nor \ccode{"} in the
+"winidx" field, this is the fraction of the length of this hit
+that overlaps with the best scoring overlapping hit marked with
+\ccode{\^} in the "olp" field (the hit index given in the
+"winidx" field), to 4 significant digits. For hits with either
+\ccode{*} or \ccode{\^} in the "olp" field, this field will
+always be \ccode{-}. For hits with \ccode{-} in the "winidx"
+field, this field will always be \ccode{-}.
+For hits with \ccode{"} in the "winidx"
+field, this field will always be \ccode{"}.
+
+\item[\emprog{winfrct2:}]
+For hits that have neither \ccode{-} nor \ccode{"} in the
+"winidx" field, this is the
+fraction of the length of the best scoring overlapping hit marked with
+\ccode{\^} in the "olp" field (the hit
+index given in the "winidx" field) that overlaps with this hit,
+to 4 significant digits.
+ For hits with either
+\ccode{*} or \ccode{\^} in the "olp" field, this field will
+always be \ccode{-}. For hits with \ccode{-} in the "winidx"
+field, this field will always be \ccode{-}.
+For hits with \ccode{"} in the "winidx"
+field, this field will always be \ccode{"}.
+
+\end{description}
+
+The tables are columnated neatly for human readability, but do not
write parsers that rely on this columnation; rely on space-delimited
fields. The pretty columnation assumes fixed maximum widths for each
field. If a field exceeds its allotted width, it will still be fully
@@ -140,9 +262,10 @@ \subsection{The target hits table}
still wouldn't be identical, because the target database size used for
E-value calculations is different (total number of target nucleotides
for \prog{cmsearch}, number of target profiles times target sequence
-length for \prog{cmscan}, and it's good not to forget this.
+length for \prog{cmscan}), and it's good not to forget this.
If some of the descriptions of these fields don't make sense to you,
it may help to go through the tutorial in
section~\ref{section:tutorial} and read section~\ref{section:pipeline}
of the manual.
+
diff --git a/documentation/userguide/titlepage.tex.in b/documentation/userguide/titlepage.tex.in
index 18d0a081..cabf7eea 100644
--- a/documentation/userguide/titlepage.tex.in
+++ b/documentation/userguide/titlepage.tex.in
@@ -12,17 +12,14 @@ sequence and secondary structure consensus} \\ }
\vspace*{\fill}
\begin{center}
-\url{http://infernal.janelia.org/}\\
+\url{http://eddylab.org/infernal}\\
Version @INFERNAL_VERSION@; @INFERNAL_DATE@ \\
\vspace*{\fill}
Eric Nawrocki and Sean Eddy\\
-for the INFERNAL Development Team\\
-Janelia Farm Research Campus\\
-19700 Helix Drive\\
-Ashburn VA 20147 USA\\
-\url{http://eddylab.org/} \\
+for the INFERNAL development team\\
+\url{github.com/EddyRivasLab/infernal/}
\end{center}
\vspace*{\fill}
diff --git a/documentation/userguide/tutorial.tex b/documentation/userguide/tutorial.tex
index 88da66f7..7d30a72c 100644
--- a/documentation/userguide/tutorial.tex
+++ b/documentation/userguide/tutorial.tex
@@ -1,6 +1,9 @@
% EPN, Mon Oct 21 12:57:38 2013
+% EPN, Mon Jun 27 12:32:24 2016 [1.1.2 release]
% Actual commands run on:
-% login-eddy
+% cbbdev13
+% $ uname -a
+% Linux cbbdev13 2.6.32-573.18.1.el6.x86_64 #1 SMP Tue Feb 9 22:46:17 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux
\section{Tutorial}
\label{section:tutorial}
@@ -197,9 +200,9 @@ \subsubsection{Step 1: build a covariance model with cmbuild}
\begin{sreoutput}
# cmbuild :: covariance model construction from multiple sequence alignments
-# INFERNAL 1.1.1 (July 2014)
-# Copyright (C) 2014 Howard Hughes Medical Institute.
-# Freely distributed under the GNU General Public License (GPLv3).
+# INFERNAL 1.1.2 (June 2016)
+# Copyright (C) 2016 Howard Hughes Medical Institute.
+# Freely distributed under a BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# CM file: tRNA5.cm
# alignment file: tutorial/tRNA5.sto
@@ -210,7 +213,7 @@ \subsubsection{Step 1: build a covariance model with cmbuild}
# ------ -------------------- -------- -------- ------ ----- ---- ---- ----- ----- -----------
1 tRNA5 5 3.73 74 72 21 2 0.783 0.489
#
-# CPU time: 0.57u 0.00s 00:00:00.56 Elapsed: 00:00:00.57
+# CPU time: 0.29u 0.00s 00:00:00.28 Elapsed: 00:00:00.30
\end{sreoutput}
If your input file had contained more than one alignment, you'd get
@@ -282,35 +285,36 @@ \subsubsection{Step 2: calibrate the model with cmcalibrate}
\begin{sreoutput}
# cmcalibrate :: fit exponential tails for CM E-values
-# INFERNAL 1.1.1 (July 2014)
-# Copyright (C) 2014 Howard Hughes Medical Institute.
-# Freely distributed under the GNU General Public License (GPLv3).
+# INFERNAL 1.1.2 (June 2016)
+# Copyright (C) 2016 Howard Hughes Medical Institute.
+# Freely distributed under a BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# CM file: tRNA5.cm
# forecast mode (no calibration): on
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
#
-# Forecasting running time for CM calibration(s) on 8 cpus:
+# Forecasting running time for CM calibration(s) on 24 cpus:
#
# predicted
# running time
# model name (hr:min:sec)
# -------------------- ------------
- tRNA5 00:06:26
+ tRNA5 00:01:00
#
-# CPU time: 0.27u 0.00s 00:00:00.27 Elapsed: 00:00:00.28
+# CPU time: 0.15u 0.00s 00:00:00.15 Elapsed: 00:00:00.16
[ok]
\end{sreoutput}
The header comes first, telling you what program you ran, on what file
-and with what options. This calibration will use 8 CPUs, your output
+and with what options. This calibration will use 24 CPUs, your output
+% ^^
may vary depending on how many cores you have available on the machine
you're using. (If you are planning to use MPI to parallelize the
calibration (see the Installation section), you can specify the number
of CPUs for the time estimate as \otext{} with the
-\otext{--nforecast } option.) Using 8 CPUs, \prog{cmcalibrate}
+\otext{--nforecast } option.) Using 24 CPUs, \prog{cmcalibrate}
estimates the time required for calibration on the machine I'm using
-at about seven minutes.
+at about one minute.
Feel free to perform the calibration yourself if you'd like (with the
command \otext{cmcalibrate tRNA5.cm}). However, we've included the file
@@ -337,13 +341,13 @@ \subsubsection{Step 3: search a sequence database with cmsearch}
\begin{sreoutput}
# cmsearch :: search CM(s) against a sequence database
-# INFERNAL 1.1.1 (July 2014)
-# Copyright (C) 2014 Howard Hughes Medical Institute.
-# Freely distributed under the GNU General Public License (GPLv3).
+# INFERNAL 1.1.2 (June 2016)
+# Copyright (C) 2016 Howard Hughes Medical Institute.
+# Freely distributed under a BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query CM file: tRNA5.cm
# target sequence database: tutorial/mrum-genome.fa
-# number of worker threads: 8
+# number of worker threads: 24
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
\end{sreoutput}
@@ -367,8 +371,8 @@ \subsubsection{Step 3: search a sequence database with cmsearch}
(12) ! 1.6e-15 61.7 0.0 NC_013790.1 2350984 2350911 - cm no 0.53 Methanobrevibacter ruminantium M1 chromosome, complete genome
(13) ! 3.3e-15 60.7 0.0 NC_013790.1 2186090 2186019 - cm no 0.54 Methanobrevibacter ruminantium M1 chromosome, complete genome
(14) ! 4.1e-15 60.4 0.0 NC_013790.1 2680159 2680233 + cm no 0.67 Methanobrevibacter ruminantium M1 chromosome, complete genome
- (15) ! 7.9e-15 59.5 0.0 NC_013790.1 2749839 2749768 - cm no 0.53 Methanobrevibacter ruminantium M1 chromosome, complete genome
- (16) ! 7.9e-15 59.5 0.0 NC_013790.1 2749945 2749874 - cm no 0.53 Methanobrevibacter ruminantium M1 chromosome, complete genome
+ (15) ! 7.9e-15 59.5 0.0 NC_013790.1 2749945 2749874 - cm no 0.53 Methanobrevibacter ruminantium M1 chromosome, complete genome
+ (16) ! 7.9e-15 59.5 0.0 NC_013790.1 2749839 2749768 - cm no 0.53 Methanobrevibacter ruminantium M1 chromosome, complete genome
(17) ! 9.8e-15 59.2 0.0 NC_013790.1 361676 361604 - cm no 0.51 Methanobrevibacter ruminantium M1 chromosome, complete genome
(18) ! 1e-14 59.2 0.0 NC_013790.1 2585073 2584999 - cm no 0.60 Methanobrevibacter ruminantium M1 chromosome, complete genome
(19) ! 1.1e-14 59.1 0.0 NC_013790.1 2130422 2130349 - cm no 0.59 Methanobrevibacter ruminantium M1 chromosome, complete genome
@@ -664,18 +668,18 @@ \subsubsection{Step 3: search a sequence database with cmsearch}
Query model(s): 1 (72 consensus positions)
Target sequences: 1 (5874406 residues searched)
Target sequences re-searched for truncated hits: 1 (360 residues re-searched)
-Windows passing local HMM SSV filter: 11200 (0.2111); expected (0.35)
+Windows passing local HMM SSV filter: 11205 (0.2116); expected (0.35)
Windows passing local HMM Viterbi filter: (off)
Windows passing local HMM Viterbi bias filter: (off)
-Windows passing local HMM Forward filter: 137 (0.002691); expected (0.005)
-Windows passing local HMM Forward bias filter: 134 (0.002621); expected (0.005)
-Windows passing glocal HMM Forward filter: 87 (0.001923); expected (0.005)
-Windows passing glocal HMM Forward bias filter: 87 (0.001923); expected (0.005)
-Envelopes passing glocal HMM envelope defn filter: 100 (0.001342); expected (0.005)
-Envelopes passing local CM CYK filter: 60 (0.0007631); expected (0.0001)
+Windows passing local HMM Forward filter: 136 (0.002693); expected (0.005)
+Windows passing local HMM Forward bias filter: 133 (0.002623); expected (0.005)
+Windows passing glocal HMM Forward filter: 84 (0.001951); expected (0.005)
+Windows passing glocal HMM Forward bias filter: 84 (0.001951); expected (0.005)
+Envelopes passing glocal HMM envelope defn filter: 98 (0.001318); expected (0.005)
+Envelopes passing local CM CYK filter: 60 (0.0007629); expected (0.0001)
Total CM hits reported: 56 (0.0007205); includes 0 truncated hit(s)
-# CPU time: 2.15u 0.03s 00:00:02.17 Elapsed: 00:00:00.89
+# CPU time: 2.01u 0.05s 00:00:02.05 Elapsed: 00:00:00.49
//
[ok]
\end{sreoutput}
@@ -730,19 +734,19 @@ \subsubsection{Step 3: search a sequence database with cmsearch}
% ^^^^
residues will pass the filter). Here, about 21\% of the database in
% ^^^^
-11,200 separate windows got through the SSV filter. For a database of
+11,205 separate windows got through the SSV filter. For a database of
%^^^^^
this size, the local Viterbi filter is turned off. The local Forward filter
is set to allow an expected 0.5\% of the database survive. Here about
% ^^^^
-0.3\% survives in 137 windows. Next, each surviving window is checked
+0.3\% survives in 136 windows. Next, each surviving window is checked
%^^
to see if the target sequence is ``obviously'' so biased in its
composition that it's unlikely to be a true homolog. This is called
the ``bias filter''\footnote{There's also a bias filter step used in
the local Viterbi filter stage, when it is used.} and applying a bit
score correction to previous filter's score for each window and
-recomputing the P-value. Three of the 137 windows fail to pass
+recomputing the P-value. Three of the 136 windows fail to pass
% ^^^^^ ^^^
the local Forward bias filter stage. Next, the Forward algorithm is
used to score each window again, but this time with the HMM configured
@@ -751,7 +755,7 @@ \subsubsection{Step 3: search a sequence database with cmsearch}
difference between Infernal and HMMER3's (v3.0) pipeline. HMMER v3.0
only uses local HMM algorithms.} As with the local stage, an
expected 0.5\% of the database is expected to survive. In this case,
-87 of the 134 windows, comprising about 0.2\% of the database,
+84 of the 134 windows, comprising about 0.2\% of the database,
%^ ^^^
survive. The bias filter is run again, this time applying a correction
to the glocal Forward scores. For this search, 0 windows are removed at
@@ -762,13 +766,13 @@ \subsubsection{Step 3: search a sequence database with cmsearch}
or more hit envelopes in each window, where each envelope contains one
putative hit. Often residues at the beginning and ends of windows are
determined to be nonhomologous and are not included in the
-envelope. In this search, 100 envelopes are defined within the 87
+envelope. In this search, 98 envelopes are defined within the 84
% ^^^ ^^
windows. Note that the envelopes comprise only about 70\% of the
% ^^^
-residues from the 87 windows, indicated by the drop of 0.1923\% to
+residues from the 84 windows, indicated by the drop of 0.1951\% to
% ^^^^^^^^
-0.1342\%.
+0.1318\%.
%%^^^^
After hit envelopes have been defined with the filter HMM, the two
@@ -794,9 +798,9 @@ \subsubsection{Step 3: search a sequence database with cmsearch}
% ^^
Finally, the running time of the search is reported, in CPU time and
-elapsed time. This search took about 1 second (wall
+elapsed time. This search took about half a second (wall
% ^
-clock time) (running on eight cores).
+clock time) (running on twenty four cores).
\subsubsection{Truncated RNA detection}
@@ -942,13 +946,13 @@ \subsubsection{Step 3: search the CM database with cmscan}
\begin{sreoutput}
# cmscan :: search sequence(s) against a CM database
-# INFERNAL 1.1.1 (July 2014)
-# Copyright (C) 2014 Howard Hughes Medical Institute.
-# Freely distributed under the GNU General Public License (GPLv3).
+# INFERNAL 1.1.2 (June 2016)
+# Copyright (C) 2016 Howard Hughes Medical Institute.
+# Freely distributed under a BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-# query sequence file: ../../tutorial/metag-example.fa
+# query sequence file: tutorial/metag-example.fa
# target CM database: minifam.cm
-# number of worker threads: 8
+# number of worker threads: 24
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query: AAGA01015927.1 [L=943]
@@ -1022,7 +1026,7 @@ \subsubsection{Step 3: search the CM database with cmscan}
Envelopes passing local CM CYK filter: 4 (0.05189); expected (0.0001)
Total CM hits reported: 3 (0.03046); includes 0 truncated hit(s)
-# CPU time: 0.21u 0.01s 00:00:00.22 Elapsed: 00:00:00.22
+# CPU time: 0.15u 0.02s 00:00:00.17 Elapsed: 00:00:00.12
//
\end{widesreoutput}
@@ -1145,9 +1149,172 @@ \subsubsection{Truncated hit and local end alignment example}
were in this EL, the \otext{PP} annotation would be a gap (\otext{.})
character.
+\subsection{Searching the Rfam CM database with a query sequence}
+
+The Rfam database \url{http://rfam.xfam.org/} is a collection
+of RNA families, each represented by a CM and multiple sequence
+alignment used to build that CM. As of June 2016, the current release
+is 12.1, which includes 2474 families. The Rfam website allows
+web-based searches using \prog{cmscan} of the Rfam CM database against
+query sequences that the user can upload. Alternatively, you can perform
+the same searches by running \prog{cmscan} locally, as shown in this
+example. By searching all of Rfam with your sequence dataset, you will
+be annotating your dataset for most known types of structural RNAs
+with a single command.
+
+To complete this step of the tutorial you'll need to download the Rfam
+12.1 CM file from here: \\
+\url{ftp://ftp.ebi.ac.uk/pub/databases/Rfam/12.1/Rfam.cm.gz}
+and gunzipping it, like this:
+
+\user{wget ftp://ftp.ebi.ac.uk/pub/databases/Rfam/12.1/Rfam.cm.gz}
+
+\user{gunzip Rfam.cm.gz}
+
+Then, as in the previous example, you'll need to run \prog{cmpress} on
+this CM database:
+
+\user{cmpress Rfam.cm}
+
+The next step is to run \prog{cmscan}. In order to reproduce how Rfam
+searches are performed \citep{Nawrocki15} several command line
+options are required. Each of these options is explained below. The
+full command is (split up into two lines so it fits on the page):
+
+\indent\indent\small\verb+> cmscan --rfam --cut_ga --nohmmonly --tblout mrum-genome.tblout --fmt 2 \+\\
+\indent\indent\small\verb+> --clanin testsuite/Rfam.12.1.clanin Rfam.cm tutorial/mrum-genome.fa > mrum-genome.cmscan+\\
+
+This command will take at least several minutes and possibly up to
+about 30 minutes depending on the number of cores and speed of your
+computer.
+
+The command line options used in the above command are as follows:
+
+\begin{sreitems}{\emprog{--nohmmonly}}
+\item[\otext{--rfam}] Specifies that the filter pipeline run in fast
+ mode, with the same strict filters that are used for Rfam searches
+ and for other sequence databases larger than 20 Gb (see
+ section~\ref{section:pipeline}).
+%
+\item[\otext{--cut\_ga}] Specifies that the special Rfam \emph{GA}
+ (gathering) thresholds be used to determine which hits are
+ reported. These thresholds are stored in the \prog{Rfam.cm} file.
+ Each model has its own GA bit score threshold, which was determined
+ by Rfam curators as the bit score at and above which all hits are
+ believed to be true homologs to the model. These determinations were made based on
+ observed hit results against the large Rfamseq database used by
+ Rfam \citep{Nawrocki15}.
+%
+\item[\otext{--nohmmonly}] All models, even those with zero basepairs,
+ are run in CM mode (not HMM mode). This ensures all GA cutoffs, which were
+ determined in CM mode for each model, are valid.
+%
+\item[\otext{--tblout}] Specifies that a tabular output
+ file should be created, see section~\ref{section:tabular}.
+%
+\item[\otext{--fmt 2}] The tabular output file will be in format 2,
+ which includes annotation of overlapping hits. See
+ page~\pageref{tabular-format2} for a complete description of this
+ format.
+%
+\item[\otext{--clanin}] Clan information should be read
+ from the file \prog{testsuite/Rfam.12.1.claninfo}. This file lists
+ which models belong to the same clan. Clans are groups of models
+ that are homologous and therefore it is expected that some hits to
+ these models will overlap. For example, the LSU\_rRNA\_archaea and
+ LSU\_rRNA\_bacteria models are both in the same clan.
+%
+\end{sreitems}
+
+When the \prog{cmscan} command finishes running, the file
+\prog{mrum-genome.cmscan} will contain the standard output of the
+program. This file will be similar to what we saw in the earlier example of
+\prog{cmscan}. The file \prog{mrum-genome.tblout} has also been
+created, which is a tabular representation of all hits, one line per
+hit. Take a look at this file. The first two lines are comment lines
+(prefixed with \prog{\#} characters) with the labels of each of the 27
+columns of data in the file. Each subsequent line has 27 space
+delimited tokens. The specific meaning of these tokens is described in
+detail in section~\ref{section:tabular}. Below I'm including the
+first 24 lines of the file, with columns 3-5, 7-9 and 13-16 removed
+(replaced with \prog{...}) so that the text will fit on this page:
+
+\begin{tinysreoutput}
+#idx target name ... clan name ... seq from seq to strand ... score E-value inc olp anyidx afrct1 afrct2 winidx wfrct1 wfrct2 description of target
+#--- ---------------------- ... --------- ... -------- -------- ------ ... ----- --------- --- --- ------ ------ ------ ------ ------ ------ ---------------------
+1 LSU_rRNA_archaea ... CL00112 ... 762872 765862 + ... 2763.5 0 ! ^ - - - - - - -
+2 LSU_rRNA_archaea ... CL00112 ... 2041329 2038338 - ... 2755.0 0 ! ^ - - - - - - -
+3 LSU_rRNA_bacteria ... CL00112 ... 762874 765862 + ... 1872.9 0 ! = 1 1.000 0.999 " " " -
+4 LSU_rRNA_bacteria ... CL00112 ... 2041327 2038338 - ... 1865.5 0 ! = 2 1.000 0.999 " " " -
+5 LSU_rRNA_eukarya ... CL00112 ... 763018 765851 + ... 1581.3 0 ! = 1 1.000 0.948 " " " -
+6 LSU_rRNA_eukarya ... CL00112 ... 2041183 2038349 - ... 1572.1 0 ! = 2 1.000 0.948 " " " -
+7 SSU_rRNA_archaea ... CL00111 ... 2043361 2041888 - ... 1552.0 0 ! ^ - - - - - - -
+8 SSU_rRNA_archaea ... CL00111 ... 760878 762351 + ... 1546.5 0 ! ^ - - - - - - -
+9 SSU_rRNA_bacteria ... CL00111 ... 2043366 2041886 - ... 1161.9 0 ! = 7 0.995 1.000 " " " -
+10 SSU_rRNA_bacteria ... CL00111 ... 760873 762353 + ... 1156.4 0 ! = 8 0.995 1.000 " " " -
+11 SSU_rRNA_eukarya ... CL00111 ... 2043361 2041891 - ... 970.4 2.5e-289 ! = 7 1.000 0.998 " " " -
+12 SSU_rRNA_eukarya ... CL00111 ... 760878 762348 + ... 963.8 2.4e-287 ! = 8 1.000 0.998 " " " -
+13 SSU_rRNA_microsporidia ... CL00111 ... 2043361 2041891 - ... 919.9 1.9e-277 ! = 7 1.000 0.998 " " " -
+14 SSU_rRNA_microsporidia ... CL00111 ... 760878 762348 + ... 917.2 1.3e-276 ! = 8 1.000 0.998 " " " -
+15 RNaseP_arch ... - ... 2614544 2614262 - ... 184.9 2.8e-50 ! * - - - - - - -
+16 Archaea_SRP ... CL00003 ... 1064321 1064634 + ... 197.6 1.7e-45 ! * - - - - - - -
+17 FMN ... - ... 193975 193837 - ... 115.2 1.7e-24 ! * - - - - - - -
+18 tRNA ... CL00001 ... 735136 735208 + ... 72.1 1.2e-12 ! * - - - - - - -
+19 tRNA ... CL00001 ... 2350593 2350520 - ... 71.0 2.5e-12 ! * - - - - - - -
+20 tRNA ... CL00001 ... 2680310 2680384 + ... 70.9 2.6e-12 ! * - - - - - - -
+21 tRNA ... CL00001 ... 2351254 2351181 - ... 69.7 5.5e-12 ! * - - - - - - -
+22 tRNA ... CL00001 ... 361676 361604 - ... 69.5 6.2e-12 ! * - - - - - - -
+\end{tinysreoutput}
+
+This tabular format includes the target model name, sequence name (in
+column 3, which is omitted above to save space), clan name, sequence
+coordinates, bit score, E-value and more. Because the \prog{--fmt 2}
+option was used, this file includes information on which hits overlap
+with other hits, starting at the column labelled ``olp'' and ending
+with ``wfrct2''. Hits with the ``*'' character in the ``olp'' column
+do not overlap with any other hits. Those with ``\verb+^+'' do overlap with
+at least one other hit, but none of those overlapping hits have a
+better score (that occurs higher in the list). Those with ``='' also
+overlap with at least one other hit that does have a better score, the
+index of which is given in the ``anyidx'' column. For more detailed
+explanation of these columns, see page~\pageref{tabular-format2}.
+
+The top two hits are both to the \prog{LSU\_rRNA\_archaea}
+model. These are the two copies of LSU rRNA in the
+\emph{Methanobrevibacter ruminantium} genome. Hits number 3 and 4
+are to the \prog{LSU\_rRNA\_bacteria} model and overlap with hits 1
+and 2 nearly completely (hit 1 is from sequence positions 762872 to 765862 and
+hit 3 is from sequence positions 762874 to 765862). This overlap is not
+surprising because the bacterial and archaeal LSU rRNA models are very
+similar, and so are assigning high scores to the same
+subsequences. Further, hit 5 is to \prog{LSU\_rRNA\_eukarya} and also
+overlaps hits 1 and 3. Because these three LSU models are all expected
+to produce overlapping hits due to their homology, Rfam has grouped
+them into the same \emph{clan}, note the ``CL00112'' value in the ``clan
+name'' column for all three hits. This clan information was provided
+in the \prog{rfam.12.1claninfo} input file we provided to \prog{cmscan}
+by using the \prog{--clanin} option.
+
+The ``olp'' column indicates that hit 1 is the highest scoring of the
+three overlapping hits because it contains the ``\verb+^+'' character. Hits 3 and 5 both have
+``='' in the ``olp'' column indicating that there is another hit to
+another model which overlaps these hits and has a better score.
+
+If you were using these results to produce annotations for the
+\emph{Methanobrevibacter ruminantium} genome, you may want to ignore
+any hits that have higher scoring overlaps. To do this you can just
+remove any hits with ``='' in the ``olp'' column. Alternatively, you
+can have these hits not printed to the tabular output file by
+additionally providing the \prog{--oskip} option to \prog{cmscan}.
+You can also modify the overlap annotation behavior with
+\prog{--oclan} option which restricts the annotation of overlaps to
+hits for models within the same clan. Overlapping hits from models
+that are not in the same clan will not be marked as
+overlaps, instead they will marked as ``*'' in the ``olp'' field.
+
\subsection{Creating multiple alignments with cmalign}
The file \otext{tutorial/mrum-tRNAs10.fa} is a FASTA file containing
-the 10 of the tRNA hits above the inclusion threshold (with an E-value
+the 10 tRNA hits above the inclusion threshold (with an E-value
less than $0.01$) found by \prog{cmsearch} in our
search of \emph{M. ruminantium} genome\footnote{The
\otext{-A } option to \prog{cmsearch} can be used to save a
@@ -1163,7 +1330,7 @@ \subsection{Creating multiple alignments with cmalign}
\begin{tinysreoutput}
# STOCKHOLM 1.0
-#=GF AU Infernal 1.1.1
+#=GF AU Infernal 1.1.2
mrum-tRNA.1 GGAGCUAUAGCUCAAU..GGC..AGAGCGUUUGGCUGACAU........................................CCAAAAGGUUAUGGGUUCGAUUCCCUUUAGCCCCA
#=GR mrum-tRNA.1 PP ****************..***..******************........................................***********************************
@@ -1293,7 +1460,7 @@ \subsubsection{cmalign assumes sequences may be truncated}
\label{cmalign-cobalamin}
\begin{sreoutput}
# STOCKHOLM 1.0
-#=GF AU Infernal 1.1.1
+#=GF AU Infernal 1.1.2
Cobalamin.1 -------------------------------GUAGGCAAAAGGAAGAGGAAGgAUGGUGGAAAUCCUUCACGGGCCCGGCCA
#=GR Cobalamin.1 PP ...............................44455566666899******989****************************
@@ -1367,7 +1534,7 @@ \subsection{Searching a sequence database for RNAs with unknown or no
structure of a collection of homologous RNAs. Currently, Infernal
itself does not have the capability of predicting structure, but it's
predecessor COVE did with the \prog{covet} program, still available at
-\url{ftp://selab.janelia.org/pub/software/cove/cove-2.4.4.tar.Z}.
+\url{eddylab.org/software/cove/cove.tar.Z}.
Infernal automatically detects when a model has zero basepairs and
uses efficient profile HMM algorithms in \prog{cmsearch} and
@@ -1393,9 +1560,9 @@ \subsection{Searching a sequence database for RNAs with unknown or no
\begin{sreoutput}
# cmbuild :: covariance model construction from multiple sequence alignments
-# INFERNAL 1.1.1 (July 2014)
-# Copyright (C) 2014 Howard Hughes Medical Institute.
-# Freely distributed under the GNU General Public License (GPLv3).
+# INFERNAL 1.1.2 (June 2016)
+# Copyright (C) 2016 Howard Hughes Medical Institute.
+# Freely distributed under a BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# CM file: tRNA5-noss.cm
# alignment file: tutorial/tRNA5.sto
@@ -1407,7 +1574,7 @@ \subsection{Searching a sequence database for RNAs with unknown or no
# ------ -------------------- -------- -------- ------ ----- ---- ---- ----- ----- -----------
1 tRNA5 5 5.00 74 72 0 0 0.552 0.552
#
-# CPU time: 0.18u 0.00s 00:00:00.18 Elapsed: 00:00:00.19
+# CPU time: 0.14u 0.00s 00:00:00.14 Elapsed: 00:00:00.14
\end{sreoutput}
The output reports that this model has 0 basepairs (``bps'') (the
@@ -1449,7 +1616,7 @@ \subsection{Searching a sequence database for RNAs with unknown or no
(10) ! 6.4e-05 24.8 0.0 NC_013790.1 1873882 1873820 - hmm - 0.63 Methanobrevibacter ruminantium M1 chromosome, complete genome
(11) ! 0.00014 23.7 0.0 NC_013790.1 360882 360824 - hmm - 0.51 Methanobrevibacter ruminantium M1 chromosome, complete genome
(12) ! 0.00059 21.8 0.0 NC_013790.1 361910 361851 - hmm - 0.38 Methanobrevibacter ruminantium M1 chromosome, complete genome
- (13) ! 0.00091 21.2 0.0 NC_013790.1 2350586 2350528 - hmm - 0.58 Methanobrevibacter ruminantium M1 chromosome, complete genome
+ (13) ! 0.00092 21.2 0.0 NC_013790.1 2350586 2350528 - hmm - 0.58 Methanobrevibacter ruminantium M1 chromosome, complete genome
(14) ! 0.0018 20.3 0.0 NC_013790.1 995341 995267 - hmm - 0.51 Methanobrevibacter ruminantium M1 chromosome, complete genome
(15) ! 0.0026 19.7 0.0 NC_013790.1 97728 97788 + hmm - 0.49 Methanobrevibacter ruminantium M1 chromosome, complete genome
(16) ! 0.0029 19.6 0.0 NC_013790.1 2186083 2186024 - hmm - 0.50 Methanobrevibacter ruminantium M1 chromosome, complete genome
@@ -1459,7 +1626,7 @@ \subsection{Searching a sequence database for RNAs with unknown or no
(20) ! 0.0074 18.3 0.0 NC_013790.1 361056 360994 - hmm - 0.40 Methanobrevibacter ruminantium M1 chromosome, complete genome
------ inclusion threshold ------
(21) ? 0.011 17.7 0.0 NC_013790.1 2151679 2151737 + hmm - 0.56 Methanobrevibacter ruminantium M1 chromosome, complete genome
- (22) ? 0.019 17.1 0.0 NC_013790.1 2327123 2327043 - hmm - 0.62 Methanobrevibacter ruminantium M1 chromosome, complete genome
+ (22) ? 0.018 17.1 0.0 NC_013790.1 2327123 2327043 - hmm - 0.62 Methanobrevibacter ruminantium M1 chromosome, complete genome
(23) ? 0.023 16.7 0.0 NC_013790.1 360973 360920 - hmm - 0.54 Methanobrevibacter ruminantium M1 chromosome, complete genome
(24) ? 0.037 16.1 0.0 NC_013790.1 2350982 2350919 - hmm - 0.50 Methanobrevibacter ruminantium M1 chromosome, complete genome
(25) ? 0.039 16.1 0.0 NC_013790.1 361671 361606 - hmm - 0.50 Methanobrevibacter ruminantium M1 chromosome, complete genome
@@ -1655,9 +1822,9 @@ \subsection{Specifying and annotating match positions with cmbuild --hand}
\begin{sreoutput}
# cmbuild :: covariance model construction from multiple sequence alignments
-# INFERNAL 1.1.1 (July 2014)
-# Copyright (C) 2014 Howard Hughes Medical Institute.
-# Freely distributed under the GNU General Public License (GPLv3).
+# INFERNAL 1.1.2 (June 2016)
+# Copyright (C) 2016 Howard Hughes Medical Institute.
+# Freely distributed under a BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# CM file: tRNA5-hand.cm
# alignment file: ../../tutorial/tRNA5-hand.sto
@@ -1669,7 +1836,7 @@ \subsection{Specifying and annotating match positions with cmbuild --hand}
# ------ -------------------- -------- -------- ------ ----- ---- ---- ----- ----- -----------
1 tRNA5-hand 5 3.59 74 74 21 2 0.763 0.476
#
-# CPU time: 0.59u 0.00s 00:00:00.59 Elapsed: 00:00:00.61
+# CPU time: 0.31u 0.00s 00:00:00.31 Elapsed: 00:00:00.32
\end{sreoutput}
The output reports that the model now has 74 match (consensus)
@@ -1687,6 +1854,7 @@ \subsection{Specifying and annotating match positions with cmbuild --hand}
search:
\user{cmsearch tutorial/tRNA5-hand.c.cm tutorial/mrum-genome.fa}
+% tutorial regression: trna-hand-mrum.cmsearch
The results are very similar to the earlier search with the
tRNA model built with default \prog{cmbuild} parameters (though not
diff --git a/release-notes/00CHECKLIST b/release-notes/00CHECKLIST
index a8609d31..045d8530 100644
--- a/release-notes/00CHECKLIST
+++ b/release-notes/00CHECKLIST
@@ -1,169 +1,195 @@
Checklist for an Infernal release.
-EPN, Mon Jun 25 14:40:53 2012
+EPN, Fri Jun 24 10:17:16 2016
-Updated for 1.1 release, based on HMMER's 00CHECKLIST.
+Updated for 1.1.2 release, based partly on SSU-ALIGN 0.1.1's 00CHECKLIST
-------------------------------------
-When editing this 00CHECKLIST, it is best to edit it only in the
-trunk, not in a release branch. It isn't included in releases anyway.
-
-Subversion repository: https://svn.janelia.org/eddylab/eddys/src/infernal
-
-Infernal, like HMMER, follows an 'unstable trunk' policy. Each major
-release goes onto a stable branch. Every release (even minor ones) is
-tagged.
-
-Release types: major releases, minor releases, and snapshots. A major
-release gets its own branch. A minor release puts bug fixes into a
-major branch. A snapshot is from the development trunk.
-
-Version naming: example
-major . 1.0
-minor .. 1.0.1
-alpha .a 1.0a1
-beta .b 1.0b3
-release candidate .rc 1.0rc1
-snapshot ..snap 1.0.snap20080325
-
-
-* Announce intent to release to all developers.
- Commit working copies on all machines.
- Check for stray uncommitted files:
- ./configure
- make distclean
- svn update
- svn status
- Clean up any stray files identified by 'svn status'.
- 'svn add' and 'svn commit' as needed to commit new or modified files.
-
-
-================================================================
-= Creating a new major release branch, if necessary
-================================================================
-
-For major public releases (1.1, 1.2): we create a Subversion branch,
-so we can continue support (with bugfixes) without disrupting
-development of the next main release.
-
-* First test the development trunk.
- Compile should be entirely clean when compiled -Wall.
- 'make check' should be clean.
- 'make dev' should be clean.
- '(cd documentation/userguide; make)' should work
-
- When trunk is clean,
- svn commit
- We're (usually) next going to move out of the trunk to the release branch.
-
-* Create stable release branch from the trunk.
- All subsequent bugfix releases will happen in this branch, while trunk keeps moving.
-
- svn copy https://svn.janelia.org/eddylab/eddys/src/infernal/trunk\
- https://svn.janelia.org/eddylab/eddys/src/infernal/branches/1.1\
- -m "created Infernal 1.1 release branch"
- svn copy https://svn.janelia.org/eddylab/eddys/src/hmmer/trunk\
- https://svn.janelia.org/eddylab/eddys/src/hmmer/branches/infernal/1.1\
- -m "created Infernal 1.1 release branch"
- svn copy https://svn.janelia.org/eddylab/eddys/easel/trunk\
- https://svn.janelia.org/eddylab/eddys/easel/branches/infernal/1.1\
- -m "created Infernal 1.1 release branch"
-
-
-==================================================================
-= Work in the current release branch (~/releases/infernal-release)
-==================================================================
-
-Once a release branch has been taken (either new, or by a merge from
-the trunk destined to become a release), work only in the release
-branch. We'll merge changes back to the trunk when the release cycle
-is complete.
-
-* Checking out a release branch for the first time, in ~/releases/
- cd ~/releases
- svn checkout https://svn.janelia.org/eddylab/eddys/src/infernal/branches/1.1 infernal-release
-
-Don't call this working directory infernal-1.1, nor infernal! Call it
-infernal-release, because later we'll create infernal-xx as its
-release, and because you want to recognize that it's different from
-src/infernal.
-
-If this is the first time (a new release branch), you also need to
-update the "svn:externals" so Easel and HMMER are checked out from
-the appropriate stable branch too.
-
- svn proplist --verbose https://svn.janelia.org/eddylab/eddys/src/infernal/branches/1.1
- svn propedit svn:externals infernal-release
- easel https://svn.janelia.org/eddylab/eddys/easel/branches/infernal/1.1
- hmmer https://svn.janelia.org/eddylab/eddys/src/hmmer/branches/infernal/1.1
- cd infernal-release
- svn update
- svn commit
-
-Note the hassle with svn:externals, because it currently only accepts
-absolute URLs. Relative paths are supposed to become available in
-Subversion 1.5, which may help. Later if we merge the branch back to
-the trunk, the merge will mess up easel's and hmmer's externals, and
-we'll have to propedit the trunk.
-
+Git repositories: https://github.com/EddyRivasLab/infernal.git
+
+ https://github.com/EddyRivasLab/hmmer.git
+
+ https://github.com/EddyRivasLab/easel.git
+
+See instructions on how to do a release using the lab's git flow
+strategy here:
+
+https://github.com/EddyRivasLab/infernal/wiki
+
+And these pages may also be helpful:
+https://github.com/EddyRivasLab/hmmer/wiki
+https://github.com/EddyRivasLab/easel/wiki
+
+==========================
+= Creating a new release =
+==========================
+
+1. Announce intent to release to all developers.
+
+2. Create release branches of easel, hmmer and infernal.
+
+ (from https://github.com/EddyRivasLab/infernal/wiki)
+
+ NOTE FOR THE 1.1.2 RELEASE I DID NOT FOLLOW THIS EXACTLY:
+ instead of finalizing the hmmer and easel releases completely
+ before the 1.1.2 release, I waited until I was sure that
+ Infernal 1.1.2 was good to go, then I finalized those releases
+ (merged to master and develop).
+ See the notes underneath this block enclosed by ~~~~~~~~~~~~~
+ for details.
+
+ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ To make a release, you're going to make a release branch of the code,
+ and of any other repos it depends on. For example, for an Infernal
+ release, you're going to make release branches in HMMER and Easel
+ too. You assign appropriate version numbers to each, test and
+ stabilize. When everything is ready, you merge to master and tag that
+ commit with the version number; then you also merge back to develop,
+ and delete the release branch.
+
+ For example, here's the git flow for an Infernal release, depending on
+ HMMER and Easel. Suppose Infernal is currently at 1.1.2, HMMER is
+ currently at 3.2.1, and Easel is currently at 0.2.3. Suppose we decide
+ this release will be Infernal 1.2, and it depends on some new features
+ in HMMER so we need to make a new HMMER 3.2.2 release, but we can use
+ the last stable Easel release as it is. Then first we go over to Easel
+ and just make a tag:
+
+ $ cd easel
+ $ git checkout master
+ $ git tag -a infernal-1.2
+ $ git push origin infernal-1.2
+
+ then we go over to make a new release from HMMER3's h3-develop branch:
+
+ $ cd hmmer3
+ $ git checkout -b release-3.2.2 h3-develop
+ # change version numbers to 3.2.2; also dates, copyrights
+ $ git commit -a -m "Version number bumped to 3.2.2"
+ # do and commit any other work needed to test/stabilize H3 release
+ $ git checkout h3-master
+ $ git merge --no-ff release-3.2.2
+ $ git tag -a 3.2.2
+ $ git tag -a infernal-1.2 # This records that Infernal 1.2 release depends on HMMER 3.2.2
+ # Now merge release branch back to develop...
+ $ git checkout h3-develop
+ $ git merge --no-ff release-3.2.2
+ $ git branch -d release-3.2.2
+
+ and finally, we do the same pattern on Infernal itself:
+
+ $ cd infernal
+ $ git checkout -b release-1.2 develop
+ # change version numbers to 1.2; also dates, copyrights
+ $ git commit -a -m "Version number bumped to 1.2"
+ # do and commit any other work needed to test/stabilize Infernal release
+ $ git checkout master
+ $ git merge --no-ff release-1.2
+ $ git tag -a 1.2
+ # Now merge release branch back to develop...
+ $ git checkout develop
+ $ git merge --no-ff release-1.2
+ Dependencies always have a tag for their own release (Easel 0.2.4),
+ and may have additional tags for packages that depend on them
+ (HMMER 3.2.2 bundles Easel 0.2.4? Then there's a hmmer-3.2.2 tag
+ pointing to that Easel commit object).
+ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+ - create easel release branch
+
+ $ cd easel
+ $ git checkout develop
+
+ # make sure develop is up to date with master (should be 0
+ # commits behind master) via github
+
+ $ git checkout -b release-0.43 develop
+
+ # bump version and release date in configure.ac
+ # make sure it builds cleanly
+ # do the following on as many systems as are available
+ # I did NCBI, my mac, EBI and Odyssey
+ # make check; make dev; testsuite/valgrind_report.pl . .
+ # (FOR 1.1.2, valgrind_report.pl didn't work at
+ # NCBI due to format of valgrind output and NCBI's
+ # version requires the --orig option for some reason.)
+ #
+ # do some anecdotal testing of miniapps, make sure
+ # version, date are correct.
+
+ # push release branch to master
+ $ git push origin release-0.43
+
+ # don't merge to master/develop or tag yet, wait
+ # until your done testing Infernal. There may be
+ # something you need to fix/change in easel.
+
+ - create hmmer release branch
+
+ $ cd hmmer
+ $ git checkout h3-develop
+
+ # make sure h3-develop is up to date with h3-master
+ # (I actually don't know how to do this because github only
+ # lists how many commits behind 'master' you are)
+
+ $ git checkout -b release-3.1b3 h3-develop
+
+ # bump version and release date of hmmer and easel
+ # in configure.ac
+ # make sure it builds cleanly
+ # do the following on as many systems as are available
+ # I did NCBI, my mac, EBI and Odyssey
+ # make check; make dev;
+ # do some anecdotal testing of programs, make sure
+ # version, date are correct.
+
+ # push release branch to master
+ $ git push origin release-3.1b3
+
+ # don't merge to master/develop or tag yet, wait
+ # until your done testing Infernal. There may be
+ # something you need to fix/change in easel.
+
+ - create infernal release branch
+
+ $ cd infernal
+ $ git checkout develop
+
+ # make sure develop is up to date with master (should be 0
+ # commits behind master) via github
+
+ $ git checkout -b release-1.1.2 develop
+
+ # bump version and release date of infernal, hmmer and easel
+ # in configure.ac
+ # make sure it builds cleanly
+ # do the following on as many systems as are available
+ # I did NCBI, my mac, EBI and Odyssey
+ # make check; make devcheck;
+ # do some anecdotal testing of programs, make sure
+ # version, date are correct.
+
+ # make sure the user guide builds on at least one system (NCBI)
+ $ cd documentation/userguide; make
+
+ # Now, prepare the distribution, which involves more testing
+ # and updating the user guide, then when you're sure you're
+ # done, commit to the release branch and merge to master then
+ # develop (instructions on this are below after the 'Preparing
+ # a distribution' section).
================================================================
-= Large merges from the trunk: try to avoid
+= Prepare the release and update the user guide
================================================================
-It's preferable to add bug fixes to the release branch, then merge
-them one at a time back to the trunk.
-
-However, there may be times when we merge the trunk to the branch in
-toto, as one big diff. To do that, if you must:
-
-first merge infernal trunk in:
- cd ~/releases
- svn checkout https://svn.janelia.org/eddylab/eddys/src/infernal/branches/1.1 infernal-release
- cd infernal-release
- svn merge https://svn.janelia.org/eddylab/eddys/src/infernal/branches/1.1 https://svn.janelia.org/eddylab/eddys/src/infernal/trunk
-
-now fix the svn:externals:
- svn propedit svn:externals infernal-release
- easel https://svn.janelia.org/eddylab/eddys/easel/branches/infernal/1.1
- hmmer https://svn.janelia.org/eddylab/eddys/src/hmmer/branches/infernal/1.1
-
-now merge into easel and hmmer:
- cd infernal-release/easel
- svn merge https://svn.janelia.org/eddylab/eddys/easel/branches/infernal/1.1 https://svn.janelia.org/eddylab/eddys/easel/trunk
- cd ../hmmer
- svn merge https://svn.janelia.org/eddylab/eddys/src/hmmer/branches/infernal/1.1 https://svn.janelia.org/eddylab/eddys/src/hmmer/trunk
-
-
-================================================================
-= Preparing a distribution
-================================================================
-
-We prepare and make a distro; later we test it thoroughly. This way
-we'll test exactly the version that's rolling out. If something goes
-wrong, it's easy enough to come back and make a new tarball.
-
-
* Write the release notes in releases/.
To gather information, check:
Infernal Bugs/BUGTRAX - update this file to mark release that fixed
bugs, and divider indicating release.
- Paper notebook since last release
- svn log since last release:
- svn log -r3022:HEAD https://svn.janelia.org/eddylab/eddys/src/hmmer/trunk
- svn log -r428:HEAD https://svn.janelia.org/eddylab/eddys/easel/trunk
-
- When done, svn add the new RELEASE-xxx file.
-
-* Edit configure.ac: make sure version, date, copyright info is set correctly.
- Do this in easel and hmmer too, they won't use their configure's
- unless someone goes in there and manually does it, but they should
- be updated (e.g. version i1.1).
- emacs configure.ac
- emacs easel/configure.ac
- emacs hmmer/configure.ac
- autoconf; (cd easel; autoconf); (cd hmmer; autoconf);
- ./configure
- . release-notes/LICENSE.sh
+
+ feature branches and commit messages on github
+
+ When done, git add the new RELEASE-xxx file.
* Edit .bashrc
I use the following environment variables in the scripting below:
@@ -178,94 +204,146 @@ wrong, it's easy enough to come back and make a new tarball.
. ~/.bashrc
-* Build versions for the Tutorial runs.
+* Update the User guide
+ Do this in the git repo you've checked out in
+ $INFERNAL_RELEASE_NOTEBOOK
-This needs to be an icc/MPI version - mpi tests are included.
-Build a previous version (${INFERNAL_OLDVERSION}) in addition to the release candidate.
+ - Update version numbers in the installation section.
+ - Redo the tutorial exercises and add new output from new version.
+ Test with regression info, hopefully in
+ $INFERNAL_OLDRELEASE_NOTEBOOK/infernal/ or
+ $INFERNAL_OLDRELEASE_NOTEBOOK/wd-infernal/.
+ - Search all .tex documents for old version and update as necessary.
+ - Commit and push all changes.
+
+================================================================
+= Preparing a distribution
+================================================================
+
+We prepare and make a distro; later we test it thoroughly. This way
+we'll test exactly the version that's rolling out. If something goes
+wrong, it's easy enough to come back and make a new tarball.
-icc 11.1 with IntelMPI; on login-eddy
-gcc 4.1.2 without mpi; on login-eddy
+* Build versions for the tests.
-Note that my .bashrc includes some configuration of the compilation
-environment. I have functions "setup_icc_intel64" and "setup_icc_ia32"
-for setting up the appropriate icc. I also have a number of Intel MPI
-environment variables set.
+This needs to be an MPI version - mpi tests are included.
+Build a previous version (${INFERNAL_OLDVERSION}) in addition to the release candidate.
+
+gcc 4.8.1 with openmpi; on cbbdev**
+gcc 4.8.1 witout mpi; on cbbdev**
Note I don't do 'make devcheck' here, simply in the interest of time
(it takes about an hour). We'll do that later to make sure everything
passes.
-On login-eddy (our compile host):
- ssh login-eddy
+On cbbdev**:
+
+If ~/releases/infernal-release does not exist, create it:
+
+ ssh cbbdev13
+ git clone https://github.com/EddyRivasLab/infernal.git infernal-release
+ cd infernal-release
+ git checkout release-1.1.2
+
+ git clone https://github.com/EddyRivasLab/hmmer.git
+ (cd hmmer; git checkout release-3.1b3)
+
+ git clone https://github.com/EddyRivasLab/easel.git
+ (cd easel; git checkout release-0.43)
+
+ autoconf
+ ./configure
+
+OR if infernal-release already exists, make sure you switch to the
+proper release branches:
+
+ cd ~/releases/infernal-release
+ git checkout release-1.1.2
+ (cd hmmer; git checkout release-3.1b3)
+ (cd easel; git checkout release-0.43)
+
+Then pick up here:
+Build new version gcc (with MPI)
+ ssh cbbdev13
cd ~/releases/infernal-release
make distclean
- rm -rf build-gcc
- mkdir build-gcc
- cd build-gcc
- ../configure > build.out 2>&1
+ rm -rf build-gcc-mpi
+ mkdir build-gcc-mpi
+ cd build-gcc-mpi
+ ../configure --enable-mpi > build.out 2>&1
make >> build.out 2>&1
make dev >> build.out 2>&1
make check >> build.out 2>&1
- ssh login-eddy
+Build new version icc (without MPI)
+ ssh cbbdev13
cd ~/releases/infernal-release
- rm -rf build-icc-mpi
- mkdir build-icc-mpi
- cd build-icc-mpi
- setup_icc_intel64
- ../configure CC=icc LDFLAGS=-static-intel --enable-mpi > build.out 2>&1
+ rm -rf build-icc
+ mkdir build-icc
+ cd build-icc
+ ../configure CC=icc > build.out 2>&1
make >> build.out 2>&1
make dev >> build.out 2>&1
make check >> build.out 2>&1
- ssh login-eddy
+Build old version gcc (with MPI)
+ ssh cbbdev12
cd ~/releases/infernal-${INFERNAL_OLDVERSION}
make distclean
- rm -rf build-gcc
- mkdir build-gcc
- cd build-gcc
- ../configure > build.out 2>&1
+ rm -rf build-gcc-mpi
+ mkdir build-gcc-mpi
+ cd build-gcc-mpi
+ ../configure --enable-mpi > build.out 2>&1
make >> build.out 2>&1
make dev >> build.out 2>&1
make check >> build.out 2>&1
- ssh login-eddy
+Build old version icc (without MPI)
+ ssh cbbdev12
cd ~/releases/infernal-${INFERNAL_OLDVERSION}
- rm -rf build-icc-mpi
- mkdir build-icc-mpi
- cd build-icc-mpi
- setup_icc_intel64
- ../configure CC=icc LDFLAGS=-static-intel --enable-mpi > build.out 2>&1
+ rm -rf build-icc
+ mkdir build-icc
+ cd build-icc
+ ../configure CC=icc > build.out 2>&1
make >> build.out 2>&1
make dev >> build.out 2>&1
make check >> build.out 2>&1
+Also build with gcc on your Mac Desktop:
+ cd ~/releases/infernal-release
+ make distclean
+ rm -rf build-gcc
+ mkdir build-gcc
+ cd build-gcc
+ ../configure > build.out 2>&1
+ make >> build.out 2>&1
+ make dev >> build.out 2>&1
+ make check >> build.out 2>&1
+Check to make sure everything built okay.
+
This sets up:
Release candidate:
srcdir ~/releases/infernal-release
- builddir (gcc) ~/releases/infernal-release/build-gcc
- builddir (icc,MPI) ~/releases/infernal-release/build-icc-mpi
+ builddir (gcc,MPI) ~/releases/infernal-release/build-gcc
+ builddir (icc) ~/releases/infernal-release/build-icc-mpi
~/releases/infernal-${INFERNAL_OLDVERSION} (old version for regression):
srcdir ~/releases/infernal-${INFERNAL_OLDVERSION}
- builddir (gcc) ~/releases/infernal-${INFERNAL_OLDVERSION}/build-gcc
- builddir (icc,MPI) ~/releases/infernal-${INFERNAL_OLDVERSION}/build-icc-mpi
-
-* Update the user guide - including the tutorial section, and
- version numbers in the installation section.
- See last ~/notebook entry for scripts.
- Don't slack off on this step - it's a useful regression test as well.
+ builddir (gcc,MPI) ~/releases/infernal-${INFERNAL_OLDVERSION}/build-gcc
+ builddir (icc) ~/releases/infernal-${INFERNAL_OLDVERSION}/build-icc-mpi
* Commit (don't forget to commit in hmmer and easel too!)
- svn status
+ git status
do any cleanup...
- svn commit
+ git commit
cd hmmer
- svn commit
+ git commit
cd ../easel
- svn commit
+ git commit
+Potentially push too, if you're doing testing on your Mac desktop and
+need the latest revisions.
================================================================
= Creating a source distribution
@@ -282,23 +360,28 @@ below should match @INFERNAL_VERSION@, @EASEL_VERSION@ and
rm -f infernal-${INFERNAL_VERSION}.tar
rm -f infernal-${INFERNAL_VERSION}.tar.gz
-* Export a snapshot, alpha, beta, or release candidate from the development trunk:
- svn export https://svn.janelia.org/eddylab/eddys/src/infernal/trunk infernal-${INFERNAL_VERSION}
+* Clone from git and checkout release branches
+ ssh cbbdev13
+ git clone https://github.com/EddyRivasLab/infernal.git infernal-${INFERNAL_VERSION}
+ cd infernal-${INFERNAL_VERSION}
+ git checkout release-${INFERNAL_VERSION}
- or: Export a major or minor release from its branch
- svn export https://svn.janelia.org/eddylab/eddys/src/infernal/branches/1.1 infernal-${INFERNAL_VERSION}
+ git clone https://github.com/EddyRivasLab/easel.git
+ cd easel
+ git checkout release-0.43
+ cd ..
- cd infernal-${INFERNAL_VERSION}
- autoconf; (cd easel; autoconf); (cd hmmer; autoconf);
- ./configure
- . release-notes/LICENSE.sh
+ git clone https://github.com/EddyRivasLab/hmmer.git
+ cd hmmer
+ git checkout release-3.1b3
+# the crucial aclocal.m4 symlink UP one dir
+ ln -s ../easel/aclocal.m4 aclocal.m4
+ cd ..
- 1.1rc1: exported 4130/774
- 1.1rc2: exported 4342/834
- 1.1rc3: exported 4478/871
- 1.1rc4: exported 4498/874
- 1.1: exported 4547/889
- 1.1.1: exported 4710/917
+ cd infernal-${INFERNAL_VERSION}
+ autoconf; (cd easel; autoconf); (cd hmmer; autoconf);
+ ./configure;
+ . release-notes/LICENSE.sh
* Check that svn has file permissions right.
Both of these should have no output.
@@ -322,43 +405,34 @@ below should match @INFERNAL_VERSION@, @EASEL_VERSION@ and
* must do Easel and HMMER first
easel/devkit/sedition EASEL_VERSION ${EASEL_VERSION} EASEL_DATE "${EASEL_DATE}" EASEL_COPYRIGHT "${EASEL_COPYRIGHT}" easel/00README
- easel/devkit/sedition EASEL_VERSION ${EASEL_VERSION} EASEL_DATE "${EASEL_DATE}" EASEL_COPYRIGHT "${EASEL_COPYRIGHT}" easel/COPYRIGHT
easel/devkit/sedition EASEL_VERSION ${EASEL_VERSION} EASEL_DATE "${EASEL_DATE}" EASEL_COPYRIGHT "${EASEL_COPYRIGHT}" easel/INSTALL
easel/devkit/sedition EASEL_VERSION ${EASEL_VERSION} EASEL_DATE "${EASEL_DATE}" EASEL_COPYRIGHT "${EASEL_COPYRIGHT}" easel/LICENSE.tag
find easel -type f -exec easel/devkit/sedition-pp LICENSE easel/LICENSE.tag {} \;
- easel/devkit/sedition HMMER_VERSION ${HMMER_VERSION} HMMER_DATE "${HMMER_DATE}" HMMER_COPYRIGHT "${HMMER_COPYRIGHT}" hmmer/README
- easel/devkit/sedition HMMER_VERSION ${HMMER_VERSION} HMMER_DATE "${HMMER_DATE}" HMMER_COPYRIGHT "${HMMER_COPYRIGHT}" hmmer/COPYRIGHT
easel/devkit/sedition HMMER_VERSION ${HMMER_VERSION} HMMER_DATE "${HMMER_DATE}" HMMER_COPYRIGHT "${HMMER_COPYRIGHT}" hmmer/INSTALL
easel/devkit/sedition HMMER_VERSION ${HMMER_VERSION} HMMER_DATE "${HMMER_DATE}" HMMER_COPYRIGHT "${HMMER_COPYRIGHT}" hmmer/release-notes/LICENSE.tag
find hmmer -type f -exec easel/devkit/sedition-pp LICENSE hmmer/release-notes/LICENSE.tag {} \;
easel/devkit/sedition INFERNAL_VERSION ${INFERNAL_VERSION} INFERNAL_DATE "${INFERNAL_DATE}" INFERNAL_COPYRIGHT "${INFERNAL_COPYRIGHT}" README
- easel/devkit/sedition INFERNAL_VERSION ${INFERNAL_VERSION} INFERNAL_DATE "${INFERNAL_DATE}" INFERNAL_COPYRIGHT "${INFERNAL_COPYRIGHT}" COPYRIGHT
easel/devkit/sedition INFERNAL_VERSION ${INFERNAL_VERSION} INFERNAL_DATE "${INFERNAL_DATE}" INFERNAL_COPYRIGHT "${INFERNAL_COPYRIGHT}" INSTALL
easel/devkit/sedition INFERNAL_VERSION ${INFERNAL_VERSION} INFERNAL_DATE "${INFERNAL_DATE}" INFERNAL_COPYRIGHT "${INFERNAL_COPYRIGHT}" release-notes/LICENSE.tag
find . -type f -exec easel/devkit/sedition-pp LICENSE release-notes/LICENSE.tag {} \;
cd documentation/manpages/
- for manpage in *.man; do\
+ for manpage in *.man; do \
../../easel/devkit/sedition INFERNAL_VERSION ${INFERNAL_VERSION} INFERNAL_DATE "${INFERNAL_DATE}" INFERNAL_COPYRIGHT "${INFERNAL_COPYRIGHT}" INFERNAL_LICENSE "${INFERNAL_LICENSE}" INFERNAL_URL "${INFERNAL_URL}" $manpage;\
done
cd ../..
* compile documentation
cd documentation/userguide
-
- *** NOTE: for 1.1.1 release I had to modify the documentation/userguide/Makefile here to point to Sean's 'rman':
- 'RMAN = /groups/eddy/home/eddys/sw/Linux/bin/rman'. I'm not sure why I had to do this for 1.1.1
- but not for 1.1?
-
+ chmod +x ../../easel/devkit/rmanprocess.pl
make
mv Userguide.pdf ../../Userguide.pdf
cd ../..
* clean up files that don't belong in the distro,
- including hmmer's easel subdir.
- (I chose to remove Manuscripts because it's big (39M))
+ IMPORTANTLY INCLUDING THE .git SUBDIRS IN INFERNAL, HMMER AND EASEL
Note: after 1.1rc1, we changed this part: documentation/userguide
in infernal and hmmer, and documentation/ in easel are no longer
@@ -370,13 +444,18 @@ below should match @INFERNAL_VERSION@, @EASEL_VERSION@ and
make distclean
cp release-notes/RELEASE-${INFERNAL_VERSION} RELEASE-NOTES
+ rm -rf .git
rm -rf Bugs
rm -rf Manuscripts
rm -rf release-notes
rm -rf autobuild
+ rm makeTAGS.sh
+
+CHECK FOR ANY WEIRD conf*** (e.g. confQy52wQ) directories, and delete if you find them
+this burned me in 1.1.2 release.
cd hmmer
- rm -rf easel
+ rm -rf .git
rm -rf bugs
rm -rf contrib
rm -rf release-notes
@@ -385,9 +464,11 @@ below should match @INFERNAL_VERSION@, @EASEL_VERSION@ and
rm -rf autom4te.cache
cd ../easel
+ rm -rf .git
rm -f 00CHECKLIST LICENSE.csh.in LICENSE.tag
cd ..
+
rm *~
* record and finish release notes
@@ -415,6 +496,8 @@ Delete TO-DO sections and clean up for public consumption.
1.1rc4: 19.2 Mb (gzipped)
1.1: 19.2 Mb (gzipped)
1.1.1: 19.5 Mb (gzipped) added large testsuite/bug-i43.cm file
+ --- git flow ---
+ 1.1.2: 19.3 Mb (gzipped)
All subsequent tests are on this source distro.
@@ -422,122 +505,120 @@ All subsequent tests are on this source distro.
= Build for testing
================================================================
-It's important to build four sets of the executables for testing. Two
-on login-eddy (build-gcc and build-icc-mpi) and two on the cluster
-(build-cluster-gcc and build-cluster-icc-mpi). The cluster versions
-are now necessary (as of 1.1rc3) b/c those machines have recently
-changed and it's recommended to compile code on the cluster that you
-run on the cluster.
+We'll build two sets of the executables on cbbdev** for testing
+(build-gcc-mpi and build-icc), for which we'll run tests locally
+(tests-fast.sh) and on the compute farm (tests-slow.sh).
-We'll use the login-eddy-built executables for any tests we run
-locally (e.g. tests-fast.sh) and the cluster-built executables for any
-tests we submit to the cluster (e.g. tests-slow.sh).
-
-On login-eddy (our compile host):
- ssh login-eddy
+On cbbdev13 (our compile host):
+ ssh cbbdev13
cd ~/releases/infernal-${INFERNAL_VERSION}
- mkdir build-gcc
- cd build-gcc
- ../configure > build.out 2>&1
+ mkdir build-gcc-mpi
+ cd build-gcc-mpi
+ ../configure --enable-mpi > build.out 2>&1
make >> build.out 2>&1
make dev >> build.out 2>&1
make check >> build.out 2>&1
make devcheck >> build.out 2>&1
-1 line: ../configure > build.out 2>&1; make >> build.out 2>&1; make dev >> build.out 2>&1; make check >> build.out 2>&1; make devcheck >> build.out 2>&1
+1 line: ../configure --enable-mpi > build.out 2>&1; make >> build.out 2>&1; make dev >> build.out 2>&1; make check >> build.out 2>&1; make devcheck >> build.out 2>&1
- ssh login-eddy
+ ssh cbbdev13
cd ~/releases/infernal-${INFERNAL_VERSION}
- mkdir build-icc-mpi
- cd build-icc-mpi
- setup_icc_intel64
- ../configure CC=icc LDFLAGS=-static-intel --enable-mpi > build.out 2>&1
+ mkdir build-icc
+ cd build-icc
+ ../configure CC=icc > build.out 2>&1
make >> build.out 2>&1
make dev >> build.out 2>&1
make check >> build.out 2>&1
make devcheck >> build.out 2>&1
-1 line: setup_icc_intel64; ../configure CC=icc LDFLAGS=-static-intel --enable-mpi > build.out 2>&1; make >> build.out 2>&1; make dev >> build.out 2>&1; make check >> build.out 2>&1; make devcheck >> build.out 2>&1
+1 line: ../configure CC=icc > build.out 2>&1; make >> build.out 2>&1; make dev >> build.out 2>&1; make check >> build.out 2>&1; make devcheck >> build.out 2>&1
- ssh login-eddy
- qlogin -pe batch 16
- cd ~/releases/infernal-${INFERNAL_VERSION}
- mkdir build-cluster-gcc
- cd build-cluster-gcc
- ../configure > build.out 2>&1
- make >> build.out 2>&1
- make dev >> build.out 2>&1
- make check >> build.out 2>&1
- make devcheck >> build.out 2>&1
+================================================================
+= Build and check on all compile farm nodes
+================================================================
-1 line: ../configure > build.out 2>&1; make >> build.out 2>&1; make dev >> build.out 2>&1; make check >> build.out 2>&1; make devcheck >> build.out 2>&1
+CURRENTLY WE HAVE NO COMPILE FARM
- ssh login-eddy
- qlogin -pe batch 16
- cd ~/releases/infernal-${INFERNAL_VERSION}
- mkdir build-cluster-icc-mpi
- cd build-cluster-icc-mpi
- setup_icc_intel64
- ../configure CC=icc LDFLAGS=-static-intel --enable-mpi > build.out 2>&1
- make >> build.out 2>&1
- make dev >> build.out 2>&1
- make check >> build.out 2>&1
- make devcheck >> build.out 2>&1
+What I'll do is test it on the following:
+cbbdev21
+my Mac Desktop
+ody (Harvard)
+EBI
+Mac laptop (if convenient)
-1 line: setup_icc_intel64; ../configure CC=icc LDFLAGS=-static-intel --enable-mpi > build.out 2>&1; make >> build.out 2>&1; make dev >> build.out 2>&1; make check >> build.out 2>&1; make devcheck >> build.out 2>&1
+One issue is that these are all different file systems, whereas I used
+to do (at Janelia) the compile farm tests from one directory because
+the file system was shared.
-================================================================
-= Build and check on all compile farm nodes
-================================================================
+For here, I'll actually copy the src tarball (via public ftp site):
+UPDATE VERSION AS NECESSARY
+ wget http://ftp.ncbi.nlm.nih.gov/pub/nawrocki/infernal-1.1.2.tar.gz
+ tar xvfz infernal-1.1.2.tar.gz
-Look at current list of compile farm nodes on the lab wiki page.
-For each machine, we manually login and build through a
-'make devcheck' and verify that all tests pass.
+Then build and run tests:
-Do this in ~/releases/infernal-${INFERNAL_VERSION}
-(not in ~/releases/infernal-release/)
+ ./configure > build.out 2>&1
+ make >> build.out 2>&1
+ make dev >> build.out 2>&1
+ make check >> build.out 2>&1
+ make devcheck >> build.out 2>&1
-(NOTE: to save time at this step in 1.1rc2 --> 1.1, I
-created a mkdir.sh file that creates all the compile farm
-build dirs and copies the build.sh files, see
-~/releases/infernal-${INFERNAL_OLDVERSION}/mkdir.sh)
+1line:./configure > build.out 2>&1;make >> build.out 2>&1;make dev >> build.out 2>&1;make check >> build.out 2>&1;make devcheck >> build.out 2>&1;
-Example:
- cd ~/releases/infernal-${INFERNAL_VERSION}
- mkdir build-cf-xcompile
- cd build-cf-xcompile/
+ Check build.out
+
+ Then do some anecdotal tests, possibly from the tutorial.
-Create build.sh:
+ Then make sure that this works:
- cat build.sh
- ../configure > build.out 2>&1
- make V=1 >> build.out 2>&1
- make V=1 dev >> build.out 2>&1
- make V=1 check >> build.out 2>&1
- make V=1 devcheck >> build.out 2>&1
+ make clean
- ssh xcompile.int.janelia.org
- cd ~/releases/infernal-${INFERNAL_VERSION}/build-cf-xcompile
- sh build.sh
+Then do the same in hmmer and easel (to test those 'release'
+versions). Actually do this by removing the src distro, unpacking it
+again, and redoing for hmmer and then easel. For hmmer, you'll need to
+copy all the easel files into hmmer.
+
+Do hmmer:
+ cd ..
+ rm -rf infernal-1.1.2
+ tar xvf infernal-1.1.2.tar.gz
+ cd infernal-1.1.2/hmmer
+ cp -r ../easel ./easel
+ sh ./configure > build.out 2>&1
+ make >> build.out 2>&1
+ make dev >> build.out 2>&1
+ make check >> build.out 2>&1
+
+1line: sh ./configure > build.out 2>&1; make >> build.out 2>&1; make dev >> build.out 2>&1; make check >> build.out 2>&1;
+
+ check build.out
+ run anecdotal tests
+ make clean
+
+And finally easel:
+ cd ../..
+ rm -rf infernal-1.1.2
+ tar xvf infernal-1.1.2.tar.gz
+ cd infernal-1.1.2/easel
+ sh ./configure > build.out 2>&1
+ make >> build.out 2>&1
+ make dev >> build.out 2>&1
+ make check >> build.out 2>&1
+
+1line: sh ./configure > build.out 2>&1; make >> build.out 2>&1; make dev >> build.out 2>&1; make check >> build.out 2>&1;
-Wait for it to finish. Then manually verify that all tests pass.
-List of all compile farm nodes that should pass all tests as of
-last release (1.1rc2):
+ check build.out
+ run anecdotal tests
+ make clean
-(See http://wiki.int.janelia.org/wiki/display/EddyLab/Compile+Farm)
- for current list and for machine-specific instructions for building)
- 1) Intel Apple OS/X (xcompile.int.janelia.org)
- 2) PowerPC IBM AIX (cf-ppc2.int.janelia.org)
- 3) Linux on an AMD Opteron (cf-suse.int.janelia.org)
- 4) Debian 6.0.3 AMD64 (cf-debian.int.janelia.org)
- 5) Ubuntu 12.04 AMD64 (cf-ubuntu.int.janelia.org)
- 6) Fedora 16 AMD64 (cf-fedora.int.janelia.org)
- 7) OpenBSD 5.0 AMD64 (cf-openbsd.int.janelia.org)
- 8) OpenSuse 12.1 AMD64 (cf-opensuse.int.janelia.org)
- 9) FreeBSD 8.2 AMD64 (cf-freebsd.int.janelia.org)
-10) Ubuntu 12.0.4.1 32-bit (cf-ubuntu32)
+ inf hmmer easel
+ncbimac2056 pass
+cbbdev21
+ebi
+ody
================================================================
= Testing
@@ -557,7 +638,7 @@ manually look at each line for errors.
These instructions should work post-1.1rc2:
Set up tests:
- ssh login-eddy
+ ssh cbbdev13
cd ${INFERNAL_RELEASE_NOTEBOOK}
mkdir tests
mkdir tests/out-files/
@@ -569,28 +650,14 @@ Set up tests:
sh cp-required-files.sh
Run tests:
-tests-fast*.sh run on login-eddy, takes about 1 minute
-tests-fast-valgrind*.sh run valgrind tests on login-eddy, takes about 30 minutes
-tests-slow*.sh submit to cluster, takes about 2.5 hours
+tests-fast*.sh run on cbbdev13, takes about 1 minute
+tests-fast-valgrind*.sh run valgrind tests on cbbdev13y, takes about 30 minutes
+tests-slow*.sh submit to compute farm, takes about 2.5 hours
time sh tests-fast.sh > tests-fast.out
time sh tests-fast-oldversion.sh > tests-fast-oldversion.out
diff tests-fast.out tests-fast-oldversion.out > tests-fast.diff
-NOTE: With 1.1rc1 and 1.1rc2, I executed 'tests-fast-valgrind.sh' and
-'tests-fast-valgrind-oldversion.sh' via 'submit-valgrind.sh', but
-starting with 1.1rc3 I run them on login-eddy. The reason is that the
-cluster nodes were showing weird valgrind errors that I could never
-account for. This happened on both the current and 'new' cluster
-nodes. The current nodes had changed since the 1.1rc2 release in that
-a new OS had been installed on them (see Feb 26 2013 email from Rob
-Lines). I never figured out the root of the problem, but decided to
-not pursue it because it could only lead to more changes in the 1.1rc3
-code, which were more likely to break something than fix anything
-broken (if anything was in fact broken!) given the stability of hmmer3
-and infernal 1.1rc1 and 1.1rc2 all of which valgrind was reporting
-problems in on the cluster nodes.
-
sh run-valgrind.sh
Takes about 1 hour. Note run-valgrind does not run jobs in parallel
@@ -602,11 +669,6 @@ leaks or errors.
diff tests-fast-valgrind.out tests-fast-valgrind-oldversion.out > tests-fast-valgrind.diff
sh tests-slow.sh
-
- *** NOTE: post-1.1rc3: before running tests-slow-oldversion.sh, change
- tests-slow-oldversion.sh directories from build-gcc to
- build-cluster-gcc and build-icc-mpi to build-cluster-icc-mpi
-
sh tests-slow-oldversion.sh
Wait for these to finish (about 3 hours)
@@ -621,29 +683,30 @@ Make sure all diff output includes only expected differences.
Make sure all err-files/* and err-oldversion-files/* (besides valg.*err) are empty.
-Remember to test on both builds (gcc and icc-mpi), the scripts above
+Remember to test on both builds (gcc-mpi and icc), the scripts above
already do this, except for the valgrind ones.
Then run some anecdotal tests.
mkdir anecdotes
Some examples:
cd anecdotes
- ~/releases/infernal-${INFERNAL_VERSION}/build-gcc/src/cmfetch ~/db/rfam_11.0/Rfam.cm.1_1 5S_rRNA > 5S.cm
- ~/releases/infernal-${INFERNAL_OLDVERSION}/build-gcc/src/cmfetch ~/db/rfam_11.0/Rfam.cm.1_1 5S_rRNA > 5S.old.cm
+ ~/releases/infernal-${INFERNAL_VERSION}/build-gcc-mpi/src/cmfetch ~/db/rfam/rfam_12.1/Rfam.cm 5S_rRNA > 5S.cm
+ ~/releases/infernal-${INFERNAL_OLDVERSION}/build-gcc-mpi/src/cmfetch ~/db/rfam/rfam_12.1/Rfam.cm 5S_rRNA > 5S.old.cm
diff 5S.cm 5S.old.cm
- ~/releases/infernal-${INFERNAL_VERSION}/build-gcc/src/cmstat 5S.cm
- ~/releases/infernal-${INFERNAL_VERSION}/build-gcc/src/cmstat 5S.old.cm
- ~/releases/infernal-${INFERNAL_VERSION}/build-gcc/src/cmsearch 5S.cm ~/genomes/hvol.fa
- ~/releases/infernal-${INFERNAL_OLDVERSION}/build-gcc/src/cmsearch 5S.cm ~/genomes/hvol.fa
- ~/releases/infernal-${INFERNAL_VERSION}/build-gcc/src/cmpress 5S.cm
- ~/releases/infernal-${INFERNAL_OLDVERSION}/build-gcc/src/cmpress 5S.old.cm
- ~/releases/infernal-${INFERNAL_VERSION}/build-gcc/src/cmscan 5S.cm ~/genomes/hvol.fa
- ~/releases/infernal-${INFERNAL_VERSION}/build-gcc/src/cmscan 5S.old.cm ~/genomes/hvol.fa
- ~/releases/infernal-${INFERNAL_VERSION}/build-gcc/src/cmsearch -A 5S.sto 5S.cm ~/genomes/hvol.fa
- ~/releases/infernal-${INFERNAL_VERSION}/build-gcc/easel/miniapps/esl-reformat fasta 5S.sto > 5S.fa
- ~/releases/infernal-${INFERNAL_VERSION}/build-gcc/src/cmalign 5S.cm 5S.fa
-
-Also, do a rmark3 benchmark with default settings and --mid.
+ ~/releases/infernal-${INFERNAL_VERSION}/build-gcc-mpi/src/cmstat 5S.cm
+ ~/releases/infernal-${INFERNAL_VERSION}/build-gcc-mpi/src/cmstat 5S.old.cm
+ ~/releases/infernal-${INFERNAL_VERSION}/build-gcc-mpi/src/cmsearch 5S.cm /panfs/pan1/infernal/db/other-genomes/hvol.fa
+ ~/releases/infernal-${INFERNAL_OLDVERSION}/build-gcc-mpi/src/cmsearch 5S.cm /panfs/pan1/infernal/db/other-genomes/hvol.fa
+ ~/releases/infernal-${INFERNAL_VERSION}/build-gcc-mpi/src/cmpress 5S.cm
+ ~/releases/infernal-${INFERNAL_OLDVERSION}/build-gcc-mpi/src/cmpress 5S.old.cm
+ ~/releases/infernal-${INFERNAL_VERSION}/build-gcc-mpi/src/cmscan 5S.cm /panfs/pan1/infernal/db/other-genomes/hvol.fa
+ ~/releases/infernal-${INFERNAL_VERSION}/build-gcc-mpi/src/cmscan 5S.old.cm /panfs/pan1/infernal/db/other-genomes/hvol.fa
+ ~/releases/infernal-${INFERNAL_VERSION}/build-gcc-mpi/src/cmsearch -A 5S.sto 5S.cm /panfs/pan1/infernal/db/other-genomes/hvol.fa
+ ~/releases/infernal-${INFERNAL_VERSION}/build-gcc-mpi/easel/miniapps/esl-reformat fasta 5S.sto > 5S.fa
+ ~/releases/infernal-${INFERNAL_VERSION}/build-gcc-mpi/src/cmalign 5S.cm 5S.fa
+
+Also, do a rmark3 benchmark with default settings and --mid for
+both new and old versions.
(These commands should work post-i1.1rc2 if you're doing a small
update release)
@@ -675,13 +738,10 @@ Edit version number (may not be necessary) in do-symlink.sh, do-all.sh, do-pp.sh
emacs do-pp.sh
sh do-symlink.sh
-NOTE: as of 1.1, do-all.sh won't work as written b/c new cluster
-doesn't accept "-l excl=true" flag. To fix it, copy the old
-~/releases/infernal-${INFERNAL_VERSION}/rmark/rmark-master.pl
-to the current dir to ./tmp-rmark-master.pl, then replace
-'-l excl=true' to '-pe batch 16' (if the cluster still has 16
-CPUs per node), then modify do-all.sh so it calls tmp-rmark-master.pl
-instead of ~/releases/infernal-${INFERNAL_VERSION}/rmark/rmark-master.pl.
+NOTE: as of 1.1, do-all.sh won't work as written b/c it's set-up
+for Janelia's cluster. As of 1.1.3 and beyond, you should be able
+to look at/copy
+${INFERNAL_OLDRELEASE_NOTEBOOK}/tests/rmark3/tmp-rmark-master.pl
sh do-all.sh
Wait for jobs to finish (approximately 20 min)
@@ -691,7 +751,7 @@ need to copy the 'rmark-rocplot' executable from a build dir into the
rmark directory, because rmark-pp.sh expects all the rmark scripts to
be in the same dir, then delete it when we're done with it:
- cp ~/releases/infernal-${INFERNAL_VERSION}/build-cluster-gcc/rmark/rmark-rocplot ~/releases/infernal-${INFERNAL_VERSION}/rmark/
+ cp ~/releases/infernal-${INFERNAL_VERSION}/build-gcc-mpi/rmark/rmark-rocplot ~/releases/infernal-${INFERNAL_VERSION}/rmark/
sh do-pp.sh
Wait for jobs to finish (approximately 5 min)
rm ~/releases/infernal-${INFERNAL_VERSION}/rmark/rmark-rocplot
@@ -701,16 +761,6 @@ ${INFERNAL_OLDRELEASE_NOTEBOOK}/tests/rmark3/
Check the userguide (Userguide.pdf).
-Ensure 'make clean' and 'make distclean' finish without errors. The
-1.1rc1 distro had a bug that caused errors for both of these. To do
-this:
- cd ~/releases/infernal-${INFERNAL_VERSION}/
- sh ./configure;
- make
- make dev
- make clean
- make distclean
-
================================================================
= Binary distros
================================================================
@@ -718,15 +768,6 @@ this:
cd ${INFERNAL_RELEASE_NOTEBOOK}
mkdir Distros; cd Distros
-After talking with Sean, we decided to distribute linux-intel-gcc
-instead of linux-intel-ia32 and linux-intel-x86_64 because of this
-warning:
- icc: warning #10237: -lcilkrts linked in dynamically, static library not available
-If this gets resolved in the future, we may go back to distributing
-binaries built with icc (64 and 32).
-
-The lcilkrts is still a problem as of 1.1.1 (July 23 2014)
-
Note: the configure call differs from the one Sean uses in hmmer. I
specify --prefix. If I don't do that I get a 'make install' error
because I don't have permission to change the permissions on the man
@@ -740,7 +781,7 @@ Three builds:
cygwin
linux-intel-gcc:
- ssh login-eddy
+ ssh cbbdev13
export INFERNAL_DISTRO=linux-intel-gcc
cd ${INFERNAL_RELEASE_NOTEBOOK}/Distros
tar zxf ~/releases/infernal-${INFERNAL_VERSION}.tar.gz
@@ -766,19 +807,23 @@ linux-intel-gcc:
gzip infernal-${INFERNAL_VERSION}-${INFERNAL_DISTRO}.tar
-macosx-intel build (on Sean's desktop):
- ssh 10.123.13.171
+macosx-intel build (on my Mac Desktop):
+You'll need to update the release notebook dir here next release
export INFERNAL_DISTRO=macosx-intel
+ export INFERNAL_RELEASE_NOTEBOOK=$UH/notebook/16_0611_inf_1p1p2_release
+ export INFERNAL_VERSION=1.1.2
cd ${INFERNAL_RELEASE_NOTEBOOK}/Distros
- tar zxf ~/releases/infernal-${INFERNAL_VERSION}.tar.gz
+ tar zxf $UH/releases/infernal-${INFERNAL_VERSION}.tar.gz
mv infernal-${INFERNAL_VERSION} infernal-${INFERNAL_VERSION}-${INFERNAL_DISTRO}
cd infernal-${INFERNAL_VERSION}-${INFERNAL_DISTRO}
mkdir binaries
mkdir build-${INFERNAL_DISTRO}
cd build-${INFERNAL_DISTRO}
- ../configure --bindir=${INFERNAL_RELEASE_NOTEBOOK}/Distros/infernal-${INFERNAL_VERSION}-${INFERNAL_DISTRO}/binaries --prefix=${INFERNAL_RELEASE_NOTEBOOK}/Distros/infernal-${INFERNAL_VERSION}-${INFERNAL_DISTRO} > ${INFERNAL_RELEASE_NOTEBOOK}/Distros/build-${INFERNAL_DISTRO}.out 2>&1
+ ../configure --bindir=${INFERNAL_RELEASE_NOTEBOOK}/Distros/infernal-${INFERNAL_VERSION}-${INFERNAL_DISTRO}/binaries \
+ --prefix=${INFERNAL_RELEASE_NOTEBOOK}/Distros/infernal-${INFERNAL_VERSION}-${INFERNAL_DISTRO} \
+ > ${INFERNAL_RELEASE_NOTEBOOK}/Distros/build-${INFERNAL_DISTRO}.out 2>&1
make >> ${INFERNAL_RELEASE_NOTEBOOK}/Distros/build-${INFERNAL_DISTRO}.out 2>&1
make dev >> ${INFERNAL_RELEASE_NOTEBOOK}/Distros/build-${INFERNAL_DISTRO}.out 2>&1
make check >> ${INFERNAL_RELEASE_NOTEBOOK}/Distros/build-${INFERNAL_DISTRO}.out 2>&1
diff --git a/release-notes/RELEASE-1.1.2 b/release-notes/RELEASE-1.1.2
new file mode 100644
index 00000000..d5894088
--- /dev/null
+++ b/release-notes/RELEASE-1.1.2
@@ -0,0 +1,29 @@
+Infernal 1.1.2 release notes
+http://eddylab.org/infernal/
+EPN, Fri Jun 24 10:50:16 2016
+________________________________________________________________
+
+Infernal 1.1.2 is the second update release for Infernal 1.1.
+
+Notable changes from 1.1.1:
+
+ - cmscan is significantly improved, and can now be used for genome
+ annotation:
+ o speed improvements due to storage of models in memory instead of
+ rereading from disk for each query sequence
+ o overlapping hits are annotated in tabular output files
+ with the --tblout --fmt 2 option combination
+ o clan membership (a la Rfam) is annotated in tabular output files
+ with the --tblout --fmt 2 --clanin option combination.
+ o there is no longer a maximum query sequence length
+
+ - the Easel and HMMER3 libraries which are included with Infernal have
+ undergone numerous bug fixes and improvements.
+
+ - Fixed bug #i44, which caused a problem with the cmalign --mapstr
+ option if only one half of a base pair in the input alignment
+ structure was modelled by a consensus position (and the other was
+ modelled as an insert).
+
+________________________________________________________________
+For more information, see http://eddylab.org/infernal/
diff --git a/rmark/rmark-create.c b/rmark/rmark-create.c
index 71942c0b..793b59a3 100644
--- a/rmark/rmark-create.c
+++ b/rmark/rmark-create.c
@@ -530,7 +530,6 @@ remove_fragments(struct cfg_s *cfg, ESL_MSA *msa, ESL_MSA **ret_filteredmsa, int
int *useme = NULL;
double len = 0.0;
int i;
- int nfrags;
int status;
/* min length is cfg->fragfrac * average length */
@@ -539,7 +538,7 @@ remove_fragments(struct cfg_s *cfg, ESL_MSA *msa, ESL_MSA **ret_filteredmsa, int
len *= cfg->fragfrac / (double) msa->nseq;
ESL_ALLOC(useme, sizeof(int) * msa->nseq);
- for (nfrags = 0, i = 0; i < msa->nseq; i++)
+ for (i = 0; i < msa->nseq; i++)
useme[i] = (esl_abc_dsqrlen(msa->abc, msa->ax[i]) < len) ? 0 : 1;
if ((status = esl_msa_SequenceSubset(msa, useme, ret_filteredmsa)) != eslOK) goto ERROR;
@@ -580,7 +579,6 @@ separate_sets(struct cfg_s *cfg, ESL_MSA *msa, int **ret_i_am_train, int **ret_i
int nc = 0;
int c;
int ctrain; /* index of the cluster that becomes the training alignment */
- int ntrain; /* number of seqs in the training alignment */
int nskip;
int i, i2;
int status;
@@ -591,7 +589,6 @@ separate_sets(struct cfg_s *cfg, ESL_MSA *msa, int **ret_i_am_train, int **ret_i
if ((status = esl_msacluster_SingleLinkage(msa, cfg->idthresh1, &assignment, &nin, &nc)) != eslOK) goto ERROR;
ctrain = esl_vec_IArgMax(nin, nc);
- ntrain = esl_vec_IMax(nin, nc);
for (i = 0; i < msa->nseq; i++) i_am_train[i] = (assignment[i] == ctrain) ? 1 : 0;
if ((status = esl_msa_SequenceSubset(msa, i_am_train, &trainmsa)) != eslOK) goto ERROR;
diff --git a/src/Rfam.12.1.claninfo b/src/Rfam.12.1.claninfo
new file mode 100644
index 00000000..fbdf3770
--- /dev/null
+++ b/src/Rfam.12.1.claninfo
@@ -0,0 +1,104 @@
+CL00001 tRNA cyano_tmRNA tRNA-Sec mt-tmRNA
+CL00003 Metazoa_SRP Bacteria_small_SRP Fungi_SRP Dictyostelium_SRP Bacteria_large_SRP Plant_SRP Protozoa_SRP Archaea_SRP
+CL00004 Telomerase-cil
+CL00008 U54 snoU54
+CL00010 Hammerhead_3 Hammerhead_1 Hammerhead_HH9 Hammerhead_II Hammerhead_HH10
+CL00011 GlmZ_SraJ GlmY_tke1
+CL00012 SAM SAM-IV
+CL00013 7SK Arthropod_7SK
+CL00014 CRISPR-DR2 CRISPR-DR4 CRISPR-DR14 CRISPR-DR17 CRISPR-DR25 CRISPR-DR43 CRISPR-DR66
+CL00015 CRISPR-DR5 CRISPR-DR7 CRISPR-DR63 CRISPR-DR64
+CL00016 FinP traJ_5
+CL00017 IRES_HCV IRES_Pesti
+CL00018 SCARNA24 SCARNA3
+CL00019 SCARNA4 SCARNA15
+CL00021 SNORA16 SNORA2 snopsi28S-3327 snR189 snR46 S_pombe_snR46
+CL00022 SNORA3 snR11
+CL00023 SNORA4 snR83
+CL00024 SNORA5 snR85
+CL00025 SNORA7 snR81
+CL00026 SNORA8 snR31
+CL00027 SNORA9 snR33 snR43 S_pombe_snR33
+CL00028 SNORA13 snR35 S_pombe_snR35
+CL00029 SNORA43 SNORA17
+CL00030 SNORA20 SNORA29
+CL00031 SNORA21 snR10 S_pombe_snR10
+CL00032 SNORA27 SNORA26 snR42 S_pombe_snR42
+CL00033 SNORA28 snopsi18S-841 snR80
+CL00034 SNORA50 SNORA54 SNORA35 SNORA76
+CL00035 SNORA36 snR36 snR44 S_pombe_snR36
+CL00036 SNORA44 SNORA58 snR161 snR9
+CL00037 SNORA48 snR86
+CL00038 SNORA66 snoR98 SNORA52 SNORA18 snoR80 snR49 snR5 S_pombe_snR5
+CL00039 SNORA56 snR8
+CL00040 SNORA62 snR3 snR82 S_pombe_snR3
+CL00041 SNORA64 snR37
+CL00042 SNORA65 snR34 snoR2
+CL00043 SNORA74 snR191
+CL00044 SNORD12 snR190
+CL00045 SNORD15 snR75 snR13 snoZ5
+CL00046 SNORD16 snR87
+CL00047 SNORD18 snoU18
+CL00048 SNORD19 SNORD19B
+CL00049 SNORD25 snR56
+CL00050 SNORD26 SNORD81
+CL00051 SNORD36 SNORD29 snoZ223 SNORD38 snosnR69 snosnR61 snosnR71 SNORD78 snoR69Y snR47 snoU36a
+CL00052 SNORD30 snoU30
+CL00053 SNORD31 snoZ17 snR67 snoR35
+CL00054 SNORD33 snoZ196 SNORD51 snosnR55 snoMe18S-Um1356 snoMe28S-Am982 snR39 snR40
+CL00055 SNORD34 snR62
+CL00056 SNORD35 snoZ161_228 snR73
+CL00057 SNORD39 snoZ7 snoZ101 SNORD65 snoR77Y snR77
+CL00058 SNORD57 SNORD41 snR51
+CL00059 SNORD43 snR70
+CL00060 SNORD44 snoZ102_R77
+CL00061 SNORD46 snR63
+CL00062 SNORD49 snoZ112 snoU49
+CL00063 SNORD52 SNORD53_SNORD92 snoZ157 snR78
+CL00064 SNORD58 SNORD99
+CL00065 snoZ159 SNORD59 snosnR54
+CL00066 SNORD60 snoR1 snosnR48 snoMe28S-G3255 sn2903
+CL00067 SNORD61 snoU61 SNORD125
+CL00068 SNORD62 snoR41 snR41
+CL00069 SNORD79 SNORD113 SNORD74 snoR44_J54 snosnR64 snoMe28S-Cm2645 SNORD64 SNORD112 SNORD109A
+CL00070 snosnR60_Z15 SNORD77 Afu_263
+CL00071 SNORD88 snR76 snoR118
+CL00072 SNORD96 SNORD2
+CL00073 snoR30 SNORD100
+CL00074 SNORD101 snoR60
+CL00075 SNORD105 snoU105B
+CL00076 SNORD110 snoR14
+CL00077 SNORND104 snR58
+CL00078 SNORA73 snR30
+CL00079 snR68 snoR27
+CL00080 snoR53 snoR53Y
+CL00081 snoZ279_R105_R108 snoU13
+CL00082 snoU89 snoU85
+CL00083 mir-6 mir-11
+CL00084 mir-3 mir-318
+CL00085 mir-16 mir-15
+CL00086 mir-28 mir-708
+CL00087 mir-34 mir-449
+CL00088 mir-36 mir-42 mir-35
+CL00089 mir-190 mir-50
+CL00090 mir-74 mir-73
+CL00091 bantam mir-81
+CL00092 mir-137 mir-234
+CL00093 mir-183 mir-182 mir-263 mir-228
+CL00094 mir-216 mir-283
+CL00095 mir-279 mir-996
+CL00096 mir-515 mir-290 mir-302 miR-430
+CL00097 mir-BART1 mir-BART3
+CL00098 MIR169_2 MIR169_5
+CL00099 MIR171_1 MIR171_2
+CL00100 U3 Fungi_U3 Plant_U3 ACEA_U3
+CL00101 Cobalamin
+CL00102 group-II-D1D4-1 group-II-D1D4-2 group-II-D1D4-3 group-II-D1D4-4 group-II-D1D4-5 group-II-D1D4-6 group-II-D1D4-7
+CL00103 SNORD11 SNORD11B
+CL00104 HBV_epsilon AHBV_epsilon
+CL00105 SraC_RyeA RyeB
+CL00106 CsrB CsrC PrrB_RsmZ RsmY TwoAYGGAY rsmX
+CL00108 suhB
+CL00110 mir-19 mir-363
+CL00111 SSU_rRNA_bacteria SSU_rRNA_archaea SSU_rRNA_eukarya SSU_rRNA_microsporidia
+CL00112 LSU_rRNA_archaea LSU_rRNA_bacteria LSU_rRNA_eukarya
diff --git a/src/bandcyk-truncation-test.c b/src/bandcyk-truncation-test.c
index dd034835..7345249b 100644
--- a/src/bandcyk-truncation-test.c
+++ b/src/bandcyk-truncation-test.c
@@ -53,7 +53,6 @@ static ESL_OPTIONS options[] = {
{ "--betaW", eslARG_REAL, "1E-5", NULL, "x>0.",NULL, NULL, NULL, "set tail probability thresh for W calculation to ", 0 },
{ "--beta1", eslARG_REAL, "1E-5", NULL, "x>0.",NULL, NULL, NULL, "set tail probability thresh for dmin1/dmax1 to ", 0 },
{ "--beta2", eslARG_REAL, "1E-6", NULL, "x>0.",NULL, NULL, NULL, "set tail probability thresh for dmin2/dmax2 to ", 0 },
- { "--verbose", eslARG_NONE, FALSE, NULL, NULL, NULL, NULL, NULL, "show output (default: silently return 0 on success)", 0 },
{ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 },
};
static char usage[] = "[-options] where width Z1 < Z2.";
@@ -80,7 +79,6 @@ main(int argc, char **argv)
double gbeta1; /* geometric decay constant, truncation error calc */
double gbeta2; /* geometric decay constant, truncation error calc */
double g; /* log of an estimated gamma[n] */
- int be_verbose;
ESL_ALPHABET *abc = NULL;
char errbuf[eslERRBUFSIZE]; /* for error messages */
CM_QDBINFO *qdbinfo1 = NULL; /* holds dmin1/dmax1 and dmin2/dmax2 for first choice of Z */
@@ -95,7 +93,6 @@ main(int argc, char **argv)
betaW = esl_opt_GetReal (go, "--betaW");
beta1 = esl_opt_GetReal (go, "--beta1");
beta2 = esl_opt_GetReal (go, "--beta2");
- be_verbose = esl_opt_GetBoolean(go, "--verbose");
if (Z1 >= Z2) cm_Fail("Please set a width Z1 < width Z2, else the check won't work right.");
diff --git a/src/cm_alidisplay.c b/src/cm_alidisplay.c
index eca937da..07e67f2f 100644
--- a/src/cm_alidisplay.c
+++ b/src/cm_alidisplay.c
@@ -76,7 +76,6 @@ cm_alidisplay_Create(CM_t *cm, char *errbuf, CM_ALNDATA *adata, const ESL_SQ *sq
int pos; /* position in growing ali */
int lc, rc; /* indices for left, right pos in consensus */
int symi, symj;
- int d;
char mode;
int lrf, rrf; /* chars in annotation line; left, right */
int lstr, rstr; /* chars in structure line; left, right */
@@ -416,7 +415,6 @@ cm_alidisplay_Create(CM_t *cm, char *errbuf, CM_ALNDATA *adata, const ESL_SQ *sq
lpost = '.'; /* init to gap, if it corresponds to a residue, we'll reset it below */
rpost = '.'; /* init to gap, if it corresponds to a residue, we'll reset it below */
}
- d = tr->emitr[ti] - tr->emitl[ti] + 1;
mode = tr->mode[ti];
/* Calculate four of the six lines: rfline, csline, model, and aseq.
diff --git a/src/cm_alndata.c b/src/cm_alndata.c
index 709a800f..e4fca5c3 100644
--- a/src/cm_alndata.c
+++ b/src/cm_alndata.c
@@ -208,7 +208,7 @@ DispatchSqBlockAlignment(CM_t *cm, char *errbuf, ESL_SQ_BLOCK *sq_block, float m
char mode; /* mode passed to DispatchSqAlignment() */
int cp9b_valid; /* passed to DispatchSqAlignment() */
- ESL_ALLOC(dataA, sizeof(CM_ALNDATA *) * sq_block->count);
+ ESL_ALLOC(dataA, sizeof(CM_ALNDATA *) * ESL_MAX(1, sq_block->count)); // avoid 0 malloc
for(j = 0; j < sq_block->count; j++) dataA[j] = NULL;
/* DispatchSqAligment() needs a mode, pipeline pass index, and
diff --git a/src/cm_dpalign.c b/src/cm_dpalign.c
index ea402391..7d7ed88c 100644
--- a/src/cm_dpalign.c
+++ b/src/cm_dpalign.c
@@ -270,7 +270,7 @@ cm_alignT_hb(CM_t *cm, char *errbuf, ESL_DSQ *dsq, int L, float size_limit, int
ESL_STACK *pda; /* stack that tracks bifurc parent of a right start */
int v,j,d,i; /* indices for state, j, subseq len */
int k; /* subseq len for bifurcs */
- int z; /* state index */
+ /*int z;*/ /* state index */
int y, yoffset; /* child state y, it's offset */
int bifparent; /* B_st parent */
int b; /* local begin state */
@@ -340,7 +340,7 @@ cm_alignT_hb(CM_t *cm, char *errbuf, ESL_DSQ *dsq, int L, float size_limit, int
if (cm->sttype[v] == B_st) {
k = shmx->kshadow[v][jp_v][dp_v]; /* k = offset len of right fragment */
- z = cm->cnum[v];
+ /*z = cm->cnum[v];*/
/* Store info about the right fragment that we'll retrieve later:
*/
@@ -2201,7 +2201,6 @@ cm_OptAccAlign(CM_t *cm, char *errbuf, ESL_DSQ *dsq, int L, float size_limit, CM
int sdr; /* StateRightDelta(cm->sttype[v] */
int j_sdr; /* j - sdr */
int d_sd; /* d - sd */
- float tsc; /* a transition score */
int have_el; /* TRUE if CM has local ends on, otherwise FALSE */
/* the DP matrices */
@@ -2244,7 +2243,6 @@ cm_OptAccAlign(CM_t *cm, char *errbuf, ESL_DSQ *dsq, int L, float size_limit, CM
/* Main recursion */
for (v = cm->M-1; v >= 0; v--) {
- float const *tsc_v = cm->tsc[v]; /* transition scores for state v */
sd = StateDelta(cm->sttype[v]);
sdr = StateRightDelta(cm->sttype[v]);
@@ -2321,7 +2319,6 @@ cm_OptAccAlign(CM_t *cm, char *errbuf, ESL_DSQ *dsq, int L, float size_limit, CM
*/
for (y = cm->cfirst[v]; y < (cm->cfirst[v] + cm->cnum[v]); y++) {
yoffset = y - cm->cfirst[v];
- tsc = tsc_v[yoffset];
j_sdr = 0;
for (j = sdr; j <= L; j++, j_sdr++) {
d_sd = 0;
@@ -3001,7 +2998,6 @@ cm_CYKOutsideAlign(CM_t *cm, char *errbuf, ESL_DSQ *dsq, int L, float size_limit
float **esc_vAA; /* ptr to cm->oesc, optimized emission scores */
float escore; /* an emission score, tmp variable */
int voffset; /* index of v in t_v(y) transition scores */
- int emitmode; /* EMITLEFT, EMITRIGHT, EMITPAIR, EMITNONE, for state y */
int sd; /* StateDelta(cm->sttype[y]) */
int sdr; /* StateRightDelta(cm->sttype[y] */
@@ -3111,7 +3107,6 @@ cm_CYKOutsideAlign(CM_t *cm, char *errbuf, ESL_DSQ *dsq, int L, float size_limit
if ((cm->flags & CMH_LOCAL_END) && NOT_IMPOSSIBLE(cm->endsc[v])) {
sdr = StateRightDelta(cm->sttype[v]); /* note sdr is for state v */
sd = StateDelta(cm->sttype[v]); /* note sd is for state v */
- emitmode = Emitmode(cm->sttype[v]); /* note emitmode is for state v */
for (j = 0; j <= L; j++) {
for (d = 0; d <= j; d++) {
@@ -4023,7 +4018,6 @@ cm_OutsideAlign(CM_t *cm, char *errbuf, ESL_DSQ *dsq, int L, float size_limit, i
float **esc_vAA; /* ptr to cm->oesc, optimized emission scores */
float escore; /* an emission score, tmp variable */
int voffset; /* index of v in t_v(y) transition scores */
- int emitmode; /* EMITLEFT, EMITRIGHT, EMITPAIR, EMITNONE, for state y */
int sd; /* StateDelta(cm->sttype[y]) */
int sdr; /* StateRightDelta(cm->sttype[y] */
@@ -4128,7 +4122,6 @@ cm_OutsideAlign(CM_t *cm, char *errbuf, ESL_DSQ *dsq, int L, float size_limit, i
if ((cm->flags & CMH_LOCAL_END) && NOT_IMPOSSIBLE(cm->endsc[v])) {
sdr = StateRightDelta(cm->sttype[v]); /* note sdr is for state v */
sd = StateDelta(cm->sttype[v]); /* note sd is for state v */
- emitmode = Emitmode(cm->sttype[v]); /* note emitmode is for state v */
for (j = 0; j <= L; j++) {
for (d = 0; d <= j; d++) {
@@ -5196,7 +5189,6 @@ cm_EmitterPosteriorHB(CM_t *cm, char *errbuf, int L, float size_limit, CM_HB_MX
int status;
int v, j, d; /* state, position, subseq length */
int i; /* sequence position */
- int sd; /* StateDelta(v) */
int ip_v; /* offset i in banded matrix */
int ip_v2; /* another offset i in banded matrix */
int jp_v; /* offset j in banded matrix */
@@ -5225,7 +5217,6 @@ cm_EmitterPosteriorHB(CM_t *cm, char *errbuf, int L, float size_limit, CM_HB_MX
* leftwise (l_pp) or rightwise (r_pp).
*/
for(v = 0; v < cm->M; v++) {
- sd = StateDelta(cm->sttype[v]);
if(cm->sttype[v] == MP_st || cm->sttype[v] == ML_st || cm->sttype[v] == IL_st) {
for(j = jmin[v]; j <= jmax[v]; j++) {
jp_v = j - jmin[v];
@@ -5450,7 +5441,7 @@ int
cm_PostCode(CM_t *cm, char *errbuf, int L, CM_EMIT_MX *emit_mx, Parsetree_t *tr, char **ret_ppstr, float *ret_avgp)
{
int status;
- int x, v, i, j, d, r; /* counters */
+ int x, v, i, j, r; /* counters */
char *ppstr; /* the PP string, created here */
float p; /* a probability */
float sum_logp; /* log of summed probability of all residues emitted thus far */
@@ -5464,7 +5455,6 @@ cm_PostCode(CM_t *cm, char *errbuf, int L, CM_EMIT_MX *emit_mx, Parsetree_t *tr,
v = tr->state[x];
i = tr->emitl[x];
j = tr->emitr[x];
- d = j-i+1;
/* Only P, L, R, and EL states have emissions. */
if(cm->sttype[v] == EL_st) { /* EL state, we have to handle this guy special */
@@ -5510,7 +5500,7 @@ int
cm_PostCodeHB(CM_t *cm, char *errbuf, int L, CM_HB_EMIT_MX *emit_mx, Parsetree_t *tr, char **ret_ppstr, float *ret_avgp)
{
int status;
- int x, v, i, j, d, r; /* counters */
+ int x, v, i, j, r; /* counters */
char *ppstr; /* the PP string, created here */
float p; /* a probability */
float sum_logp; /* log of summed probability of all residues emitted thus far */
@@ -5533,7 +5523,6 @@ cm_PostCodeHB(CM_t *cm, char *errbuf, int L, CM_HB_EMIT_MX *emit_mx, Parsetree_t
v = tr->state[x];
i = tr->emitl[x];
j = tr->emitr[x];
- d = j-i+1;
/* Only P, L, R, and EL states have emissions. */
if(cm->sttype[v] == EL_st) { /* EL state, we have to handle this guy special */
diff --git a/src/cm_dpalign_trunc.c b/src/cm_dpalign_trunc.c
index 41746efd..e3a69a1a 100644
--- a/src/cm_dpalign_trunc.c
+++ b/src/cm_dpalign_trunc.c
@@ -9217,7 +9217,6 @@ cm_TrEmitterPosteriorHB(CM_t *cm, char *errbuf, int L, float size_limit, char pr
int status;
int v, j, d; /* state, position, subseq length */
int i; /* sequence position */
- int sd; /* StateDelta(v) */
int fill_L, fill_R; /* do we need to fill Ll_pp/Rr_pp matrices? */
int jp_v; /* j-jmin[v] for current j, and current v */
int jp_v2; /* another offset j in banded matrix */
@@ -9253,7 +9252,6 @@ cm_TrEmitterPosteriorHB(CM_t *cm, char *errbuf, int L, float size_limit, char pr
* leftwise (*l_pp) or rightwise (*r_pp).
*/
for(v = 0; v < cm->M; v++) {
- sd = StateDelta(cm->sttype[v]);
if(cm->sttype[v] == MP_st || cm->sttype[v] == ML_st || cm->sttype[v] == IL_st) {
if(cm->cp9b->Jvalid[v]) {
for(j = jmin[v]; j <= jmax[v]; j++) {
@@ -9588,7 +9586,7 @@ int
cm_TrPostCode(CM_t *cm, char *errbuf, int L, CM_TR_EMIT_MX *emit_mx, Parsetree_t *tr, char **ret_ppstr, float *ret_avgp)
{
int status;
- int x, v, i, j, d, r; /* counters */
+ int x, v, i, j, r; /* counters */
char *ppstr; /* the PP string, created here */
float p; /* a probability */
float sum_logp; /* log of summed probability of all residues emitted thus far */
@@ -9606,7 +9604,6 @@ cm_TrPostCode(CM_t *cm, char *errbuf, int L, CM_TR_EMIT_MX *emit_mx, Parsetree_t
v = tr->state[x];
i = tr->emitl[x];
j = tr->emitr[x];
- d = j-i+1;
mode = tr->mode[x];
/* Only P, L, R, and EL states have emissions. */
@@ -9694,7 +9691,7 @@ int
cm_TrPostCodeHB(CM_t *cm, char *errbuf, int L, CM_TR_HB_EMIT_MX *emit_mx, Parsetree_t *tr, char **ret_ppstr, float *ret_avgp)
{
int status;
- int x, v, i, j, d, r; /* counters */
+ int x, v, i, j, r; /* counters */
char *ppstr; /* the PP string, created here */
float p; /* a probability */
float sum_logp; /* log of summed probability of all residues emitted thus far */
@@ -9721,7 +9718,6 @@ cm_TrPostCodeHB(CM_t *cm, char *errbuf, int L, CM_TR_HB_EMIT_MX *emit_mx, Parset
v = tr->state[x];
i = tr->emitl[x];
j = tr->emitr[x];
- d = j-i+1;
mode = tr->mode[x];
/* Only P, L, R, and EL states have emissions. */
diff --git a/src/cm_dpsearch.c b/src/cm_dpsearch.c
index d7fb7c60..04f0c3ee 100644
--- a/src/cm_dpsearch.c
+++ b/src/cm_dpsearch.c
@@ -745,7 +745,6 @@ RefCYKScan(CM_t *cm, char *errbuf, CM_SCAN_MX *smx, int qdbidx, ESL_DSQ *dsq, in
int dn_w, dx_w; /* minimum/maximum valid d for state w */
int *dmin; /* [0..v..cm->M-1] minimum d allowed for this state */
int *dmax; /* [0..v..cm->M-1] maximum d allowed for this state */
- int cnum; /* number of children for current state */
int *jp_wA; /* rolling pointer index for B states, gets precalc'ed */
float **init_scAA; /* [0..v..cm->M-1][0..d..W] initial score for each v, d for all j */
double **act; /* [0..j..W-1][0..a..abc->K-1], alphabet count, count of residue a in dsq from 1..jp where j = jp%(W+1) */
@@ -869,7 +868,6 @@ RefCYKScan(CM_t *cm, char *errbuf, CM_SCAN_MX *smx, int qdbidx, ESL_DSQ *dsq, in
jp_v = (cm->stid[v] == BEGL_S) ? (j % (W+1)) : cur;
jp_y = (StateRightDelta(cm->sttype[v]) > 0) ? prv : cur;
sd = StateDelta(cm->sttype[v]);
- cnum = cm->cnum[v];
dn = dnA[v];
dx = dxA[v];
/* if we emit right, precalc score of emitting res j from state v */
@@ -2388,7 +2386,6 @@ RefIInsideScan(CM_t *cm, char *errbuf, CM_SCAN_MX *smx, int qdbidx, ESL_DSQ *dsq
int dn_w, dx_w; /* minimum/maximum valid d for state w */
int *dmin; /* [0..v..cm->M-1] minimum d allowed for this state */
int *dmax; /* [0..v..cm->M-1] maximum d allowed for this state */
- int cnum; /* number of children for current state */
int *jp_wA; /* rolling pointer index for B states, gets precalc'ed */
int **init_scAA; /* [0..v..cm->M-1][0..d..W] initial score for each v, d for all j */
double **act; /* [0..j..W-1][0..a..abc->K-1], alphabet count, count of residue a in dsq from 1..jp where j = jp%(W+1) */
@@ -2512,7 +2509,6 @@ RefIInsideScan(CM_t *cm, char *errbuf, CM_SCAN_MX *smx, int qdbidx, ESL_DSQ *dsq
jp_v = (cm->stid[v] == BEGL_S) ? (j % (W+1)) : cur;
jp_y = (StateRightDelta(cm->sttype[v]) > 0) ? prv : cur;
sd = StateDelta(cm->sttype[v]);
- cnum = cm->cnum[v];
dn = dnA[v];
dx = dxA[v];
/* if we emit right, precalc score of emitting res j from state v */
@@ -2768,7 +2764,6 @@ RefFInsideScan(CM_t *cm, char *errbuf, CM_SCAN_MX *smx, int qdbidx, ESL_DSQ *dsq
int dn_w, dx_w; /* minimum/maximum valid d for state w */
int *dmin; /* [0..v..cm->M-1] minimum d allowed for this state */
int *dmax; /* [0..v..cm->M-1] maximum d allowed for this state */
- int cnum; /* number of children for current state */
int *jp_wA; /* rolling pointer index for B states, gets precalc'ed */
float **init_scAA; /* [0..v..cm->M-1][0..d..W] initial score for each v, d for all j */
double **act; /* [0..j..W-1][0..a..abc->K-1], alphabet count, count of residue a in dsq from 1..jp where j = jp%(W+1) */
@@ -2891,7 +2886,6 @@ RefFInsideScan(CM_t *cm, char *errbuf, CM_SCAN_MX *smx, int qdbidx, ESL_DSQ *dsq
jp_v = (cm->stid[v] == BEGL_S) ? (j % (W+1)) : cur;
jp_y = (StateRightDelta(cm->sttype[v]) > 0) ? prv : cur;
sd = StateDelta(cm->sttype[v]);
- cnum = cm->cnum[v];
dn = dnA[v];
dx = dxA[v];
/* if we emit right, precalc score of emitting res j from state v */
diff --git a/src/cm_dpsearch_trunc.c b/src/cm_dpsearch_trunc.c
index e220092d..2c5631f7 100644
--- a/src/cm_dpsearch_trunc.c
+++ b/src/cm_dpsearch_trunc.c
@@ -111,7 +111,6 @@ RefTrCYKScan(CM_t *cm, char *errbuf, CM_TR_SCAN_MX *trsmx, int qdbidx, int pass_
int dx_w; /* maximum valid d for state w */
int kn, kx; /* minimum/maximum valid k for current d in B_st recursion */
int *dmax; /* [0..v..cm->M-1] maximum d allowed for this state */
- int cnum; /* number of children for current state */
int *jp_wA; /* rolling pointer index for B states, gets precalc'ed */
float **init_scAA; /* [0..v..cm->M-1][0..d..W] initial score for each v, d for all j */
double **act; /* [0..j..W-1][0..a..abc->K-1], alphabet count, count of residue a in dsq from 1..jp where j = jp%(W+1) */
@@ -260,7 +259,6 @@ RefTrCYKScan(CM_t *cm, char *errbuf, CM_TR_SCAN_MX *trsmx, int qdbidx, int pass_
jp_y = (StateRightDelta(cm->sttype[v]) > 0) ? prv : cur;
jq_y = (StateRightDelta(cm->sttype[v]) > 0) ? cur : prv;
sd = StateDelta(cm->sttype[v]);
- cnum = cm->cnum[v];
/* if we emit right, precalc score of emitting res j from state v */
float esc_j = IMPOSSIBLE;
float rmesc_j = IMPOSSIBLE;
@@ -768,7 +766,6 @@ RefITrInsideScan(CM_t *cm, char *errbuf, CM_TR_SCAN_MX *trsmx, int qdbidx, int p
int dx_y; /* maximum valid d for state y */
int dx_w; /* maximum valid d for state w */
int *dmax; /* [0..v..cm->M-1] maximum d allowed for this state */
- int cnum; /* number of children for current state */
int *jp_wA; /* rolling pointer index for B states, gets precalc'ed */
int **init_scAA; /* [0..v..cm->M-1][0..d..W] initial score for each v, d for all j */
double **act; /* [0..j..W-1][0..a..abc->K-1], alphabet count, count of residue a in dsq from 1..jp where j = jp%(W+1) */
@@ -917,7 +914,6 @@ RefITrInsideScan(CM_t *cm, char *errbuf, CM_TR_SCAN_MX *trsmx, int qdbidx, int p
jp_y = (StateRightDelta(cm->sttype[v]) > 0) ? prv : cur;
jq_y = (StateRightDelta(cm->sttype[v]) > 0) ? cur : prv;
sd = StateDelta(cm->sttype[v]);
- cnum = cm->cnum[v];
/* if we emit right, precalc score of emitting res j from state v */
int esc_j = -INFTY;
int rmesc_j = -INFTY;
diff --git a/src/cm_modelmaker.c b/src/cm_modelmaker.c
index ed7f0df1..6b339f40 100644
--- a/src/cm_modelmaker.c
+++ b/src/cm_modelmaker.c
@@ -1831,7 +1831,7 @@ cm_check_before_detaching(CM_t *cm, int insert1, int insert2)
int ret_val;
int i, yoffset;
int to_detach;
- int to_keep;
+ /*int to_keep;*/
float diff;
ret_val = FALSE;
@@ -1843,7 +1843,7 @@ cm_check_before_detaching(CM_t *cm, int insert1, int insert2)
{
ret_val = TRUE;
to_detach = insert1;
- to_keep = insert2;
+ /*to_keep = insert2;*/
}
if(cm->sttype[insert2+1] == E_st)
{
@@ -1851,7 +1851,7 @@ cm_check_before_detaching(CM_t *cm, int insert1, int insert2)
cm_Fail("ERROR: in cm_check_before_detaching() insert1: %d and insert2: %d both map to END_E-1 states.\n", insert1, insert2);
ret_val = TRUE;
to_detach = insert2;
- to_keep = insert1;
+ /*to_keep = insert1;*/
}
/* check to make sure we have 0.0 counts in to_detach */
diff --git a/src/cm_mx.c b/src/cm_mx.c
index 0d71c0ee..037b79d0 100644
--- a/src/cm_mx.c
+++ b/src/cm_mx.c
@@ -894,7 +894,7 @@ cm_hb_mx_Create(int M)
/* level 3: dp cell memory, when creating only allocate 1 cell per state, for j = 0, d = 0 */
ESL_ALLOC(mx->dp_mem, sizeof(float) * (M+1) * (allocL) * (allocW));
- ESL_ALLOC(mx->nrowsA, sizeof(int) * (M+1));
+ ESL_ALLOC(mx->nrowsA, sizeof(int) * (M+1));
for (v = 0; v <= M; v++) {
ESL_ALLOC(mx->dp[v], sizeof(float *) * (allocL));
mx->nrowsA[v] = allocL;
@@ -2162,11 +2162,9 @@ cm_shadow_mx_SizeNeeded(CM_t *cm, char *errbuf, int L, int64_t *ret_ny_cells, in
int64_t y_ncells;
int64_t k_ncells;
float Mb_needed;
- int nbifs;
y_ncells = 0;
k_ncells = 0;
- nbifs = CMCountStatetype(cm, B_st);
Mb_needed = (float)
(sizeof(CM_SHADOW_MX) +
((cm->M) * sizeof(char **)) + /* mx->yshadow[] ptrs */
@@ -2776,7 +2774,6 @@ cm_tr_shadow_mx_SizeNeeded(CM_t *cm, char *errbuf, int L, int64_t *ret_Jny_cells
int64_t Rk_ncells;
int64_t Tk_ncells;
float Mb_needed;
- int nbifs;
Jy_ncells = 0;
Ly_ncells = 0;
@@ -2785,7 +2782,6 @@ cm_tr_shadow_mx_SizeNeeded(CM_t *cm, char *errbuf, int L, int64_t *ret_Jny_cells
Lk_ncells = 0;
Rk_ncells = 0;
Tk_ncells = 0;
- nbifs = CMCountStatetype(cm, B_st);
Mb_needed = (float)
(sizeof(CM_TR_SHADOW_MX) +
(3 * (cm->M) * sizeof(char **)) + /* mx->{J,L,R}yshadow[] ptrs */
@@ -3195,13 +3191,11 @@ cm_hb_shadow_mx_SizeNeeded(CM_t *cm, char *errbuf, CP9Bands_t *cp9b, int64_t *re
int64_t y_ncells, k_ncells;
int jbw;
float Mb_needed;
- int nbifs;
/* contract check */
if(cp9b == NULL) ESL_FAIL(eslEINCOMPAT, errbuf, "cm_hb_shadow_mx_SizeNeeded() entered with cp9b == NULL.\n");
y_ncells = k_ncells = 0;
- nbifs = CMCountStatetype(cm, B_st);
Mb_needed = (float)
(sizeof(CM_HB_SHADOW_MX) +
@@ -3302,15 +3296,15 @@ cm_tr_hb_shadow_mx_Create(CM_t *cm)
ESL_ALLOC(mx->Rkshadow, sizeof(int **) * M);
ESL_ALLOC(mx->Tkshadow, sizeof(int **) * M);
- ESL_ALLOC(mx->Lkmode, sizeof(char **) * M);
- ESL_ALLOC(mx->Rkmode, sizeof(char **) * M);
+ ESL_ALLOC(mx->Lkmode, sizeof(char **) * M);
+ ESL_ALLOC(mx->Rkmode, sizeof(char **) * M);
/* level 3: matrix cell memory, when creating only allocate 1 cell per state, for j = 0, d = 0 */
ESL_ALLOC(mx->Jyshadow_mem, (sizeof(char) * (M-B) * (allocL) * (allocW)));
ESL_ALLOC(mx->Lyshadow_mem, (sizeof(char) * (M-B) * (allocL) * (allocW)));
ESL_ALLOC(mx->Ryshadow_mem, (sizeof(char) * (M-B) * (allocL) * (allocW)));
- ESL_ALLOC(mx->Jkshadow_mem, sizeof(int) * ESL_MAX(1, B * allocL * allocW));
+ ESL_ALLOC(mx->Jkshadow_mem, sizeof(int) * ESL_MAX(1, B * allocL * allocW)); // avoid 0 malloc
ESL_ALLOC(mx->Lkshadow_mem, sizeof(int) * ESL_MAX(1, B * allocL * allocW));
ESL_ALLOC(mx->Rkshadow_mem, sizeof(int) * ESL_MAX(1, B * allocL * allocW));
ESL_ALLOC(mx->Tkshadow_mem, sizeof(int) * ESL_MAX(1, B * allocL * allocW));
@@ -3662,7 +3656,7 @@ cm_tr_hb_shadow_mx_GrowTo(CM_t *cm, CM_TR_HB_SHADOW_MX *mx, char *errbuf, CP9Ban
if(jbw > mx->LnrowsA[v]) {
if(mx->Lkshadow[v] != NULL) ESL_RALLOC(mx->Lkshadow[v], p, sizeof(int *) * jbw);
else ESL_ALLOC (mx->Lkshadow[v], sizeof(int *) * jbw);
- if(mx->Lkmode[v] != NULL) ESL_RALLOC(mx->Lkmode[v], p, sizeof(char *) * jbw);
+ if(mx->Lkmode[v] != NULL) ESL_RALLOC(mx->Lkmode[v], p, sizeof(char *) * jbw);
else ESL_ALLOC (mx->Lkmode[v], sizeof(char *) * jbw);
mx->LnrowsA[v] = jbw;
}
@@ -3992,7 +3986,6 @@ cm_tr_hb_shadow_mx_SizeNeeded(CM_t *cm, char *errbuf, CP9Bands_t *cp9b, int64_t
int64_t Tk_ncells;
int jbw;
float Mb_needed;
- int nbifs;
/* contract check */
if(cp9b == NULL) ESL_FAIL(eslEINCOMPAT, errbuf, "cm_tr_hb_shadow_mx_SizeNeeded() entered with cp9b == NULL.\n");
@@ -4004,7 +3997,6 @@ cm_tr_hb_shadow_mx_SizeNeeded(CM_t *cm, char *errbuf, CP9Bands_t *cp9b, int64_t
Lk_ncells = 0;
Rk_ncells = 0;
Tk_ncells = 0;
- nbifs = CMCountStatetype(cm, B_st);
Mb_needed = (float)
(sizeof(CM_TR_HB_SHADOW_MX) +
(3 * (cp9b->cm_M) * sizeof(char **)) + /* mx->{J,L,R}yshadow[] ptrs */
@@ -6003,7 +5995,7 @@ cm_scan_mx_integerize(CM_t *cm, CM_SCAN_MX *smx, char *errbuf)
smx->ncells_alpha_begl = (smx->W+1);
smx->ncells_alpha_begl *= n_begl;
smx->ncells_alpha_begl *= (smx->W+1);
- ESL_ALLOC(smx->ialpha_begl_mem, sizeof(int) * ESL_MAX(1, smx->ncells_alpha_begl));
+ ESL_ALLOC(smx->ialpha_begl_mem, sizeof(int) * ESL_MAX(1, smx->ncells_alpha_begl)); // avoid 0 malloc
/* we used to define ncells_alpha_begl this way:
* smx->ncells_alpha_begl = (smx->W+1) * n_begl * (smx->W+1);
* but that overflows for large models (even though ncells_alpha_begl is an int64_t, I guess
@@ -6667,9 +6659,9 @@ cm_tr_scan_mx_floatize(CM_t *cm, CM_TR_SCAN_MX *trsmx, char *errbuf)
trsmx->ncells_alpha_begl = (trsmx->W+1);
trsmx->ncells_alpha_begl *= n_begl;
trsmx->ncells_alpha_begl *= (trsmx->W+1);
- ESL_ALLOC(trsmx->fJalpha_begl_mem, sizeof(float) * (trsmx->ncells_alpha_begl));
- ESL_ALLOC(trsmx->fLalpha_begl_mem, sizeof(float) * (trsmx->ncells_alpha_begl));
- ESL_ALLOC(trsmx->fRalpha_begl_mem, sizeof(float) * (trsmx->ncells_alpha_begl));
+ ESL_ALLOC(trsmx->fJalpha_begl_mem, sizeof(float) * ESL_MAX(1, trsmx->ncells_alpha_begl)); // avoid 0 malloc
+ ESL_ALLOC(trsmx->fLalpha_begl_mem, sizeof(float) * ESL_MAX(1, trsmx->ncells_alpha_begl));
+ ESL_ALLOC(trsmx->fRalpha_begl_mem, sizeof(float) * ESL_MAX(1, trsmx->ncells_alpha_begl));
cur_cell = 0;
for (v = 0; v < cm->M; v++) {
@@ -6813,9 +6805,9 @@ cm_tr_scan_mx_integerize(CM_t *cm, CM_TR_SCAN_MX *trsmx, char *errbuf)
trsmx->ncells_alpha_begl = (trsmx->W+1);
trsmx->ncells_alpha_begl *= n_begl;
trsmx->ncells_alpha_begl *= (trsmx->W+1);
- ESL_ALLOC(trsmx->iJalpha_begl_mem, sizeof(int) * (trsmx->ncells_alpha_begl));
- ESL_ALLOC(trsmx->iLalpha_begl_mem, sizeof(int) * (trsmx->ncells_alpha_begl));
- ESL_ALLOC(trsmx->iRalpha_begl_mem, sizeof(int) * (trsmx->ncells_alpha_begl));
+ ESL_ALLOC(trsmx->iJalpha_begl_mem, sizeof(int) * ESL_MAX(1, trsmx->ncells_alpha_begl));
+ ESL_ALLOC(trsmx->iLalpha_begl_mem, sizeof(int) * ESL_MAX(1, trsmx->ncells_alpha_begl));
+ ESL_ALLOC(trsmx->iRalpha_begl_mem, sizeof(int) * ESL_MAX(1, trsmx->ncells_alpha_begl));
cur_cell = 0;
for (v = 0; v < cm->M; v++) {
diff --git a/src/cm_p7_modelmaker.c b/src/cm_p7_modelmaker.c
index bae5c498..769dc661 100644
--- a/src/cm_p7_modelmaker.c
+++ b/src/cm_p7_modelmaker.c
@@ -351,7 +351,6 @@ cm_p7_Tau(ESL_RANDOMNESS *r, char *errbuf, P7_OPROFILE *om, P7_PROFILE *gm, P7_B
double gmu, glam;
int status;
int i;
- int M;
int do_generic;
if(om == NULL && gm == NULL) { status = eslEINVAL; goto ERROR; }
@@ -361,12 +360,10 @@ cm_p7_Tau(ESL_RANDOMNESS *r, char *errbuf, P7_OPROFILE *om, P7_PROFILE *gm, P7_B
if(do_generic) {
gx = p7_gmx_Create(gm->M, L); /* DP matrix: for ForwardParser, L rows */
if (gx == NULL) { status = eslEMEM; goto ERROR; }
- M = gm->M;
}
else {
ox = p7_omx_Create(om->M, 0, L); /* DP matrix: for ForwardParser, L rows */
if (ox == NULL) { status = eslEMEM; goto ERROR; }
- M = om->M;
}
ESL_ALLOC(xv, sizeof(double) * N);
diff --git a/src/cm_parsetree.c b/src/cm_parsetree.c
index fda3c081..df6e9360 100644
--- a/src/cm_parsetree.c
+++ b/src/cm_parsetree.c
@@ -2621,7 +2621,7 @@ cm_StochasticParsetree(CM_t *cm, char *errbuf, ESL_DSQ *dsq, int L, CM_MX *mx, E
int el_is_possible; /* TRUE if we can jump to EL from current state (and we're in local mode) FALSE if not */
float fsc = 0.; /* score of the parsetree we're sampling */
int choice; /* index represeting sampled choice */
- int sd, sdl, sdr; /* state delta, state left delta, state right delta */
+ int sd, sdr; /* state delta, state right delta */
/* the DP matrix, filled by prior call to cm_InsideAlign() */
float ***alpha = mx->dp; /* pointer to the alpha DP matrix */
@@ -2703,7 +2703,6 @@ cm_StochasticParsetree(CM_t *cm, char *errbuf, ESL_DSQ *dsq, int L, CM_MX *mx, E
/* add in emission score (or 0.0 if we're a non-emitter) */
fsc += get_femission_score(cm, dsq, v, i, j);
sd = StateDelta(cm->sttype[v]);
- sdl = StateLeftDelta(cm->sttype[v]);
sdr = StateRightDelta(cm->sttype[v]);
/* set pA[] as (float-ized) log odds scores for each child we can transit to,
@@ -2860,7 +2859,7 @@ cm_StochasticParsetreeHB(CM_t *cm, char *errbuf, ESL_DSQ *dsq, int L, CM_HB_MX *
int jp_z, kp_z; /* j - jmin[z], d - hdmin[z][jp_z] */
int jp_y_sdr; /* j - jmin[y] - vms_sdr */
int dp_y_sd; /* hdmin[y][jp_y_vms_sdr] - vms_sd */
- int jp_0; /* L offset in ROOT_S's (v==0) j band */
+ int jp_0; /* j offset in ROOT_S's (v==0) j band */
int Lp_0; /* L offset in ROOT_S's (v==0) d band */
int kmin, kmax; /* min/max k */
diff --git a/src/cm_pipeline.c b/src/cm_pipeline.c
index 73002a44..b7b40b78 100644
--- a/src/cm_pipeline.c
+++ b/src/cm_pipeline.c
@@ -24,8 +24,6 @@
#include "infernal.h"
-#define DEBUG_NOW 0
-
static int pli_p7_filter (CM_PIPELINE *pli, P7_OPROFILE *om, P7_BG *bg, float *p7_evparam, P7_SCOREDATA *msvdata, const ESL_SQ *sq, int64_t **ret_ws, int64_t **ret_we, float **ret_wb, int *ret_nwin);
static int pli_p7_env_def (CM_PIPELINE *pli, P7_OPROFILE *om, P7_BG *bg, float *p7_evparam, const ESL_SQ *sq, int64_t *ws, int64_t *we, int nwin, P7_HMM **opt_hmm, P7_PROFILE **opt_gm,
P7_PROFILE **opt_Rgm, P7_PROFILE **opt_Lgm, P7_PROFILE **opt_Tgm, int64_t **ret_es, int64_t **ret_ee, float **ret_eb, int *ret_nenv);
@@ -1325,7 +1323,7 @@ cm_Pipeline(CM_PIPELINE *pli, off_t cm_offset, P7_OPROFILE *om, P7_BG *bg, float
have3term = (sq->end == 1) ? TRUE : FALSE;
}
-#if DEBUG_NOW
+#if eslDEBUGLEVEL >= 3
/*printf("\nPIPELINE ENTRANCE %s %s %" PRId64 " residues (pli->maxW: %d om->max_length: %d cm->W: %d)\n", sq->name, sq->desc, sq->n, pli->maxW, om->max_length, (*opt_cm)->W);*/
printf("\nPIPELINE ENTRANCE %-15s %15s (n: %6" PRId64 " start: %6" PRId64 " end: %6" PRId64 " C: %6" PRId64 " W: %6" PRId64 " L: %6" PRId64 " have5term: %d have3term: %d)\n",
sq->name, om->name, sq->n, sq->start, sq->end, sq->C, sq->W, sq->L, have5term, have3term);
@@ -1454,7 +1452,7 @@ cm_Pipeline(CM_PIPELINE *pli, off_t cm_offset, P7_OPROFILE *om, P7_BG *bg, float
* A. pli_p7_filter(): MSV, Viterbi, local Forward filters
* B. pli_final_stage_hmmonly(): use H3 local domain definition to define HMM hits
********************************************************************************************************/
-#if DEBUG_NOW
+#if eslDEBUGLEVEL >= 3
printf("\nHMM ONLY PIPELINE calling p7_filter() %s %" PRId64 " residues (pass: %d)\n", sq2search->name, sq2search->n, p);
#endif
if((status = pli_p7_filter(pli, om, bg, p7_evparam, msvdata, sq2search, &ws, &we, &wb, &nwin)) != eslOK) return status;
@@ -1472,7 +1470,7 @@ cm_Pipeline(CM_PIPELINE *pli, off_t cm_offset, P7_OPROFILE *om, P7_BG *bg, float
* A. pli_p7_filter(): SSV, Viterbi, local Forward filters
* B. pli_p7_env_def(): glocal Forward, and glocal (usually) HMM envelope definition, then
*/
-#if DEBUG_NOW
+#if eslDEBUGLEVEL >= 3
printf("\nPIPELINE calling p7_filter() %s %" PRId64 " residues (pass: %d)\n", sq2search->name, sq2search->n, p);
#endif
if((status = pli_p7_filter(pli, om, bg, p7_evparam, msvdata, sq2search, &ws, &we, &wb, &nwin)) != eslOK) return status;
@@ -1521,17 +1519,17 @@ cm_Pipeline(CM_PIPELINE *pli, off_t cm_offset, P7_OPROFILE *om, P7_BG *bg, float
}
}
else {
-#if DEBUG_NOW
+#if eslDEBUGLEVEL >= 3
printf("\nPIPELINE calling p7_env_def() %s %" PRId64 " residues (pass: %d)\n", sq2search->name, sq2search->n, p);
#endif
if((status = pli_p7_env_def(pli, om, bg, p7_evparam, sq2search, ws, we, nwin, opt_hmm, opt_gm, opt_Rgm, opt_Lgm, opt_Tgm, &(p7esAA[p]), &(p7eeAA[p]), &(p7ebAA[p]), &(np7envA[p]))) != eslOK) return status;
}
} /* end of if(pli->do_edef) */
- if(ws != NULL) { free(ws); ws = NULL; }
- if(we != NULL) { free(we); we = NULL; }
- if(wb != NULL) { free(wb); wb = NULL; }
- nwin = 0;
- }
+ } /* end of 'else' entered if p != PLI_PASS_HMM_ONLY_ANY */
+ if(ws != NULL) { free(ws); ws = NULL; }
+ if(we != NULL) { free(we); we = NULL; }
+ if(wb != NULL) { free(wb); wb = NULL; }
+ nwin = 0;
} /* end of 'for(p = PLI_PASS_STD_ANY; p <= PLI_NPASSES; p++)', first loop over pipeline passes */
if(pli->do_one_cmpass) {
@@ -1597,15 +1595,15 @@ cm_Pipeline(CM_PIPELINE *pli, off_t cm_offset, P7_OPROFILE *om, P7_BG *bg, float
/* 1. Banded CYK on the envelopes defined by the p7 HMM in the pipeline pass above (if pli->do_edef == TRUE) */
if(pli->do_edef) {
if(pli->do_fcyk) {
- #if DEBUG_NOW
+ #if eslDEBUGLEVEL >= 3
printf("\nPIPELINE calling pli_cyk_env_filter() %s %" PRId64 " residues (pass: %d)\n", sq2search->name, sq2search->n, p);
#endif
if((status = pli_cyk_env_filter(pli, cm_offset, sq2search, p7esAA[p], p7eeAA[p], np7envA[p], opt_cm, &es, &ee, &nenv)) != eslOK) return status;
if(pli->do_time_F4 || pli->do_time_F5) return status;
}
else { /* defined envelopes with HMM, but CYK filter is off: act as if all p7-defined envelopes survived CYK */
- ESL_ALLOC(es, sizeof(int64_t) * np7envA[p]);
- ESL_ALLOC(ee, sizeof(int64_t) * np7envA[p]);
+ ESL_ALLOC(es, sizeof(int64_t) * ESL_MAX(1, np7envA[p])); // avoid 0 malloc
+ ESL_ALLOC(ee, sizeof(int64_t) * ESL_MAX(1, np7envA[p]));
for(i = 0; i < np7envA[p]; i++) { es[i] = p7esAA[p][i]; ee[i] = p7eeAA[p][i]; }
nenv = np7envA[p];
}
@@ -1613,7 +1611,7 @@ cm_Pipeline(CM_PIPELINE *pli, off_t cm_offset, P7_OPROFILE *om, P7_BG *bg, float
/* 2. Using CYK to define envelopes on full sequences (if pli->do_edef == FALSE && pli->fcyk = TRUE) */
else if((! pli->do_edef) && pli->do_fcyk) {
/* Defining envelopes with CYK */
-#if DEBUG_NOW
+#if eslDEBUGLEVEL >= 3
printf("\nPIPELINE calling pli_cyk_seq_filter() %s %" PRId64 " residues (pass: %d)\n", sq2search->name, sq2search->n, p);
#endif
if((status = pli_cyk_seq_filter(pli, cm_offset, sq2search, opt_cm, &es, &ee, &nenv)) != eslOK) return status;
@@ -1628,12 +1626,12 @@ cm_Pipeline(CM_PIPELINE *pli, off_t cm_offset, P7_OPROFILE *om, P7_BG *bg, float
/* Filters are finished. Final stage of pipeline (always run).
*/
-#if DEBUG_NOW
+#if eslDEBUGLEVEL >= 3
printf("\nPIPELINE calling FinalStage() %s %" PRId64 " residues model: %s (pass: %d) nhits: %" PRId64 "\n", sq2search->name, sq2search->n, om->name, p, hitlist->N);
#endif
prv_ntophits = hitlist->N;
if((status = pli_final_stage(pli, cm_offset, sq2search, es, ee, nenv, hitlist, opt_cm)) != eslOK) return status;
-#if DEBUG_NOW
+#if eslDEBUGLEVEL >= 3
printf("\nPIPELINE back from FinalStage() %s %" PRId64 " residues model: %s (pass: %d) nhits: %" PRId64 "\n", sq2search->name, sq2search->n, om->name, p, hitlist->N);
#endif
@@ -2436,7 +2434,6 @@ pli_p7_filter(CM_PIPELINE *pli, P7_OPROFILE *om, P7_BG *bg, float *p7_evparam, P
int64_t *new_we = NULL; /* used when copying/modifying we */
float *new_wb = NULL; /* used when copying/modifying wb */
int nsurv_fwd; /* number of windows that survive fwd filter */
- int new_nsurv_fwd; /* used when merging fwd survivors */
ESL_DSQ *subdsq; /* a ptr to the first position of a window */
int have_rest; /* do we have the full read in? */
P7_HMM_WINDOWLIST wlist; /* list of windows, structure taken by p7_MSVFilter_longtarget() */
@@ -2473,7 +2470,7 @@ pli_p7_filter(CM_PIPELINE *pli, P7_OPROFILE *om, P7_BG *bg, float *p7_evparam, P
p7_oprofile_ReconfigMSVLength(om, pli->maxW);
om->max_length = pli->maxW;
- #if DEBUG_NOW
+ #if eslDEBUGLEVEL >= 3
printf("\nPIPELINE pli_p7_filter() %s %" PRId64 " residues\n", sq->name, sq->n);
#endif
@@ -2590,7 +2587,7 @@ pli_p7_filter(CM_PIPELINE *pli, P7_OPROFILE *om, P7_BG *bg, float *p7_evparam, P
p7_bg_SetLength(bg, wlen);
p7_bg_NullOne (bg, subdsq, wlen, &nullsc);
-#if DEBUG_NOW
+#if eslDEBUGLEVEL >= 3
if(cur_do_msv) printf("SURVIVOR window %5d [%10" PRId64 "..%10" PRId64 "] survived SSV ? bits ? P\n", i, ws[i], we[i]);
#endif
survAA[p7_SURV_F1][i] = TRUE;
@@ -2618,7 +2615,7 @@ pli_p7_filter(CM_PIPELINE *pli, P7_OPROFILE *om, P7_BG *bg, float *p7_evparam, P
pli->acct[pli->cur_pass_idx].n_past_msvbias++;
survAA[p7_SURV_F1b][i] = TRUE;
-#if DEBUG_NOW
+#if eslDEBUGLEVEL >= 3
if(cur_do_msv && cur_do_msvbias) printf("SURVIVOR window %5d [%10" PRId64 "..%10" PRId64 "] survived MSV-Bias ? bits P ?\n", i, ws[i], we[i]);
#endif
if(pli->do_time_F1) return eslOK;
@@ -2653,7 +2650,7 @@ pli_p7_filter(CM_PIPELINE *pli, P7_OPROFILE *om, P7_BG *bg, float *p7_evparam, P
pli->acct[pli->cur_pass_idx].n_past_vit++;
survAA[p7_SURV_F2][i] = TRUE;
-#if DEBUG_NOW
+#if eslDEBUGLEVEL >= 3
if (cur_do_vit) printf("SURVIVOR window %5d [%10" PRId64 "..%10" PRId64 "] survived Vit %6.2f bits P %g\n", i, ws[i], we[i], wb[i], wp[i]);
#endif
@@ -2664,7 +2661,7 @@ pli_p7_filter(CM_PIPELINE *pli, P7_OPROFILE *om, P7_BG *bg, float *p7_evparam, P
}
have_filtersc = TRUE;
wsc = (vfsc - filtersc) / eslCONST_LOG2;
- P = esl_gumbel_surv(wb[i], p7_evparam[CM_p7_LVMU], p7_evparam[CM_p7_LVLAMBDA]);
+ P = esl_gumbel_surv(wsc, p7_evparam[CM_p7_LVMU], p7_evparam[CM_p7_LVLAMBDA]);
wp[i] = P;
wb[i] = wsc;
if (P > cur_F2b) continue;
@@ -2673,7 +2670,7 @@ pli_p7_filter(CM_PIPELINE *pli, P7_OPROFILE *om, P7_BG *bg, float *p7_evparam, P
pli->acct[pli->cur_pass_idx].n_past_vitbias++;
survAA[p7_SURV_F2b][i] = TRUE;
-#if DEBUG_NOW
+#if eslDEBUGLEVEL >= 3
if (cur_do_vit && cur_do_vitbias) printf("SURVIVOR window %5d [%10" PRId64 "..%10" PRId64 "] survived Vit-Bias %6.2f bits P %g\n", i, ws[i], we[i], wb[i], wp[i]);
#endif
if(pli->do_time_F2) continue;
@@ -2694,7 +2691,7 @@ pli_p7_filter(CM_PIPELINE *pli, P7_OPROFILE *om, P7_BG *bg, float *p7_evparam, P
pli->acct[pli->cur_pass_idx].n_past_fwd++;
survAA[p7_SURV_F3][i] = TRUE;
-#if DEBUG_NOW
+#if eslDEBUGLEVEL >= 3
if(cur_do_fwd) printf("SURVIVOR window %5d [%10" PRId64 "..%10" PRId64 "] survived Fwd %6.2f bits P %g\n", i, ws[i], we[i], wb[i], wp[i]);
#endif
@@ -2714,7 +2711,7 @@ pli_p7_filter(CM_PIPELINE *pli, P7_OPROFILE *om, P7_BG *bg, float *p7_evparam, P
nsurv_fwd++;
survAA[p7_SURV_F3b][i] = TRUE;
-#if DEBUG_NOW
+#if eslDEBUGLEVEL >= 3
if(cur_do_fwd && cur_do_fwdbias) printf("SURVIVOR window %5d [%10" PRId64 "..%10" PRId64 "] survived Fwd-Bias %6.2f bits P %g\n", i, ws[i], we[i], wb[i], wp[i]);
#endif
}
@@ -2763,7 +2760,6 @@ pli_p7_filter(CM_PIPELINE *pli, P7_OPROFILE *om, P7_BG *bg, float *p7_evparam, P
}
}
/* we could have overlapping windows, merge those that do overlap */
- new_nsurv_fwd = 0;
ESL_ALLOC(useme, sizeof(int) * nsurv_fwd);
esl_vec_ISet(useme, nsurv_fwd, FALSE);
i2 = 0;
@@ -2912,13 +2908,13 @@ pli_p7_env_def(CM_PIPELINE *pli, P7_OPROFILE *om, P7_BG *bg, float *p7_evparam,
do_local_envdef = (pli->cur_pass_idx == PLI_PASS_5P_AND_3P_ANY) ? TRUE : FALSE;
nenv_alloc = nwin;
- ESL_ALLOC(es, sizeof(int64_t) * nenv_alloc);
- ESL_ALLOC(ee, sizeof(int64_t) * nenv_alloc);
- ESL_ALLOC(eb, sizeof(float) * nenv_alloc);
+ ESL_ALLOC(es, sizeof(int64_t) * ESL_MAX(1, nenv_alloc)); // avoid 0 malloc
+ ESL_ALLOC(ee, sizeof(int64_t) * ESL_MAX(1, nenv_alloc));
+ ESL_ALLOC(eb, sizeof(float) * ESL_MAX(1, nenv_alloc));
nenv = 0;
seq = esl_sq_CreateDigital(sq->abc);
-#if DEBUG_NOW
+#if eslDEBUGLEVEL >= 3
printf("\nPIPELINE p7EnvelopeDef() %s %" PRId64 " residues\n", sq->name, sq->n);
#endif
@@ -2973,7 +2969,7 @@ pli_p7_env_def(CM_PIPELINE *pli, P7_OPROFILE *om, P7_BG *bg, float *p7_evparam,
Tgm = *opt_Tgm;
for (i = 0; i < nwin; i++) {
-#if DEBUG_NOW
+#if eslDEBUGLEVEL >= 3
printf("p7 envdef win: %4d of %4d [%6" PRId64 "..%6" PRId64 "] pass: %" PRId64 "\n", i, nwin, ws[i], we[i], pli->cur_pass_idx);
#endif
/* if we require first or final residue, and don't have it, then
@@ -3064,7 +3060,7 @@ pli_p7_env_def(CM_PIPELINE *pli, P7_OPROFILE *om, P7_BG *bg, float *p7_evparam,
P = esl_exp_surv (sc_for_pvalue, p7_evparam[CM_p7_GFMU], p7_evparam[CM_p7_GFLAMBDA]);
}
-#if DEBUG_NOW
+#if eslDEBUGLEVEL >= 3
if(P > pli->F4) {
printf("KILLED window %5d [%10" PRId64 "..%10" PRId64 "] gFwd %6.2f bits P %g\n", i, ws[i], we[i], sc_for_pvalue, P);
}
@@ -3075,7 +3071,7 @@ pli_p7_env_def(CM_PIPELINE *pli, P7_OPROFILE *om, P7_BG *bg, float *p7_evparam,
pli->acct[pli->cur_pass_idx].n_past_gfwd++;
pli->acct[pli->cur_pass_idx].pos_past_gfwd += wlen;
-#if DEBUG_NOW
+#if eslDEBUGLEVEL >= 3
printf("SURVIVOR window %5d [%10" PRId64 "..%10" PRId64 "] survived gFwd %6.2f bits P %g\n", i, ws[i], we[i], sc_for_pvalue, P);
#endif
@@ -3098,7 +3094,7 @@ pli_p7_env_def(CM_PIPELINE *pli, P7_OPROFILE *om, P7_BG *bg, float *p7_evparam,
P = esl_exp_surv (sc_for_pvalue, p7_evparam[CM_p7_GFMU], p7_evparam[CM_p7_GFLAMBDA]);
}
if(P > pli->F4b) continue;
-#if DEBUG_NOW
+#if eslDEBUGLEVEL >= 3
printf("SURVIVOR window %5d [%10" PRId64 "..%10" PRId64 "] survived gFwdBias %6.2f bits P %g\n", i, ws[i], we[i], sc_for_pvalue, P);
#endif
pli->acct[pli->cur_pass_idx].n_past_gfwdbias++;
@@ -3182,7 +3178,7 @@ pli_p7_env_def(CM_PIPELINE *pli, P7_OPROFILE *om, P7_BG *bg, float *p7_evparam,
continue;
}
-#if DEBUG_NOW
+#if eslDEBUGLEVEL >= 3
printf("SURVIVOR envelope [%10" PRId64 "..%10" PRId64 "] survived F5 %6.2f bits P %g\n", pli->ddef->dcl[d].ienv + ws[i] - 1, pli->ddef->dcl[d].jenv + ws[i] - 1, env_sc_for_pvalue, P);
#endif
pli->acct[pli->cur_pass_idx].n_past_edef++;
@@ -3206,7 +3202,7 @@ pli_p7_env_def(CM_PIPELINE *pli, P7_OPROFILE *om, P7_BG *bg, float *p7_evparam,
continue;
}
}
-#if DEBUG_NOW
+#if eslDEBUGLEVEL >= 3
printf("SURVIVOR envelope [%10" PRId64 "..%10" PRId64 "] survived F5-bias %6.2f bits P %g\n", pli->ddef->dcl[d].ienv + ws[i] - 1, pli->ddef->dcl[d].jenv + ws[i] - 1, env_sc_for_pvalue, P);
#endif
pli->acct[pli->cur_pass_idx].n_past_edefbias++;
@@ -3322,12 +3318,12 @@ pli_cyk_env_filter(CM_PIPELINE *pli, off_t cm_offset, const ESL_SQ *sq, int64_t
*/
cyk_env_cutoff = cm->expA[pli->fcyk_cm_exp_mode]->mu_extrap + (log(pli->F6env) / (-1 * cm->expA[pli->fcyk_cm_exp_mode]->lambda));
-#if DEBUG_NOW
+#if eslDEBUGLEVEL >= 3
printf("\nPIPELINE EnvCYKFilter() %s %" PRId64 " residues\n", sq->name, sq->n);
#endif
for (i = 0; i < np7env; i++) {
-#if DEBUG_NOW
+#if eslDEBUGLEVEL >= 3
printf("\nSURVIVOR Envelope %5d [%10ld..%10ld] being passed to EnvCYKFilter pass: %" PRId64 "\n", i, p7es[i], p7ee[i], pli->cur_pass_idx);
#endif
cm->search_opts = pli->fcyk_cm_search_opts;
@@ -3355,7 +3351,7 @@ pli_cyk_env_filter(CM_PIPELINE *pli, off_t cm_offset, const ESL_SQ *sq, int64_t
p7ee[i] = cyk_envj;
}
-#if DEBUG_NOW
+#if eslDEBUGLEVEL >= 3
printf("SURVIVOR envelope [%10" PRId64 "..%10" PRId64 "] survived EnvCYKFilter %6.2f bits P %g\n", p7es[i], p7ee[i], sc, P);
#endif
}
@@ -3500,7 +3496,7 @@ pli_cyk_seq_filter(CM_PIPELINE *pli, off_t cm_offset, const ESL_SQ *sq, CM_t **o
iwin = ESL_MAX(1, sq_hitlist->hit[h]->stop - (cm->W-1));
jwin = ESL_MIN(sq->n, sq_hitlist->hit[h]->start + (cm->W-1));
-#if DEBUG_NOW
+#if eslDEBUGLEVEL >= 3
double P = esl_exp_surv(sq_hitlist->hit[h]->score, cm->expA[pli->fcyk_cm_exp_mode]->mu_extrap, cm->expA[pli->fcyk_cm_exp_mode]->lambda);
printf("SURVIVOR window [%10" PRId64 "..%10" PRId64 "] survived SeqCYKFilter %6.2f bits P %g\n", iwin, jwin, sq_hitlist->hit[h]->score, P);
#endif
@@ -3603,7 +3599,7 @@ pli_final_stage(CM_PIPELINE *pli, off_t cm_offset, const ESL_SQ *sq, int64_t *es
save_tau = cm->tau;
for (i = 0; i < nenv; i++) {
-#if DEBUG_NOW
+#if eslDEBUGLEVEL >= 3
printf("\nSURVIVOR Envelope %5d [%10ld..%10ld] being passed to Final stage pass: %" PRId64 "\n", i, es[i], ee[i], pli->cur_pass_idx);
#endif
nhit = hitlist->N;
@@ -3660,7 +3656,7 @@ pli_final_stage(CM_PIPELINE *pli, off_t cm_offset, const ESL_SQ *sq, int64_t *es
if ((status = esl_strdup(cm->acc, -1, &(hit->acc))) != eslOK) ESL_FAIL(eslEMEM, pli->errbuf, "allocation failure");
if ((status = esl_strdup(cm->desc, -1, &(hit->desc))) != eslOK) ESL_FAIL(eslEMEM, pli->errbuf, "allocation failure");
}
-#if DEBUG_NOW
+#if eslDEBUGLEVEL >= 3
printf("SURVIVOR envelope [%10ld..%10ld] survived Inside %6.2f bits P %g\n", hit->start, hit->stop, hit->score, hit->pvalue);
#endif
/* Get an alignment of the hit.
@@ -3814,7 +3810,7 @@ pli_final_stage_hmmonly(CM_PIPELINE *pli, off_t cm_offset, P7_OPROFILE *om, P7_B
nullsc2 = (float)loc_window_length * log((float)loc_window_length/(loc_window_length+1)) + log(1./(loc_window_length+1));
for (i = 0; i < nwin; i++) {
-#if DEBUG_NOW
+#if eslDEBUGLEVEL >= 3
printf("p7 final stage win: %4d of %4d [%6" PRId64 "..%6" PRId64 "] pass: %" PRId64 "\n", i, nwin, ws[i], we[i], pli->cur_pass_idx);
#endif
@@ -3908,7 +3904,7 @@ pli_final_stage_hmmonly(CM_PIPELINE *pli, off_t cm_offset, P7_OPROFILE *om, P7_B
p7_alidisplay_Destroy(pli->ddef->dcl[d].ad);
pli->ddef->dcl[d].ad = NULL;
-#if DEBUG_NOW
+#if eslDEBUGLEVEL >= 3
printf("SURVIVOR envelope [%10ld..%10ld] survived Final HMM ONLY stage %6.2f bits P %g\n", hit->start, hit->stop, hit->score, hit->pvalue);
#endif
@@ -4514,10 +4510,10 @@ merge_windows_from_two_lists(int64_t *ws1, int64_t *we1, double *wp1, int *wl1,
for(i2 = 0; i2 < nwin2; i2++) if(ws2[i2] > we2[i2]) return eslEINVAL;
nalloc = nwin1 + nwin2; /* we'll never exceed this */
- ESL_ALLOC(mws, sizeof(int64_t) * nalloc);
- ESL_ALLOC(mwe, sizeof(int64_t) * nalloc);
- ESL_ALLOC(mwp, sizeof(double) * nalloc);
- ESL_ALLOC(mwl, sizeof(int) * nalloc);
+ ESL_ALLOC(mws, sizeof(int64_t) * ESL_MAX(1, nalloc)); // avoid 0 malloc
+ ESL_ALLOC(mwe, sizeof(int64_t) * ESL_MAX(1, nalloc));
+ ESL_ALLOC(mwp, sizeof(double) * ESL_MAX(1, nalloc));
+ ESL_ALLOC(mwl, sizeof(int) * ESL_MAX(1, nalloc));
i1 = 0;
i2 = 0;
diff --git a/src/cm_submodel.c b/src/cm_submodel.c
index a5c744cf..bc623698 100644
--- a/src/cm_submodel.c
+++ b/src/cm_submodel.c
@@ -423,7 +423,6 @@ map_orig2sub_cm_helper(CM_t *orig_cm, CM_t *sub_cm, CMSubMap_t *submap, int orig
{
int sub_nd;
int orig_nd;
- int is_insert;
/*printf("\nin helper: orig_v: %d sub_v: %d\n", orig_v, sub_v);*/
@@ -437,10 +436,8 @@ map_orig2sub_cm_helper(CM_t *orig_cm, CM_t *sub_cm, CMSubMap_t *submap, int orig
orig_nd = orig_cm->ndidx[orig_v];
sub_nd = sub_cm->ndidx[sub_v];
- is_insert = FALSE;
if(sub_cm->sttype[sub_v] == IL_st || sub_cm->sttype[sub_v] == IR_st)
{
- is_insert = TRUE;
/* Make sure that neither orig_v nor sub_v is a detached insert state,
* if either is, we return b/c it's irrelevant, and we don't store that info in the maps */
if(orig_cm->sttype[(orig_v+1)] == E_st || sub_cm->sttype[(sub_v+1)] == E_st)
@@ -861,9 +858,7 @@ CP9NodeForPosn(CP9_t *hmm, int i0, int j0, int x, CP9_MX *post,
'1' for insert */
int max_sc; /* score (log probability) from post matrix for max_k node max_type state type */
int k; /* counter over nodes */
- int reached_mass; /* TRUE if we've reached our pmass */
- reached_mass = FALSE;
if(!is_start) pmass = 1. - pmass; /* we move left to right */
/*printf("in CP9NodeForPosn is_start: %d pmass: %f\n", is_start, pmass);*/
@@ -2046,9 +2041,6 @@ check_sub_cm_by_sampling(CM_t *orig_cm, CM_t *sub_cm, char *errbuf, ESL_RANDOMNE
CP9_t *sub_hmm; /* constructed CP9 HMM from the sub_cm */
CP9Map_t *orig_cp9map; /* maps the orig_cm to the orig_hmm and vice versa */
CP9Map_t *sub_cp9map; /* maps the sub_cm to the sub_hmm and vice versa */
- int debug_level;
-
- debug_level = 0;
/* Build two CP9 HMMs, one for the orig_cm and one for the sub_cm */
if((status = build_cp9_hmm(orig_cm, errbuf, FALSE, 0.0001, print_flag, &orig_hmm, &orig_cp9map)) != eslOK) return status;
@@ -3329,7 +3321,6 @@ sub_cm2cm_parsetree(CM_t *orig_cm, CM_t *sub_cm, Parsetree_t **ret_orig_tr, Pars
int orig_v2;
int orig_nd1;
int orig_nd2;
- int nodes_used;
int cm_nd;
int i;
int parent_tr_nd;
@@ -3594,7 +3585,6 @@ sub_cm2cm_parsetree(CM_t *orig_cm, CM_t *sub_cm, Parsetree_t **ret_orig_tr, Pars
}
orig_tr = CreateParsetree(100);
- nodes_used = 0;
for(cm_nd = 0; cm_nd < orig_cm->nodes; cm_nd++)
{
emitl_flag = 0;
diff --git a/src/cm_tophits.c b/src/cm_tophits.c
index 6864d880..54129f7b 100644
--- a/src/cm_tophits.c
+++ b/src/cm_tophits.c
@@ -189,7 +189,8 @@ cm_tophits_CreateNextHit(CM_TOPHITS *h, CM_HIT **ret_hit)
return status;
}
-/* hit_sorter_by_evalue(), hit_sorter_for_overlap_removal and hit_sorter_by_position: qsort's pawns, below */
+/* hit_sorter_by_evalue(), hit_sorter_for_overlap_removal, hit_sorter_for_overlap_markup_clans_only,
+ * hit_sorter_for_overlap_markup_clans_agnostic and hit_sorter_by_position: qsort's pawns, below */
static int
hit_sorter_by_evalue(const void *vh1, const void *vh2)
{
@@ -242,7 +243,7 @@ hit_sorter_for_overlap_removal(const void *vh1, const void *vh2)
}
static int
-hit_sorter_for_overlap_markup(const void *vh1, const void *vh2)
+hit_sorter_for_overlap_markup_clans_only(const void *vh1, const void *vh2)
{
CM_HIT *h1 = *((CM_HIT **) vh1); /* don't ask. don't change. Don't Panic. */
CM_HIT *h2 = *((CM_HIT **) vh2);
@@ -254,7 +255,7 @@ hit_sorter_for_overlap_markup(const void *vh1, const void *vh2)
if (h1->in_rc > h2->in_rc) return 1; /* second key, strand (h1->in_rc = 1, h1->in_rc = 0), forward, then reverse */
else if(h1->in_rc < h2->in_rc) return -1; /* (h1->in_rc = 0, h2->in_rc = 1), forward, then reverse */
else {
- if (h1->clan_idx > h2->clan_idx) return 1; /* third key is clan_idx, low to high (often these will all be -1) */
+ if (h1->clan_idx > h2->clan_idx) return 1; /* third key is clan_idx, low to high */
else if(h1->clan_idx < h2->clan_idx) return -1;
else {
if (h1->evalue > h2->evalue) return 1; /* fourth key is E-value, low to high */
@@ -278,6 +279,38 @@ hit_sorter_for_overlap_markup(const void *vh1, const void *vh2)
}
static int
+hit_sorter_for_overlap_markup_clans_agnostic(const void *vh1, const void *vh2)
+{
+ CM_HIT *h1 = *((CM_HIT **) vh1); /* don't ask. don't change. Don't Panic. */
+ CM_HIT *h2 = *((CM_HIT **) vh2);
+
+ if (h1->seq_idx > h2->seq_idx) return 1; /* first key, seq_idx (unique id for sequences), low to high */
+ else if (h1->seq_idx < h2->seq_idx) return -1;
+ else {
+ /* same sequence; sort by strand, then E-value, then score, then start position, then CM index */
+ if (h1->in_rc > h2->in_rc) return 1; /* second key, strand (h1->in_rc = 1, h1->in_rc = 0), forward, then reverse */
+ else if(h1->in_rc < h2->in_rc) return -1; /* (h1->in_rc = 0, h2->in_rc = 1), forward, then reverse */
+ else {
+ if (h1->evalue > h2->evalue) return 1; /* fourth key is E-value, low to high */
+ else if(h1->evalue < h2->evalue) return -1;
+ else {
+ if (h1->score < h2->score) return 1; /* fifth key is bit score, high to low */
+ else if(h1->score > h2->score) return -1;
+ else {
+ if (h1->start > h2->start) return 1; /* sixth key is start position, low to high (irregardless of in_rc value) */
+ else if(h1->start < h2->start) return -1;
+ else {
+ if (h1->cm_idx > h2->cm_idx) return 1; /* seventh key is cm_idx (unique id for models), low to high */
+ else if(h1->cm_idx < h2->cm_idx) return -1;
+ else return 0;
+ }
+ }
+ }
+ }
+ }
+}
+
+static int
hit_sorter_by_position(const void *vh1, const void *vh2)
{
CM_HIT *h1 = *((CM_HIT **) vh1); /* don't ask. don't change. Don't Panic. */
@@ -390,10 +423,14 @@ cm_tophits_SortForOverlapRemoval(CM_TOPHITS *h)
* to low), fifth is start position (low to high) and
* sixth key is CM idx (unique id for models, low to high).
*
+ * Args: do_clans_only - TRUE: we are only marking overlaps within clans
+ * FALSE: we are marking all overlaps
+ * This has implications on how we sort.
+ *
* Returns: on success.
*/
int
-cm_tophits_SortForOverlapMarkup(CM_TOPHITS *h)
+cm_tophits_SortForOverlapMarkup(CM_TOPHITS *h, int do_clans_only)
{
int i;
@@ -405,7 +442,14 @@ cm_tophits_SortForOverlapMarkup(CM_TOPHITS *h)
}
/* initialize hit ptrs, this also unsorts if already sorted by score */
for (i = 0; i < h->N; i++) h->hit[i] = h->unsrt + i;
- if (h->N > 1) qsort(h->hit, h->N, sizeof(CM_HIT *), hit_sorter_for_overlap_markup);
+ if (h->N > 1) {
+ if(do_clans_only) {
+ qsort(h->hit, h->N, sizeof(CM_HIT *), hit_sorter_for_overlap_markup_clans_only);
+ }
+ else {
+ qsort(h->hit, h->N, sizeof(CM_HIT *), hit_sorter_for_overlap_markup_clans_agnostic);
+ }
+ }
h->is_sorted_by_evalue = FALSE;
h->is_sorted_by_position = FALSE;
h->is_sorted_for_overlap_removal = FALSE;
@@ -1114,7 +1158,7 @@ int remove_or_mark_overlaps_one_seq_memeff(CM_TOPHITS *th, int64_t idx1, int64_t
* th->is_sorted_for_overlap_markup flags, exactly one
* of which must be true, otherwise we'll die.
*
- * : TRUE to only markup overlaps for hits in
+ * : TRUE to only markup overlaps for hits in
* the same clan, FALSE to markup overlaps between all
* hits. IRRELEVANT if th->is_sorted_for_overlap_removal.
*
@@ -1124,7 +1168,7 @@ int remove_or_mark_overlaps_one_seq_memeff(CM_TOPHITS *th, int64_t idx1, int64_t
* eslEMEM if we run out of memory, errbuf filled
*/
int
-cm_tophits_RemoveOrMarkOverlaps(CM_TOPHITS *th, int do_clans, char *errbuf)
+cm_tophits_RemoveOrMarkOverlaps(CM_TOPHITS *th, int do_clans_only, char *errbuf)
{
int status;
int64_t i, j;
@@ -1151,7 +1195,7 @@ cm_tophits_RemoveOrMarkOverlaps(CM_TOPHITS *th, int do_clans, char *errbuf)
else {
ESL_FAIL(eslEINVAL, errbuf, "cm_tophits_RemoveOrMarkOverlaps() list is not sorted appropriately");
}
- if(do_remove && do_clans) {
+ if(do_remove && do_clans_only) {
ESL_FAIL(eslEINVAL, errbuf, "cm_tophits_RemoveOrMarkOverlaps() list is sorted for overlap removal and we're trying to respect clan membership...shouldn't happen");
}
@@ -1164,17 +1208,17 @@ cm_tophits_RemoveOrMarkOverlaps(CM_TOPHITS *th, int do_clans, char *errbuf)
((! do_remove) || (th->hit[j]->cm_idx == th->hit[i]->cm_idx)) &&
th->hit[j]->seq_idx == th->hit[i]->seq_idx &&
th->hit[j]->in_rc == th->hit[i]->in_rc &&
- ((! do_clans) || (th->hit[j]->clan_idx == th->hit[i]->clan_idx))) {
+ ((! do_clans_only) || (th->hit[j]->clan_idx == th->hit[i]->clan_idx))) {
j++;
}
- if(j != (i+1) && /* more than one hit in set i..j-1 */
- ((! do_clans) || th->hit[i]->clan_idx != -1)) { /* we're not only marking overlaps within same clan OR
- * we are and all hits are in same clan, this way if
- * do_clans is TRUE we won't remove overlaps between
- * hits in families that are not members of any clan */
+ if(j != (i+1) && /* more than one hit in set i..j-1 */
+ ((! do_clans_only) || th->hit[i]->clan_idx != -1)) { /* we're not only marking overlaps within same clan OR
+ * we are and all hits are in same clan, this way if
+ * do_clans_only is TRUE we won't remove overlaps between
+ * hits in families that are not members of any clan */
/* Hits i to j-1 form a set of hits that all share cm_idx (if
* 'do_remove == TRUE'), seq_idx, in_rc and clan_idx (if
- * 'do_clans == TRUE'). Remove overlaps from this set in 1 of 2
+ * 'do_clans_only == TRUE'). Remove overlaps from this set in 1 of 2
* ways, depending on length of source sequence and number of
* hits. remove_overlaps_one_seq_fast() will need to allocate a
* char array of size srcL, but it is significantly faster when
@@ -1726,7 +1770,7 @@ cm_tophits_HitAlignmentStatistics(FILE *ofp, CM_TOPHITS *th, int used_hb, int us
int is_reported;
int is_included;
int is_removed_duplicate;
- int is_marked_duplicate;
+ /*int is_marked_duplicate;*/ /* not used, currently */
/* variables for alignments for all hits */
int64_t all_naln = 0; /* total number alignments */
@@ -1792,7 +1836,7 @@ cm_tophits_HitAlignmentStatistics(FILE *ofp, CM_TOPHITS *th, int used_hb, int us
is_reported = (th->unsrt[h].flags & CM_HIT_IS_REPORTED) ? TRUE : FALSE;
is_included = (th->unsrt[h].flags & CM_HIT_IS_INCLUDED) ? TRUE : FALSE;
is_removed_duplicate = (th->unsrt[h].flags & CM_HIT_IS_REMOVED_DUPLICATE) ? TRUE : FALSE;
- is_marked_duplicate = (th->unsrt[h].flags & CM_HIT_IS_MARKED_OVERLAP) ? TRUE : FALSE;
+ /*is_marked_duplicate = (th->unsrt[h].flags & CM_HIT_IS_MARKED_OVERLAP) ? TRUE : FALSE;*/
if(th->unsrt[h].ad != NULL) {
all_naln++;
all_tot_matrix_Mb += th->unsrt[h].ad->matrix_Mb;
@@ -2167,7 +2211,7 @@ cm_tophits_TabularTargets1(FILE *ofp, char *qname, char *qacc, CM_TOPHITS *th, C
for (h = 0; h < th->N; h++) {
if (th->hit[h]->flags & CM_HIT_IS_REPORTED) {
// fprintf(ofp, "%-*s %-*s %-*s %-*s %3s %8d %8d %*" PRId64 " %*" PRId64 " %6s %5s %4d %4.2f %5.1f %6.1f %9.2g %-3s %s\n",
- fprintf(ofp, "%-*s %-*s %-*s %-*s %3s %8d %8d %*" PRId64 " %*" PRId64 " %6s %5s %4d %4.2f %5.1f %6.1f %9.2g %c%c %s\n",
+ fprintf(ofp, "%-*s %-*s %-*s %-*s %3s %8d %8d %*" PRId64 " %*" PRId64 " %6s %5s %4d %4.2f %5.1f %6.1f %9.2g %-3s %s\n",
tnamew, th->hit[h]->name,
taccw, ((th->hit[h]->acc != NULL && th->hit[h]->acc[0] != '\0') ? th->hit[h]->acc : "-"),
qnamew, qname,
@@ -2183,8 +2227,7 @@ cm_tophits_TabularTargets1(FILE *ofp, char *qname, char *qacc, CM_TOPHITS *th, C
th->hit[h]->bias,
th->hit[h]->score,
th->hit[h]->evalue,
- (th->hit[h]->flags & CM_HIT_IS_INCLUDED ? '!' : '?'),
- ((pli->mode == CM_SCAN_MODELS) ? (th->hit[h]->flags & CM_HIT_IS_MARKED_OVERLAP ? '=' : '*') : ' '),
+ (th->hit[h]->flags & CM_HIT_IS_INCLUDED ? "!" : "?"),
(th->hit[h]->desc != NULL) ? th->hit[h]->desc : "-");
}
}
@@ -2305,25 +2348,27 @@ cm_tophits_TabularTargets2(FILE *ofp, char *qname, char *qacc, CM_TOPHITS *th, C
for(i = 0; i < clanw; i++) { clanstr[i] = '-'; } clanstr[clanw] = '\0';
for(i = 0; i < posw; i++) { posstr[i] = '-'; } posstr[posw] = '\0';
- ESL_ALLOC(sorted_idxA, sizeof(int64_t) * th->N);
- for(h = 0; h < th->N; h++) sorted_idxA[h] = -1;
- ESL_ALLOC(output_idxA, sizeof(int64_t) * th->N);
- for(h = 0; h < th->N; h++) output_idxA[h] = -1;
- ESL_ALLOC(has_overlapA, sizeof(int) * th->N);
- /* determine which hits are listed as any_oidx or win_oidx for any other hits */
- for(h = 0; h < th->N; h++) has_overlapA[h] = FALSE;
- for(h = 0; h < th->N; h++) {
- if(th->hit[h]->any_oidx != -1) has_overlapA[th->hit[h]->any_oidx] = TRUE;
- if(th->hit[h]->win_oidx != -1) has_overlapA[th->hit[h]->win_oidx] = TRUE;
- sorted_idxA[th->hit[h]->hit_idx] = h; /* save sorted idx */
- /* and save the output index we'll use for this hit */
- if ((th->hit[h]->flags & CM_HIT_IS_REPORTED) && /* hit is REPORTED */
- (skip_overlaps == FALSE || (! (th->hit[h]->flags & CM_HIT_IS_MARKED_OVERLAP)))) { /* hit won't be skipped b/c it's an overlap */
- noutput++;
- output_idxA[h] = noutput; /* save output idx */
+ if(th->N > 0) {
+ ESL_ALLOC(sorted_idxA, sizeof(int64_t) * th->N);
+ ESL_ALLOC(output_idxA, sizeof(int64_t) * th->N);
+ ESL_ALLOC(has_overlapA, sizeof(int) * th->N);
+ for(h = 0; h < th->N; h++) sorted_idxA[h] = -1;
+ for(h = 0; h < th->N; h++) output_idxA[h] = -1;
+ for(h = 0; h < th->N; h++) has_overlapA[h] = FALSE;
+ /* determine which hits are listed as any_oidx or win_oidx for any other hits */
+ for(h = 0; h < th->N; h++) {
+ if(th->hit[h]->any_oidx != -1) has_overlapA[th->hit[h]->any_oidx] = TRUE;
+ if(th->hit[h]->win_oidx != -1) has_overlapA[th->hit[h]->win_oidx] = TRUE;
+ sorted_idxA[th->hit[h]->hit_idx] = h; /* save sorted idx */
+ /* and save the output index we'll use for this hit */
+ if ((th->hit[h]->flags & CM_HIT_IS_REPORTED) && /* hit is REPORTED */
+ (skip_overlaps == FALSE || (! (th->hit[h]->flags & CM_HIT_IS_MARKED_OVERLAP)))) { /* hit won't be skipped b/c it's an overlap */
+ noutput++;
+ output_idxA[h] = noutput; /* save output idx */
+ }
}
+ noutput = 0; /* very impt to reset this, so we list first hit as index 1, and not th->N+1 */
}
- noutput = 0; /* very impt to reset this, so we list first hit as index 1, and not th->N+1 */
if (show_header) {
if(pli->do_trm_F3) { /* terminated after F3, more compact output (we don't have all the info for the default output mode) */
@@ -2485,9 +2530,10 @@ cm_tophits_TabularTargets2(FILE *ofp, char *qname, char *qacc, CM_TOPHITS *th, C
if(any_ofctstr2 != NULL) free(any_ofctstr2);
if(win_ofctstr1 != NULL) free(win_ofctstr1);
if(win_ofctstr2 != NULL) free(win_ofctstr2);
- if(has_overlapA != NULL) free(has_overlapA);
+ if(clannamestr != NULL) free(clannamestr);
if(sorted_idxA != NULL) free(sorted_idxA);
if(output_idxA != NULL) free(output_idxA);
+ if(has_overlapA != NULL) free(has_overlapA);
return eslOK;
@@ -2507,9 +2553,10 @@ cm_tophits_TabularTargets2(FILE *ofp, char *qname, char *qacc, CM_TOPHITS *th, C
if(any_ofctstr2 != NULL) free(any_ofctstr2);
if(win_ofctstr1 != NULL) free(win_ofctstr1);
if(win_ofctstr2 != NULL) free(win_ofctstr2);
- if(has_overlapA != NULL) free(has_overlapA);
+ if(clannamestr != NULL) free(clannamestr);
if(sorted_idxA != NULL) free(sorted_idxA);
if(output_idxA != NULL) free(output_idxA);
+ if(has_overlapA != NULL) free(has_overlapA);
return status;
}
@@ -3046,19 +3093,19 @@ main(int argc, char **argv)
if(esl_opt_GetBoolean(go, "-v")) cm_tophits_Dump(stdout, h[0]);
- if((status = cm_tophits_RemoveOrMarkOverlaps(h[0], errbuf)) != eslOK) cm_Fail(errbuf);
+ if((status = cm_tophits_RemoveOrMarkOverlaps(h[0], /*do_clans_only=*/FALSE, errbuf)) != eslOK) cm_Fail(errbuf);
esl_stopwatch_Stop(w);
esl_stopwatch_Display(stdout, w, "# CPU time cm_tophits_RemoveOrMarkOverlaps() (removing): ");
esl_stopwatch_Start(w);
- cm_tophits_SortForOverlapMarkup(h[0]);
+ cm_tophits_SortForOverlapMarkup(h[0], FALSE);
esl_stopwatch_Stop(w);
esl_stopwatch_Display(stdout, w, "# CPU time cm_tophits_SortForOverlapMarkup(): ");
esl_stopwatch_Start(w);
- if((status = cm_tophits_RemoveOrMarkOverlaps(h[0], errbuf)) != eslOK) cm_Fail(errbuf);
+ if((status = cm_tophits_RemoveOrMarkOverlaps(h[0], /*do_clans=*/FALSE, errbuf)) != eslOK) cm_Fail(errbuf);
if(esl_opt_GetBoolean(go, "-v")) cm_tophits_Dump(stdout, h[0]);
@@ -3357,14 +3404,14 @@ main(int argc, char **argv)
hit->srcL = L+1;
cm_tophits_SortForOverlapRemoval(h1);
- if((status = cm_tophits_RemoveOrMarkOverlaps(h1, /*do_clans=*/FALSE, errbuf)) != eslOK) cm_Fail(errbuf);
+ if((status = cm_tophits_RemoveOrMarkOverlaps(h1, /*do_clans_only=*/FALSE, errbuf)) != eslOK) cm_Fail(errbuf);
cm_tophits_SortByEvalue(h1);
if (strcmp(h1->hit[0]->name, "third") != 0) esl_fatal("sort 1 failed (top is %s = %f)", h1->hit[0]->name, h1->hit[0]->score);
if (strcmp(h1->hit[N+1]->name, "thirdtolast") != 0) esl_fatal("sort 1 failed (last is %s = %f)", h1->hit[N+1]->name, h1->hit[N+1]->score);
cm_tophits_Merge(h1, h2);
cm_tophits_SortForOverlapRemoval(h1);
- if((status = cm_tophits_RemoveOrMarkOverlaps(h1, /*do_clans=*/FALSE, errbuf)) != eslOK) cm_Fail(errbuf);
+ if((status = cm_tophits_RemoveOrMarkOverlaps(h1, /*do_clans_only=*/FALSE, errbuf)) != eslOK) cm_Fail(errbuf);
cm_tophits_SortByEvalue(h1);
if (strcmp(h1->hit[0]->name, "second") != 0) esl_fatal("sort 2 failed (top is %s = %f)", h1->hit[0]->name, h1->hit[0]->score);
if (strcmp(h1->hit[1]->name, "third") != 0) esl_fatal("sort 2 failed (second is %s = %f)", h1->hit[1]->name, h1->hit[1]->score);
@@ -3377,7 +3424,7 @@ main(int argc, char **argv)
cm_tophits_Merge(h1, h3);
cm_tophits_SortForOverlapRemoval(h1);
- if((status = cm_tophits_RemoveOrMarkOverlaps(h1, /*do_clans=*/FALSE, errbuf)) != eslOK) cm_Fail(errbuf);
+ if((status = cm_tophits_RemoveOrMarkOverlaps(h1, /*do_clans_only=*/FALSE, errbuf)) != eslOK) cm_Fail(errbuf);
cm_tophits_SortByEvalue(h1);
if (strcmp(h1->hit[0]->name, "first") != 0) esl_fatal("sort 3 failed (top is %s = %f)", h1->hit[0]->name, h1->hit[0]->score);
if (strcmp(h1->hit[1]->name, "second") != 0) esl_fatal("sort 3 failed (second is %s = %f)", h1->hit[1]->name, h1->hit[1]->score);
@@ -3395,7 +3442,7 @@ main(int argc, char **argv)
/* test markup, first sort for removal and make sure we don't mark up any overlaps of different models */
cm_tophits_Merge(h1, h4);
cm_tophits_SortForOverlapRemoval(h1);
- if((status = cm_tophits_RemoveOrMarkOverlaps(h1, /*do_clans=*/FALSE, errbuf)) != eslOK) cm_Fail(errbuf);
+ if((status = cm_tophits_RemoveOrMarkOverlaps(h1, /*do_clans_only=*/FALSE, errbuf)) != eslOK) cm_Fail(errbuf);
cm_tophits_SortByEvalue(h1);
if (strcmp(h1->hit[0]->name, "Bfirst") != 0) esl_fatal("sort 4 failed (first is %s = %f)", h1->hit[0]->name, h1->hit[0]->score);
if (strcmp(h1->hit[1]->name, "first") != 0) esl_fatal("sort 4 failed (second is %s = %f)", h1->hit[1]->name, h1->hit[1]->score);
@@ -3415,8 +3462,8 @@ main(int argc, char **argv)
if (h1->hit[4*N+7]->flags & CM_HIT_IS_REMOVED_DUPLICATE) esl_fatal("RemoveOrMarkOverlaps failed 14");
/* second sort for markup and make sure we DO mark up overlaps of different models */
- cm_tophits_SortForOverlapMarkup(h1);
- if((status = cm_tophits_RemoveOrMarkOverlaps(h1, /*do_clans=*/FALSE, errbuf)) != eslOK) cm_Fail(errbuf);
+ cm_tophits_SortForOverlapMarkup(h1, /*do_clans_only=*/FALSE);
+ if((status = cm_tophits_RemoveOrMarkOverlaps(h1, /*do_clans_only=*/FALSE, errbuf)) != eslOK) cm_Fail(errbuf);
cm_tophits_SortByEvalue(h1);
if (strcmp(h1->hit[0]->name, "Bfirst") != 0) esl_fatal("sort 5 failed (first is %s = %f)", h1->hit[0]->name, h1->hit[0]->score);
if (strcmp(h1->hit[1]->name, "first") != 0) esl_fatal("sort 5 failed (second is %s = %f)", h1->hit[1]->name, h1->hit[1]->score);
@@ -3521,9 +3568,9 @@ main(int argc, char **argv)
}
cm_tophits_SortForOverlapRemoval(h5);
- if((status = cm_tophits_RemoveOrMarkOverlaps(h5, /*do_clans=*/FALSE, errbuf)) != eslOK) cm_Fail(errbuf);
- cm_tophits_SortForOverlapMarkup(h5);
- if((status = cm_tophits_RemoveOrMarkOverlaps(h5, /*do_clans=*/FALSE, errbuf)) != eslOK) cm_Fail(errbuf);
+ if((status = cm_tophits_RemoveOrMarkOverlaps(h5, /*do_clans_only=*/FALSE, errbuf)) != eslOK) cm_Fail(errbuf);
+ cm_tophits_SortForOverlapMarkup(h5, /*do_clans_only=*/FALSE);
+ if((status = cm_tophits_RemoveOrMarkOverlaps(h5, /*do_clans_only=*/FALSE, errbuf)) != eslOK) cm_Fail(errbuf);
cm_tophits_SortByEvalue(h5);
if (strcmp(h5->hit[0]->name, "hit1") != 0) esl_fatal("sort 6 failed pass %d (first is %s = %f)", p+1, h5->hit[0]->name, h5->hit[0]->score);
diff --git a/src/cm_trunc.c b/src/cm_trunc.c
index 29b9a1f7..1c1a5cb1 100644
--- a/src/cm_trunc.c
+++ b/src/cm_trunc.c
@@ -86,7 +86,7 @@ cm_tr_penalties_Create(CM_t *cm, int ignore_inserts, char *errbuf)
*
* Important note: For this discussion we assume that sequences can
* only be truncated at consensus positions, which means we don't
- * have to worry about truncated begins into this is an
+ * have to worry about truncated begins into inserts. This is an
* approximation (also made by Diana and Sean in the 2009 trCYK
* paper) that greatly simplifies the explanation of the calculation
* of the truncation penalties. The examples in my ELN3 notebook
diff --git a/src/cmalign.c b/src/cmalign.c
index 122722fa..fee98f3f 100644
--- a/src/cmalign.c
+++ b/src/cmalign.c
@@ -456,7 +456,7 @@ serial_master(ESL_GETOPTS *go, struct cfg_s *cfg)
}
#ifdef HMMER_THREADS
- ESL_ALLOC(init_sqA, sizeof(ESL_SQ *) * (ncpus * 2));
+ ESL_ALLOC(init_sqA, sizeof(ESL_SQ *) * ESL_MAX(1, ncpus * 2)); // avoid malloc of 0
for (k = 0; k < ncpus * 2; k++) {
init_sqA[k] = NULL;
if((init_sqA[k] = esl_sq_CreateDigital(cfg->abc)) == NULL) cm_Fail("Failed to allocate a sequence");
@@ -487,7 +487,7 @@ serial_master(ESL_GETOPTS *go, struct cfg_s *cfg)
/* Read the first block */
sq_block = esl_sq_CreateDigitalBlock(CMALIGN_MAX_NSEQ, cfg->abc);
- sstatus = esl_sqio_ReadBlock(cfg->sqfp, sq_block, CM_MAX_RESIDUE_COUNT, CMALIGN_MAX_NSEQ, FALSE); /* FALSE says: read complete sequences */
+ sstatus = esl_sqio_ReadBlock(cfg->sqfp, sq_block, -1, -1, FALSE); /* FALSE says: read complete sequences */
nxt_sq_block = sq_block; /* special case of first block read */
while(sstatus == eslOK) {
@@ -517,7 +517,7 @@ serial_master(ESL_GETOPTS *go, struct cfg_s *cfg)
* fine for a while.
*/
nxt_sq_block = esl_sq_CreateDigitalBlock(CMALIGN_MAX_NSEQ, cfg->abc);
- sstatus = esl_sqio_ReadBlock(cfg->sqfp, nxt_sq_block, CM_MAX_RESIDUE_COUNT, CMALIGN_MAX_NSEQ, FALSE); /* FALSE says: read complete sequences */
+ sstatus = esl_sqio_ReadBlock(cfg->sqfp, nxt_sq_block, -1, -1, FALSE); /* FALSE says: read complete sequences */
if(sstatus == eslEOF) {
reached_eof = TRUE; /* nxt_sq_block will not have been filled */
esl_sq_DestroyBlock(nxt_sq_block);
@@ -536,7 +536,7 @@ serial_master(ESL_GETOPTS *go, struct cfg_s *cfg)
/* create a single array of all CM_ALNDATA objects, in original (input) order */
nmap_cur = (nali == 0) ? nmap_data : 0;
nmerged = nseq_cur + nmap_cur;
- ESL_ALLOC(merged_dataA, sizeof(CM_ALNDATA *) * nmerged);
+ ESL_ALLOC(merged_dataA, sizeof(CM_ALNDATA *) * ESL_MAX(1, nmerged)); // avoid malloc of 0
/* prepend mapali data if nec */
if(nmap_cur > 0) {
for(i = 0; i < nmap_cur; i++) merged_dataA[i] = map_dataA[i];
@@ -980,7 +980,7 @@ mpi_master(ESL_GETOPTS *go, struct cfg_s *cfg)
/* Read the first block */
sq_block = esl_sq_CreateDigitalBlock(CMALIGN_MAX_NSEQ, cfg->abc);
- sstatus = esl_sqio_ReadBlock(cfg->sqfp, sq_block, -1, FALSE); /* FALSE says: read complete sequences */
+ sstatus = esl_sqio_ReadBlock(cfg->sqfp, sq_block, -1, -1, FALSE); /* FALSE says: read complete sequences */
nxt_sq_block = sq_block; /* special case of first block read */
#if DEBUGMPI
@@ -1009,7 +1009,7 @@ mpi_master(ESL_GETOPTS *go, struct cfg_s *cfg)
* fine for a while.
*/
nxt_sq_block = esl_sq_CreateDigitalBlock(CMALIGN_MAX_NSEQ, cfg->abc);
- sstatus = esl_sqio_ReadBlock(cfg->sqfp, nxt_sq_block, -1, FALSE); /* FALSE says: read complete sequences */
+ sstatus = esl_sqio_ReadBlock(cfg->sqfp, nxt_sq_block, -1, -1, FALSE); /* FALSE says: read complete sequences */
if(sstatus == eslEOF) {
reached_eof = TRUE; /* nxt_sq_block will not have been filled */
esl_sq_DestroyBlock(nxt_sq_block);
@@ -1019,7 +1019,7 @@ mpi_master(ESL_GETOPTS *go, struct cfg_s *cfg)
/* allocate an array for all CM_ALNDATA objects we'll receive from workers */
nmap_cur = (nali == 0) ? nmap_data : 0;
nmerged = nseq_cur + nmap_cur;
- ESL_ALLOC(merged_dataA, sizeof(CM_ALNDATA *) * (nseq_cur + nmap_cur));
+ ESL_ALLOC(merged_dataA, sizeof(CM_ALNDATA *) * ESL_MAX(1, nseq_cur + nmap_cur)); // avoid malloc of 0
/* prepend mapali data if nec */
if(nmap_cur > 0) {
for(i = 0; i < nmap_cur; i++) merged_dataA[i] = map_dataA[i];
@@ -2081,7 +2081,7 @@ create_and_output_final_msa(const ESL_GETOPTS *go, const struct cfg_s *cfg, char
int cur_clen; /* consensus length (non-gap #=GC RF length) of current alignment */
int apos; /* alignment position */
ESL_MSA *fmsa = NULL; /* the merged alignment created by merging all alignments in msaA */
- int alen_fmsa; /* number of columns in merged MSA */
+ /*int alen_fmsa;*/ /* number of columns in merged MSA */
int *ngap_insA = NULL; /* [0..alen] number of insert gap columns to add after each alignment column when merging */
int *ngap_elA = NULL; /* [0..alen] number of missing data ('~') gap columns to add after each alignment column when merging */
int *ngap_eitherA = NULL; /* [0..apos..alen] = ngap_insA[apos] + ngap_elA[apos] */
@@ -2165,7 +2165,7 @@ create_and_output_final_msa(const ESL_GETOPTS *go, const struct cfg_s *cfg, char
* final (3rd) pass we'll output aligned data.
*/
fmsa = esl_msa_Create(nseq_tot, -1);
- alen_fmsa = cm->clen + esl_vec_ISum(maxins, (cm->clen+1));
+ /*alen_fmsa = cm->clen + esl_vec_ISum(maxins, (cm->clen+1));*/
/* if there was any GS annotation in any of the individual alignments,
* do second pass through alignment files, outputting GS annotation as we go. */
@@ -2483,7 +2483,6 @@ inflate_gc_with_gaps_and_els(FILE *ofp, ESL_MSA *msa, int *ngap_insA, int *ngap_
int apos = 0;
int apos2print = 0;
int i;
- int prv_cpos = -1;
int alen2print = 0;
char *rf2print;
char *ss_cons2print;
@@ -2509,7 +2508,6 @@ inflate_gc_with_gaps_and_els(FILE *ofp, ESL_MSA *msa, int *ngap_insA, int *ngap_
if(apos < msa->alen) {
rf2print[apos2print] = msa->rf[apos];
ss_cons2print[apos2print++] = msa->ss_cons[apos];
- if(! esl_abc_CIsGap(msa->abc, msa->rf[apos])) prv_cpos = apos;
}
}
diff --git a/src/cmbuild.c b/src/cmbuild.c
index 07d1057a..12f814a5 100644
--- a/src/cmbuild.c
+++ b/src/cmbuild.c
@@ -1611,21 +1611,17 @@ static P7_PRIOR * cm_p7_prior_CreateNucleic(void);
static int
set_model_cutoffs(const ESL_GETOPTS *go, const struct cfg_s *cfg, char *errbuf, ESL_MSA *msa, CM_t *cm)
{
- int cutoff_was_set = FALSE;
if(msa->cutset[eslMSA_TC1]) {
cm->tc = msa->cutoff[eslMSA_TC1];
cm->flags |= CMH_TC;
- cutoff_was_set = TRUE;
}
if(msa->cutset[eslMSA_GA1]) {
cm->ga = msa->cutoff[eslMSA_GA1];
cm->flags |= CMH_GA;
- cutoff_was_set = TRUE;
}
if(msa->cutset[eslMSA_NC1]) {
cm->nc = msa->cutoff[eslMSA_NC1];
cm->flags |= CMH_NC;
- cutoff_was_set = TRUE;
}
return eslOK;
}
@@ -2521,7 +2517,7 @@ MSADivide(ESL_MSA *mmsa, int do_all, int do_mindiff, int do_nc, float mindiff, i
* I'm leaving it in the code because later code relies on it
* (see note on rounding of diff values in "Mode 3" comment block below)
*/
- ESL_ALLOC(diff, (sizeof(double) * (T->N - 1))); /* one for each node */
+ ESL_ALLOC(diff, (sizeof(double) * ESL_MAX(1, T->N - 1))); /* one for each node, avoid 0 malloc */
for (n = (T->N-2); n >= 0; n--) {
diff[n] = T->ld[n]; /* or we could set it to T->rd[n], they're identical */
diff[n] *= 1000.;
@@ -2761,7 +2757,7 @@ find_mindiff(ESL_TREE *T, double *diff, int target_nc, int **ret_clust, int *ret
float high = 1.0;
float low = 0.0;
int high_nc = 0;
- int low_nc = 0;
+ /*int low_nc = 0;*/
float mindiff = 0.5;
int curr_nc = -1;
int curr_best = -1;
@@ -2785,7 +2781,7 @@ find_mindiff(ESL_TREE *T, double *diff, int target_nc, int **ret_clust, int *ret
}
else {/* curr_nc >= target_nc */
low = mindiff;
- low_nc = curr_nc;
+ /*low_nc = curr_nc;*/
mindiff += (high - mindiff) / 2.;
if(fabs(high-low) < thresh) keep_going = FALSE; /* stop, high and low have converged */
/*printf("GREATER nc: %d mindiff: %f low: %f high: %f\n", curr_nc, mindiff, low, high);*/
diff --git a/src/cmcalibrate.c b/src/cmcalibrate.c
index 58db9be6..f2d291fc 100644
--- a/src/cmcalibrate.c
+++ b/src/cmcalibrate.c
@@ -441,7 +441,6 @@ serial_master(ESL_GETOPTS *go, struct cfg_s *cfg)
int cmi; /* CM index, which model we're working on */
char time_buf[128]; /* string for printing elapsed time (safely holds up to 10^14 years) */
int exp_mode; /* ctr over exp tail modes */
- double asec; /* actual number of seconds for calibrating current CM */
double psec; /* predicted number of seconds for calibrating current CM */
double total_psec = 0.; /* predicted number of seconds for calibrating all CMs */
double total_asec = 0.; /* actual number of seconds for calibrating all CMs */
@@ -628,7 +627,6 @@ serial_master(ESL_GETOPTS *go, struct cfg_s *cfg)
FormatTimeString(time_buf, cfg->w->elapsed, FALSE);
printf("] %12s\n", time_buf);
fflush(stdout);
- asec = cfg->w->elapsed;
total_asec += cfg->w->elapsed;
} /* end of if(! esl_opt_IsUsed(go, "--forecast")) */
diff --git a/src/cmscan.c b/src/cmscan.c
index 2c30725a..99a62cab 100644
--- a/src/cmscan.c
+++ b/src/cmscan.c
@@ -152,21 +152,17 @@ static ESL_OPTIONS options[] = {
/* Other options */
{ "--notrunc", eslARG_NONE, FALSE, NULL, NULL, NULL, NULL, "--anytrunc,--onlytrunc,--5trunc,--3trunc", "do not allow truncated hits at sequence termini", 7 },
{ "--anytrunc", eslARG_NONE, FALSE, NULL, NULL, NULL, NULL, TRUNCOPTS, "allow full and truncated hits anywhere within sequences", 7 },
- { "--onlytrunc", eslARG_NONE, FALSE, NULL, NULL, NULL, NULL, TRUNCOPTS, "allow only truncated hits, anywhere within sequences", 7 },
- { "--5trunc", eslARG_NONE, FALSE, NULL, NULL, NULL, NULL, TRUNCOPTS, "allow truncated hits only at 5' ends of sequences", 7 },
- { "--3trunc", eslARG_NONE, FALSE, NULL, NULL, NULL, NULL, TRUNCOPTS, "allow truncated hits only at 3' ends of sequences", 7 },
+ { "--nohmmonly", eslARG_NONE, FALSE, NULL, NULL, NULL, NULL, "--hmmmax", "never run HMM-only mode, not even for models with 0 basepairs", 7 },
{ "--nonull3", eslARG_NONE, FALSE, NULL, NULL, NULL, NULL, NULL, "turn off the NULL3 post hoc additional null model", 7 },
{ "--mxsize", eslARG_REAL, NULL, NULL, "x>0.1", NULL, NULL, NULL, "set max allowed alnment mx size to Mb [df: autodetermined]", 7 },
{ "--smxsize", eslARG_REAL, "128.", NULL, "x>0.1", NULL, NULL, NULL, "set max allowed size of search DP matrices to Mb", 7 },
{ "--cyk", eslARG_NONE, FALSE, NULL, NULL, NULL, NULL, NULL, "use scanning CM CYK algorithm, not Inside in final stage", 7 },
{ "--acyk", eslARG_NONE, FALSE, NULL, NULL, NULL, NULL, NULL, "align hits with CYK, not optimal accuracy", 7 },
{ "--wcx", eslARG_REAL, FALSE, NULL, "x>=1.25",NULL, NULL,"--nohmm,--qdb,--fqdb", "set W (expected max hit len) as * cm->clen (model len)", 7 },
- { "--onepass", eslARG_NONE, FALSE, NULL, NULL, NULL, NULL,"--nohmm,--qdb,--fqdb", "use CM only for best scoring HMM pass for full seq envelopes", 7 },
{ "--toponly", eslARG_NONE, FALSE, NULL, NULL, NULL, NULL, NULL, "only search the top strand", 7 },
{ "--bottomonly", eslARG_NONE, FALSE, NULL, NULL, NULL, NULL, NULL, "only search the bottom strand", 7 },
{ "--qformat", eslARG_STRING, NULL, NULL, NULL, NULL, NULL, NULL, "assert query is in format : no autodetection", 7 },
{ "--glist", eslARG_INFILE, NULL, NULL, NULL, NULL, NULL, "-g", "configure CMs listed in file in glocal mode, others in local", 7 },
- { "--block", eslARG_INT, NULL, NULL, "n>0", NULL, NULL, NULL, "set block size (number of models per worker/thread) to ", 7 },
{ "--clanin", eslARG_INFILE, NULL, NULL, NULL, NULL, "--fmt",NULL, "read clan information from file ", 7 },
{ "--oclan", eslARG_NONE, FALSE, NULL, NULL, NULL, "--fmt,--clanin",NULL, "w/'--fmt 2' and '--tblout', only mark overlaps within clans", 7 },
{ "--oskip", eslARG_NONE, FALSE, NULL, NULL, NULL, "--fmt",NULL, "w/'--fmt 2' and '--tblout', do not output lower scoring overlaps", 7 },
@@ -210,7 +206,6 @@ static ESL_OPTIONS options[] = {
{ "--hmmF3", eslARG_REAL, "1e-5", NULL, "x>0", NULL, NULL, "--nohmmonly", "in HMM-only mode, set stage 3 (Fwd) P value threshold to ", 102 },
{ "--hmmnobias", eslARG_NONE, FALSE, NULL, NULL, NULL, NULL, "--nohmmonly", "in HMM-only mode, turn off the bias composition filter", 102 },
{ "--hmmnonull2", eslARG_NONE, FALSE, NULL, NULL, NULL, NULL, "--nohmmonly", "in HMM-only mode, turn off the null2 score correction", 102 },
- { "--nohmmonly", eslARG_NONE, FALSE, NULL, NULL, NULL, NULL, "--hmmmax", "never run HMM-only mode, not even for models with 0 basepairs",102 },
/* Options for precise control of HMM envelope definition */
/* name type default env range toggles reqs incomp help docgroup*/
{ "--rt1", eslARG_REAL, "0.25", NULL, NULL, NULL, NULL, "--nohmm,--max", "set domain/envelope definition rt1 parameter as ", 103 },
@@ -233,23 +228,31 @@ static ESL_OPTIONS options[] = {
{ "--qdb", eslARG_NONE, FALSE, NULL, NULL, NULL, NULL, NULL, "use QDBs (instead of HMM bands) in final Inside round", 105 },
{ "--beta", eslARG_REAL,"1e-15", NULL, "1E-18", 105 },
{ "--nonbanded", eslARG_NONE, FALSE, NULL, NULL, NULL, NULL,"--tau,--sums,--qdb,--beta", "do not use QDBs or HMM bands in final Inside round of CM search", 105 },
+ /* Options for terminating after individual pipeline stages, currently only works for F3 */
+ /* name type default env range toggles reqs incomp help docgroup*/
+ { "--trmF3", eslARG_NONE, FALSE, NULL, NULL, NULL,"--noali,--nohmmonly,--notrunc", NULL, "terminate after Stage 3 Fwd and output surviving windows", 106 },
+ /* Options for control of what types of truncated hits are allowed */
/* Options for timing individual pipeline stages */
/* name type default env range toggles reqs incomp help docgroup*/
- { "--timeF1", eslARG_NONE, FALSE, NULL, NULL, NULL, NULL, TIMINGOPTS, "abort after Stage 1 SSV; for timing expts", 106 },
- { "--timeF2", eslARG_NONE, FALSE, NULL, NULL, NULL, NULL, TIMINGOPTS, "abort after Stage 2 Vit; for timing expts", 106 },
- { "--timeF3", eslARG_NONE, FALSE, NULL, NULL, NULL, NULL, TIMINGOPTS, "abort after Stage 3 Fwd; for timing expts", 106 },
- { "--timeF4", eslARG_NONE, FALSE, NULL, NULL, NULL, NULL, TIMINGOPTS, "abort after Stage 4 glocal Fwd; for timing expts", 106 },
- { "--timeF5", eslARG_NONE, FALSE, NULL, NULL, NULL, NULL, TIMINGOPTS, "abort after Stage 5 envelope def; for timing expts", 106 },
- { "--timeF6", eslARG_NONE, FALSE, NULL, NULL, NULL, NULL, TIMINGOPTS, "abort after Stage 6 CYK; for timing expts", 106 },
+ { "--timeF1", eslARG_NONE, FALSE, NULL, NULL, NULL, NULL, TIMINGOPTS, "abort after Stage 1 SSV; for timing expts", 107 },
+ { "--timeF2", eslARG_NONE, FALSE, NULL, NULL, NULL, NULL, TIMINGOPTS, "abort after Stage 2 Vit; for timing expts", 107 },
+ { "--timeF3", eslARG_NONE, FALSE, NULL, NULL, NULL, NULL, TIMINGOPTS, "abort after Stage 3 Fwd; for timing expts", 107 },
+ { "--timeF4", eslARG_NONE, FALSE, NULL, NULL, NULL, NULL, TIMINGOPTS, "abort after Stage 4 glocal Fwd; for timing expts", 107 },
+ { "--timeF5", eslARG_NONE, FALSE, NULL, NULL, NULL, NULL, TIMINGOPTS, "abort after Stage 5 envelope def; for timing expts", 107 },
+ { "--timeF6", eslARG_NONE, FALSE, NULL, NULL, NULL, NULL, TIMINGOPTS, "abort after Stage 6 CYK; for timing expts", 107 },
/* Other expert options */
- { "--trmF3", eslARG_NONE, FALSE, NULL, NULL, NULL,"--noali,--nohmmonly,--notrunc", NULL, "terminate after Stage 3 Fwd and output surviving windows", 107 },
- /* name type default env range toggles reqs incomp help docgroup*/
- { "--nogreedy", eslARG_NONE, FALSE, NULL, NULL, NULL, NULL, NULL, "do not resolve hits with greedy algorithm, use optimal one", 108 },
- { "--cp9noel", eslARG_NONE, FALSE, NULL, NULL, NULL, NULL, "-g,--glist", "turn off local ends in cp9 HMMs", 108 },
- { "--cp9gloc", eslARG_NONE, FALSE, NULL, NULL, NULL, NULL, "-g,--glist,--cp9noel", "configure cp9 HMM in glocal mode", 108 },
- { "--null2", eslARG_NONE, FALSE, NULL, NULL, NULL, NULL, NULL, "turn on null 2 biased composition HMM score corrections", 108 },
- { "--maxtau", eslARG_REAL, "0.05", NULL,"0 when tightening HMM bands", 108 },
- { "--seed", eslARG_INT, "181", NULL, "n>=0", NULL, NULL, NULL, "set RNG seed to (if 0: one-time arbitrary seed)", 108 },
+ /* name type default env range toggles reqs incomp help docgroup*/
+ { "--nogreedy", eslARG_NONE, FALSE, NULL, NULL, NULL, NULL, NULL, "do not resolve hits with greedy algorithm, use optimal one", 108 },
+ { "--cp9noel", eslARG_NONE, FALSE, NULL, NULL, NULL, NULL, "-g,--glist", "turn off local ends in cp9 HMMs", 108 },
+ { "--cp9gloc", eslARG_NONE, FALSE, NULL, NULL, NULL, NULL, "-g,--glist,--cp9noel", "configure cp9 HMM in glocal mode", 108 },
+ { "--null2", eslARG_NONE, FALSE, NULL, NULL, NULL, NULL, NULL, "turn on null 2 biased composition HMM score corrections", 108 },
+ { "--maxtau", eslARG_REAL, "0.05", NULL,"0 when tightening HMM bands", 108 },
+ { "--seed", eslARG_INT, "181", NULL, "n>=0", NULL, NULL, NULL, "set RNG seed to (if 0: one-time arbitrary seed)", 108 },
+ { "--block", eslARG_INT, NULL, NULL, "n>0", NULL, NULL, NULL, "set block size (number of models per worker/thread) to ", 108 },
+ { "--onepass", eslARG_NONE, FALSE, NULL, NULL, NULL, NULL,"--nohmm,--qdb,--fqdb", "use CM only for best scoring HMM pass for full seq envelopes", 108 },
+ { "--onlytrunc", eslARG_NONE, FALSE, NULL, NULL, NULL, NULL, TRUNCOPTS, "allow only truncated hits, anywhere within sequences", 108 },
+ { "--5trunc", eslARG_NONE, FALSE, NULL, NULL, NULL, NULL, TRUNCOPTS, "allow truncated hits only at 5' ends of sequences", 108 },
+ { "--3trunc", eslARG_NONE, FALSE, NULL, NULL, NULL, NULL, TRUNCOPTS, "allow truncated hits only at 3' ends of sequences", 108 },
{ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 },
};
@@ -661,7 +664,7 @@ serial_master(ESL_GETOPTS *go, struct cfg_s *cfg)
if((status = cm_tophits_RemoveOrMarkOverlaps(tinfo[0].th, FALSE, errbuf)) != eslOK) cm_Fail(errbuf);
/* Resort in order to markup overlapping hits from different models (only within clans if --oclan) */
- cm_tophits_SortForOverlapMarkup(tinfo[0].th);
+ cm_tophits_SortForOverlapMarkup(tinfo[0].th, esl_opt_GetBoolean(go, "--oclan"));
if((status = cm_tophits_RemoveOrMarkOverlaps(tinfo[0].th, esl_opt_GetBoolean(go, "--oclan"), errbuf)) != eslOK) cm_Fail(errbuf);
/* Resort: by score (usually) or by position (if in special 'terminate after F3' mode) */
@@ -677,7 +680,7 @@ serial_master(ESL_GETOPTS *go, struct cfg_s *cfg)
for (i = 0; i < tinfo[0].th->N; i++) {
if ((tinfo[0].th->hit[i]->flags & CM_HIT_IS_REPORTED) || (tinfo[0].th->hit[i]->flags & CM_HIT_IS_INCLUDED)) {
tinfo[0].pli->acct[tinfo[0].th->hit[i]->pass_idx].n_output++;
- tinfo[0].pli->acct[tinfo[0].th->hit[i]->pass_idx].pos_output += abs(tinfo[0].th->hit[i]->stop - tinfo[0].th->hit[i]->start) + 1;
+ tinfo[0].pli->acct[tinfo[0].th->hit[i]->pass_idx].pos_output += llabs(tinfo[0].th->hit[i]->stop - tinfo[0].th->hit[i]->start) + 1;
}
}
if(tinfo[0].pli->do_trm_F3) {
@@ -943,8 +946,6 @@ thread_loop(ESL_THREADS *obj, ESL_WORK_QUEUE *queue, READER_INFO *rinfo, CM_FILE
/* variables related to --clanin */
int have_clans; /* set to TRUE if we have information on clans, else FALSE */
- int clan_idx = -1; /* clan index, -1 if current family is not part of a clan */
- int clan_fam_idx = -1; /* index of current family in clan_fam_kh, if it exists, else -1 */
/* do we have clan info? */
have_clans = (rinfo->clan_fam_kh != NULL && rinfo->clan_mapA != NULL) ? TRUE : FALSE;
@@ -977,8 +978,6 @@ thread_loop(ESL_THREADS *obj, ESL_WORK_QUEUE *queue, READER_INFO *rinfo, CM_FILE
rinfo->msvdataA[cm_idx] = block->msvdataA[i];
/* figure out clan_idx and set it in the block and rinfo */
- clan_idx = -1;
- clan_fam_idx = -1;
if(have_clans) { block->clan_idxA[i] = determine_clan_index(rinfo->omA[cm_idx]->name, rinfo->clan_fam_kh, rinfo->clan_mapA); }
else { block->clan_idxA[i] = -1; }
rinfo->clan_idxA[cm_idx] = block->clan_idxA[i];
@@ -1271,6 +1270,12 @@ mpi_master(ESL_GETOPTS *go, struct cfg_s *cfg)
int sstatus = eslOK;
int dest;
+ /* variables only used if --clanin is used */
+ ESL_KEYHASH *clan_name_kh = NULL; /* these are clan names */
+ ESL_KEYHASH *clan_fam_kh = NULL; /* these are family names in a clan, members of same clan are contiguous */
+ int *clan_mapA = NULL; /* [0..i..nfam-1] = c; family index i in belongs to clan
+ * index c in . */
+
char *mpi_buf = NULL; /* buffer used to pack/unpack structures */
int mpi_size = 0; /* size of the allocated buffer */
BLOCK_LIST *list = NULL;
@@ -1323,7 +1328,12 @@ mpi_master(ESL_GETOPTS *go, struct cfg_s *cfg)
cfg->Z = (int64_t) cmfp->ssi->nprimary;
cfg->Z_setby = CM_ZSETBY_SSI_AND_QLENGTH; /* we will multiply Z by each query sequence length */
}
- cm_file_Close(cmfp);
+ /* If nec, open and read the clan info file, while CM file is open */
+ if (esl_opt_IsOn(go, "--clanin")) {
+ if((status = read_clan_info_file(esl_opt_GetString(go, "--clanin"), errbuf, cmfp, &clan_name_kh, &clan_fam_kh, &clan_mapA)) != eslOK) cm_Fail(errbuf);
+ }
+
+ cm_file_Close(cmfp); /* important to do this after the read_clan_info_file() call above, which uses cmfp */
/* Open the query sequence database */
status = esl_sqfile_OpenDigital(abc, cfg->seqfile, seqfmt, NULL, &sqfp);
@@ -1351,7 +1361,7 @@ mpi_master(ESL_GETOPTS *go, struct cfg_s *cfg)
}
else {
bsize = nmodels / (cfg->nproc - 1);
- if(nmodels % (cfg->nproc - 1) != 0) bsize++;;
+ if(nmodels % (cfg->nproc - 1) != 0) bsize++;
}
output_header(ofp, go, cfg->cmfile, cfg->seqfile, cfg->nproc);
@@ -1500,11 +1510,11 @@ mpi_master(ESL_GETOPTS *go, struct cfg_s *cfg)
/* Sort by sequence index/position and remove duplicates found because we searched overlapping chunks */
cm_tophits_SortForOverlapRemoval(th);
- if((status = cm_tophits_RemoveOrMarkOverlaps(th, errbuf)) != eslOK) mpi_failure(errbuf);
+ if((status = cm_tophits_RemoveOrMarkOverlaps(th, FALSE, errbuf)) != eslOK) mpi_failure(errbuf);
- /* Resort in order to markup overlapping hits from different models */
- cm_tophits_SortForOverlapMarkup(th);
- if((status = cm_tophits_RemoveOrMarkOverlaps(th, errbuf)) != eslOK) mpi_failure(errbuf);
+ /* Resort in order to markup overlapping hits from different models (only within clans if --oclan) */
+ cm_tophits_SortForOverlapMarkup(th, esl_opt_GetBoolean(go, "--oclan"));
+ if((status = cm_tophits_RemoveOrMarkOverlaps(th, esl_opt_GetBoolean(go, "--oclan"), errbuf)) != eslOK) cm_Fail(errbuf);
/* Resort: by score (usually) or by position (if in special 'terminate after F3' mode) */
if(pli->do_trm_F3) cm_tophits_SortByPosition(th);
@@ -1519,7 +1529,7 @@ mpi_master(ESL_GETOPTS *go, struct cfg_s *cfg)
for (i = 0; i < th->N; i++) {
if ((th->hit[i]->flags & CM_HIT_IS_REPORTED) || (th->hit[i]->flags & CM_HIT_IS_INCLUDED)) {
pli->acct[th->hit[i]->pass_idx].n_output++;
- pli->acct[th->hit[i]->pass_idx].pos_output += abs(th->hit[i]->stop - th->hit[i]->start) + 1;
+ pli->acct[th->hit[i]->pass_idx].pos_output += llabs(th->hit[i]->stop - th->hit[i]->start) + 1;
}
}
@@ -1544,11 +1554,18 @@ mpi_master(ESL_GETOPTS *go, struct cfg_s *cfg)
}
}
- if (tblfp) {
- if(pli->do_trm_F3) cm_tophits_F3TabularTargets(tblfp, th, pli, (seq_idx == 1));
- else cm_tophits_TabularTargets (tblfp, qsq->name, qsq->acc, th, pli, (seq_idx == 1));
+ if (tblfp != NULL) {
+ if((! esl_opt_IsUsed(go, "--fmt")) || (esl_opt_GetInteger(go, "--fmt") == 1)) { /* fmt defaults to 1 */
+ if(pli->do_trm_F3) cm_tophits_F3TabularTargets1(tblfp, th, pli, (seq_idx == 1));
+ else cm_tophits_TabularTargets1 (tblfp, qsq->name, qsq->acc, th, pli, (seq_idx == 1));
+ }
+ else if(esl_opt_GetInteger(go, "--fmt") == 2) {
+ if((status = cm_tophits_TabularTargets2(tblfp, qsq->name, qsq->acc, th, pli, (seq_idx == 1), clan_name_kh, esl_opt_GetBoolean(go, "--oskip"), errbuf)) != eslOK) {
+ mpi_failure(errbuf);
+ }
+ }
}
-
+
esl_stopwatch_Stop(w);
cm_pli_Statistics(ofp, pli, w);
fprintf(ofp, "//\n");
@@ -1602,8 +1619,11 @@ mpi_master(ESL_GETOPTS *go, struct cfg_s *cfg)
esl_sq_Destroy(qsq);
esl_alphabet_Destroy(abc);
esl_sqfile_Close(sqfp);
- if(w != NULL) esl_stopwatch_Destroy(w);
- if(mw != NULL) esl_stopwatch_Destroy(mw);
+ if(w != NULL) esl_stopwatch_Destroy(w);
+ if(mw != NULL) esl_stopwatch_Destroy(mw);
+ if(clan_name_kh != NULL) esl_keyhash_Destroy(clan_name_kh);
+ if(clan_fam_kh != NULL) esl_keyhash_Destroy(clan_fam_kh);
+ if(clan_mapA != NULL) free(clan_mapA);
if (ofp != stdout) fclose(ofp);
if (tblfp) fclose(tblfp);
@@ -1629,7 +1649,7 @@ mpi_worker(ESL_GETOPTS *go, struct cfg_s *cfg)
P7_PROFILE *Rgm = NULL; /* generic query profile HMM for env defn for 5' truncated hits */
P7_PROFILE *Lgm = NULL; /* generic query profile HMM for env defn for 3' truncated hits */
P7_PROFILE *Tgm = NULL; /* generic query profile HMM for env defn for 5' and 3'truncated hits */
- P7_MSVDATA *msvdata = NULL; /* MSV/SSV specific data structure */
+ P7_SCOREDATA *msvdata = NULL; /* MSV/SSV specific data structure */
ESL_STOPWATCH *w = NULL; /* timing */
ESL_SQ *qsq = NULL; /* query sequence */
@@ -1646,11 +1666,10 @@ mpi_worker(ESL_GETOPTS *go, struct cfg_s *cfg)
ESL_KEYHASH *glocal_kh = NULL; /* list of models to configure globally, only created if --glist */
/* variables only used if --clanin is used */
- FIX ME
- ESL_KEYHASH *clan_kh = NULL; /* list of models in clans */
- char **clan_namesA = NULL; /* [0..c..nclan-1] name of clan */
- int64_t *clan_sidxA = NULL; /* [0..c..nclan-1] starting index in clan_kh for clan */
- int nclan = 0; /* number of clans, size of clan_namesA and clan_sidxA */
+ ESL_KEYHASH *clan_name_kh = NULL; /* these are clan names */
+ ESL_KEYHASH *clan_fam_kh = NULL; /* these are family names in a clan, members of same clan are contiguous */
+ int *clan_mapA = NULL; /* [0..i..nfam-1] = c; family index i in belongs to clan
+ * index c in . */
char *mpi_buf = NULL; /* buffer used to pack/unpack structures */
int mpi_size = 0; /* size of the allocated buffer */
@@ -1659,6 +1678,8 @@ mpi_worker(ESL_GETOPTS *go, struct cfg_s *cfg)
double eZ; /* effective database size */
int64_t prv_posn = 0; /* position of previous chunk for cur seq, 0 if first chunk */
ESL_DSQ *save_dsq = NULL; /* pointer to original qsq->dsq data */
+ int have_clans; /* set to TRUE if we have information on clans, else FALSE */
+ int clan_idx = -1; /* clan index, -1 if current family is not part of a clan */
MPI_Status mpistatus;
char errbuf[eslERRBUFSIZE];
@@ -1681,7 +1702,7 @@ mpi_worker(ESL_GETOPTS *go, struct cfg_s *cfg)
if(hstatus == eslEFORMAT) mpi_failure("bad file format in CM file %s\n%s", cfg->cmfile, cmfp->errbuf);
else if (hstatus != eslOK) mpi_failure("Unexpected error in reading CMs from %s\n%s", cfg->cmfile, cmfp->errbuf);
- /* Determine database size: default is to updated as we read target CMs */
+ /* Determine database size: default is to update as we read target CMs */
if(esl_opt_IsUsed(go, "-Z")) {
cfg->Z = (int64_t) esl_opt_GetReal(go, "-Z");
cfg->Z_setby = CM_ZSETBY_OPTION;
@@ -1698,6 +1719,10 @@ mpi_worker(ESL_GETOPTS *go, struct cfg_s *cfg)
/* If nec, open and read the clan info file, while CM file is open */
if (esl_opt_IsOn(go, "--clanin")) {
if((status = read_clan_info_file(esl_opt_GetString(go, "--clanin"), errbuf, cmfp, &clan_name_kh, &clan_fam_kh, &clan_mapA)) != eslOK) cm_Fail(errbuf);
+ have_clans = TRUE;
+ }
+ else {
+ have_clans = FALSE;
}
nmodels = (int64_t) cmfp->ssi->nprimary;
@@ -1785,11 +1810,14 @@ mpi_worker(ESL_GETOPTS *go, struct cfg_s *cfg)
if(rinfo->omA[cm_idx] != NULL) mpi_failure("Worker was supposed to read MSVs but already had one...\n");
hstatus = cm_p7_oprofile_ReadMSV(cmfp, TRUE, &(rinfo->abc), &(rinfo->cm_offsetA[cm_idx]), &(rinfo->cm_clenA[cm_idx]), &(rinfo->cm_WA[cm_idx]),
&(rinfo->cm_nbpA[cm_idx]), &(rinfo->gfmuA[cm_idx]), &(rinfo->gflambdaA[cm_idx]), &(rinfo->omA[cm_idx]));
+ /* determine clan idx if nec */
+ if(have_clans) { rinfo->clan_idxA[cm_idx] = determine_clan_index(rinfo->omA[cm_idx]->name, rinfo->clan_fam_kh, rinfo->clan_mapA); }
+ else { rinfo->clan_idxA[cm_idx] = -1; }
}
if(hstatus == eslOK) {
if(rinfo->msvdataA[cm_idx] == NULL) {
- rinfo->msvdataA[cm_idx] = p7_hmm_MSVDataCreate(rinfo->omA[cm_idx], FALSE);
+ rinfo->msvdataA[cm_idx] = p7_hmm_ScoreDataCreate(rinfo->omA[cm_idx], FALSE);
}
/* set pointers for convenience */
@@ -1801,10 +1829,10 @@ mpi_worker(ESL_GETOPTS *go, struct cfg_s *cfg)
gflambda = rinfo->gflambdaA[cm_idx];
om = rinfo->omA[cm_idx];
msvdata = rinfo->msvdataA[cm_idx];
+ clan_idx = rinfo->clan_idxA[cm_idx];
length = om->eoff - block.offset + 1;
-
esl_vec_FCopy(om->evparam, p7_NEVPARAM, p7_evparam);
p7_evparam[CM_p7_GFMU] = gfmu;
p7_evparam[CM_p7_GFLAMBDA] = gflambda;
@@ -2021,15 +2049,17 @@ process_commandline(int argc, char **argv, ESL_GETOPTS **ret_go, char **ret_cmfi
esl_opt_DisplayHelp(stdout, go, 104, 2, 80);
puts("\nOptions for precise control of the final stage:");
esl_opt_DisplayHelp(stdout, go, 105, 2, 80);
- puts("\nOptions for timing pipeline stages:");
+ puts("\nOptions for terminating after individual pipeline stages:");
esl_opt_DisplayHelp(stdout, go, 106, 2, 80);
+ puts("\nOptions for timing pipeline stages:");
+ esl_opt_DisplayHelp(stdout, go, 107, 2, 80);
}
printf("\nOther options%s:\n", do_dev ? "" : devmsg);
esl_opt_DisplayHelp(stdout, go, 7, 2, 80);
if(do_dev) {
printf("\nOther expert options%s:\n", do_dev ? "" : devmsg);
- esl_opt_DisplayHelp(stdout, go, 107, 2, 80);
+ esl_opt_DisplayHelp(stdout, go, 108, 2, 80);
}
else {
puts("\n*Use --devhelp to show additional expert options.");
@@ -2087,6 +2117,23 @@ process_commandline(int argc, char **argv, ESL_GETOPTS **ret_go, char **ret_cmfi
}
}
+ /* '--clanin' and '--oclan' only make sense with '--fmt 2',
+ * esl_getopts enforces --fmt is used, but not necessarily
+ * with '2' as the argument.
+ */
+ if(esl_opt_IsUsed(go, "--clanin")) {
+ if((! esl_opt_IsUsed(go, "--fmt")) || (esl_opt_GetInteger(go, "--fmt") != 2)) {
+ printf("Failed to parse command line: with --clanin, the additional option of --fmt is required with == 2");
+ goto ERROR;
+ }
+ }
+ if(esl_opt_IsUsed(go, "--oclan")) {
+ if((! esl_opt_IsUsed(go, "--fmt")) || (esl_opt_GetInteger(go, "--fmt") != 2)) {
+ printf("Failed to parse command line: with --oclan, the additional option of --fmt is required with == 2");
+ goto ERROR;
+ }
+ }
+
/* Finally, check for incompatible option combinations I *do* know
* how to disallow with esl_getopts, but that would require an error
* message like: "Option 'x' is incompatible with options
@@ -2583,16 +2630,6 @@ read_clan_info_file(char *filename, char *errbuf, CM_FILE *cmfp, ESL_KEYHASH **r
if(nclan == 0) ESL_FAIL(status, errbuf, "Error reading %s, no clans present in file\n", filename);
- /* debug print */
- for(i = 0; i < nclan; i++) {
- printf("clan %d %s\n", i, esl_keyhash_Get(clan_name_kh, i));
- }
- printf("\n\n");
- for(i = 0; i < nfam; i++) {
- printf("fam %d %s clan: %d\n", i, esl_keyhash_Get(clan_fam_kh, i), clan_mapA[i]);
- }
- printf("\n\n");
-
*ret_clan_name_kh = clan_name_kh;
*ret_clan_fam_kh = clan_fam_kh;
*ret_clan_mapA = clan_mapA;
diff --git a/src/cmsearch.c b/src/cmsearch.c
index 89c44adb..77e4081e 100644
--- a/src/cmsearch.c
+++ b/src/cmsearch.c
@@ -132,21 +132,16 @@ static ESL_OPTIONS options[] = {
/* name type default env range toggles reqs incomp help docgroup*/
{ "--notrunc", eslARG_NONE, FALSE, NULL, NULL, NULL, NULL, "--anytrunc,--onlytrunc,--5trunc,--3trunc", "do not allow truncated hits at sequence termini", 7 },
{ "--anytrunc", eslARG_NONE, FALSE, NULL, NULL, NULL, NULL, TRUNCOPTS, "allow full and truncated hits anywhere within sequences", 7 },
- { "--onlytrunc", eslARG_NONE, FALSE, NULL, NULL, NULL, NULL, TRUNCOPTS, "allow only truncated hits, anywhere within sequences", 7 },
- { "--5trunc", eslARG_NONE, FALSE, NULL, NULL, NULL, NULL, TRUNCOPTS, "allow truncated hits only at 5' ends of sequences", 7 },
- { "--3trunc", eslARG_NONE, FALSE, NULL, NULL, NULL, NULL, TRUNCOPTS, "allow truncated hits only at 3' ends of sequences", 7 },
{ "--nonull3", eslARG_NONE, FALSE, NULL, NULL, NULL, NULL, NULL, "turn off the NULL3 post hoc additional null model", 7 },
{ "--mxsize", eslARG_REAL, NULL, NULL, "x>0.1", NULL, NULL, NULL, "set max allowed alnment mx size to Mb [df: autodetermined]", 7 },
{ "--smxsize", eslARG_REAL, "128.", NULL, "x>0.1", NULL, NULL, NULL, "set max allowed size of search DP matrices to Mb", 7 },
{ "--cyk", eslARG_NONE, FALSE, NULL, NULL, NULL, NULL, NULL, "use scanning CM CYK algorithm, not Inside in final stage", 7 },
{ "--acyk", eslARG_NONE, FALSE, NULL, NULL, NULL, NULL, NULL, "align hits with CYK, not optimal accuracy", 7 },
{ "--wcx", eslARG_REAL, FALSE, NULL, "x>=1.25",NULL, NULL,"--nohmm,--qdb,--fqdb", "set W (expected max hit len) as * cm->clen (model len)", 7 },
- { "--onepass", eslARG_NONE, FALSE, NULL, NULL, NULL, NULL,"--nohmm,--qdb,--fqdb", "use CM only for best scoring HMM pass for full seq envelopes", 7 },
{ "--toponly", eslARG_NONE, FALSE, NULL, NULL, NULL, NULL, NULL, "only search the top strand", 7 },
{ "--bottomonly", eslARG_NONE, FALSE, NULL, NULL, NULL, NULL, NULL, "only search the bottom strand", 7 },
{ "--tformat", eslARG_STRING, NULL, NULL, NULL, NULL, NULL, NULL, "assert target is in format : no autodetection", 7 },
{ "--glist", eslARG_INFILE, NULL, NULL, NULL, NULL, NULL, NULL, "BOGUS OPTION, NEVER ALLOWED", 999 },
- { "--block", eslARG_INT, NULL, NULL, "n>0", NULL, NULL, NULL, "BOGUS OPTION, NEVER ALLOWED", 999 },
{ "--clanin", eslARG_INFILE, NULL, NULL, NULL, NULL, NULL, NULL, "BOGUS OPTION, NEVER ALLOWED", 999 },
{ "--oclan", eslARG_NONE, FALSE, NULL, NULL, NULL, NULL, NULL, "BOGUS OPTION, NEVER ALLOWED", 999 },
{ "--oskip", eslARG_NONE, FALSE, NULL, NULL, NULL, NULL, NULL, "BOGUS OPTION, NEVER ALLOWED", 999 },
@@ -213,25 +208,29 @@ static ESL_OPTIONS options[] = {
{ "--qdb", eslARG_NONE, FALSE, NULL, NULL, NULL, NULL, NULL, "use QDBs (instead of HMM bands) in final Inside round", 105 },
{ "--beta", eslARG_REAL,"1e-15", NULL, "1E-18", 105 },
{ "--nonbanded", eslARG_NONE, FALSE, NULL, NULL, NULL, NULL,"--tau,--sums,--qdb,--beta", "do not use QDBs or HMM bands in final Inside round of CM search", 105 },
+ /* Options for terminating after individual pipeline stages, currently only works for F3 */
+ { "--trmF3", eslARG_NONE, FALSE, NULL, NULL, NULL,"--noali,--nohmmonly,--notrunc",TIMINGOPTS, "terminate after Stage 3 Fwd and output surviving windows", 106 },
/* Options for timing individual pipeline stages */
/* name type default env range toggles reqs incomp help docgroup*/
- { "--timeF1", eslARG_NONE, FALSE, NULL, NULL, NULL, NULL, TIMINGOPTS, "abort after Stage 1 SSV; for timing expts", 106 },
- { "--timeF2", eslARG_NONE, FALSE, NULL, NULL, NULL, NULL, TIMINGOPTS, "abort after Stage 2 Vit; for timing expts", 106 },
- { "--timeF3", eslARG_NONE, FALSE, NULL, NULL, NULL, NULL, TIMINGOPTS, "abort after Stage 3 Fwd; for timing expts", 106 },
- { "--timeF4", eslARG_NONE, FALSE, NULL, NULL, NULL, NULL, TIMINGOPTS, "abort after Stage 4 glocal Fwd; for timing expts", 106 },
- { "--timeF5", eslARG_NONE, FALSE, NULL, NULL, NULL, NULL, TIMINGOPTS, "abort after Stage 5 envelope def; for timing expts", 106 },
- { "--timeF6", eslARG_NONE, FALSE, NULL, NULL, NULL, NULL, TIMINGOPTS, "abort after Stage 6 CYK; for timing expts", 106 },
- /* Options for terminating after individual pipeline stages, currently only works for F3 */
- { "--trmF3", eslARG_NONE, FALSE, NULL, NULL, NULL,"--noali,--nohmmonly,--notrunc",TIMINGOPTS, "terminate after Stage 3 Fwd and output surviving windows", 107 },
-
+ { "--timeF1", eslARG_NONE, FALSE, NULL, NULL, NULL, NULL, TIMINGOPTS, "abort after Stage 1 SSV; for timing expts", 107 },
+ { "--timeF2", eslARG_NONE, FALSE, NULL, NULL, NULL, NULL, TIMINGOPTS, "abort after Stage 2 Vit; for timing expts", 107 },
+ { "--timeF3", eslARG_NONE, FALSE, NULL, NULL, NULL, NULL, TIMINGOPTS, "abort after Stage 3 Fwd; for timing expts", 107 },
+ { "--timeF4", eslARG_NONE, FALSE, NULL, NULL, NULL, NULL, TIMINGOPTS, "abort after Stage 4 glocal Fwd; for timing expts", 107 },
+ { "--timeF5", eslARG_NONE, FALSE, NULL, NULL, NULL, NULL, TIMINGOPTS, "abort after Stage 5 envelope def; for timing expts", 107 },
+ { "--timeF6", eslARG_NONE, FALSE, NULL, NULL, NULL, NULL, TIMINGOPTS, "abort after Stage 6 CYK; for timing expts", 107 },
/* Other expert options */
- /* name type default env range toggles reqs incomp help docgroup*/
- { "--nogreedy", eslARG_NONE, FALSE, NULL, NULL, NULL, NULL, NULL, "do not resolve hits with greedy algorithm, use optimal one", 108 },
- { "--cp9noel", eslARG_NONE, FALSE, NULL, NULL, NULL, NULL, "-g", "turn off local ends in cp9 HMMs", 108 },
- { "--cp9gloc", eslARG_NONE, FALSE, NULL, NULL, NULL, NULL, "-g,--cp9noel", "configure cp9 HMM in glocal mode", 108 },
- { "--null2", eslARG_NONE, FALSE, NULL, NULL, NULL, NULL, NULL, "turn on null 2 biased composition HMM score corrections", 108 },
- { "--maxtau", eslARG_REAL, "0.05", NULL,"0 when tightening HMM bands", 108 },
- { "--seed", eslARG_INT, "181", NULL, "n>=0", NULL, NULL, NULL, "set RNG seed to (if 0: one-time arbitrary seed)", 108 },
+ /* name type default env range toggles reqs incomp help docgroup*/
+ { "--nogreedy", eslARG_NONE, FALSE, NULL, NULL, NULL, NULL, NULL, "do not resolve hits with greedy algorithm, use optimal one", 108 },
+ { "--cp9noel", eslARG_NONE, FALSE, NULL, NULL, NULL, NULL, "-g", "turn off local ends in cp9 HMMs", 108 },
+ { "--cp9gloc", eslARG_NONE, FALSE, NULL, NULL, NULL, NULL, "-g,--cp9noel", "configure cp9 HMM in glocal mode", 108 },
+ { "--null2", eslARG_NONE, FALSE, NULL, NULL, NULL, NULL, NULL, "turn on null 2 biased composition HMM score corrections", 108 },
+ { "--maxtau", eslARG_REAL, "0.05", NULL,"0 when tightening HMM bands", 108 },
+ { "--seed", eslARG_INT, "181", NULL, "n>=0", NULL, NULL, NULL, "set RNG seed to (if 0: one-time arbitrary seed)", 108 },
+ { "--block", eslARG_INT, NULL, NULL, "n>0", NULL, NULL, NULL, "BOGUS OPTION, NEVER ALLOWED", 999 },
+ { "--onepass", eslARG_NONE, FALSE, NULL, NULL, NULL, NULL,"--nohmm,--qdb,--fqdb", "use CM only for best scoring HMM pass for full seq envelopes", 108 },
+ { "--onlytrunc", eslARG_NONE, FALSE, NULL, NULL, NULL, NULL, TRUNCOPTS, "allow only truncated hits, anywhere within sequences", 108 },
+ { "--5trunc", eslARG_NONE, FALSE, NULL, NULL, NULL, NULL, TRUNCOPTS, "allow truncated hits only at 5' ends of sequences", 108 },
+ { "--3trunc", eslARG_NONE, FALSE, NULL, NULL, NULL, NULL, TRUNCOPTS, "allow truncated hits only at 3' ends of sequences", 108 },
#ifdef HAVE_MPI
/* Searching only a subset of sequences in the target database, currently requires MPI b/c SSI is required */
{ "--sidx", eslARG_INT, NULL, NULL, "n>0", NULL,"--mpi", NULL, "start searching at sequence index in target db SSI index" , 108 },
@@ -558,8 +557,6 @@ serial_master(ESL_GETOPTS *go, struct cfg_s *cfg)
cm_idx++;
esl_stopwatch_Start(w);
- printf("CM size: %.2f Mb\n", cm_Sizeof(cm));
-
/* create a new template info, and point it to the cm we just read */
tinfo = create_info(go);
tinfo->cm = cm;
@@ -665,7 +662,7 @@ serial_master(ESL_GETOPTS *go, struct cfg_s *cfg)
for (i = 0; i < info->th->N; i++) {
if ((info[0].th->hit[i]->flags & CM_HIT_IS_REPORTED) || (info[0].th->hit[i]->flags & CM_HIT_IS_INCLUDED)) {
info[0].pli->acct[info[0].th->hit[i]->pass_idx].n_output++;
- info[0].pli->acct[info[0].th->hit[i]->pass_idx].pos_output += abs(info[0].th->hit[i]->stop - info[0].th->hit[i]->start) + 1;
+ info[0].pli->acct[info[0].th->hit[i]->pass_idx].pos_output += llabs(info[0].th->hit[i]->stop - info[0].th->hit[i]->start) + 1;
}
}
@@ -783,7 +780,6 @@ serial_loop(WORKER_INFO *info, ESL_SQFILE *dbfp, int64_t *srcL)
int status;
int wstatus;
int prv_pli_ntophits; /* number of top hits before each cm_Pipeline() */
- int prv_seq_ntophits; /* number of top hits before each target sequence */
int64_t seq_idx = 0;
ESL_SQ *dbsq = esl_sq_CreateDigital(info->cm->abc);
@@ -803,7 +799,6 @@ serial_loop(WORKER_INFO *info, ESL_SQFILE *dbfp, int64_t *srcL)
if(dbsq->start == 1) dbsq->L = srcL[seq_idx-1];
cm_pli_NewSeq(info->pli, dbsq, seq_idx-1);
- prv_seq_ntophits = info->th->N;
if (info->pli->do_top) {
prv_pli_ntophits = info->th->N;
@@ -965,8 +960,6 @@ pipeline_thread(void *arg)
ESL_SQ_BLOCK *block = NULL;
void *newBlock;
int prv_pli_ntophits; /* number of top hits before each cm_Pipeline() */
- int prv_seq_ntophits; /* number of top hits before each target sequence */
-
#ifdef HAVE_FLUSH_ZERO_MODE
/* In order to avoid the performance penalty dealing with sub-normal
@@ -994,7 +987,6 @@ pipeline_thread(void *arg)
ESL_SQ *dbsq = block->list + i;
cm_pli_NewSeq(info->pli, dbsq, block->first_seqidx + i);
- prv_seq_ntophits = info->th->N;
if (info->pli->do_top) {
prv_pli_ntophits = info->th->N;
@@ -1349,7 +1341,7 @@ mpi_master(ESL_GETOPTS *go, struct cfg_s *cfg)
for (i = 0; i < info->th->N; i++) {
if ((info->th->hit[i]->flags & CM_HIT_IS_REPORTED) || (info->th->hit[i]->flags & CM_HIT_IS_INCLUDED)) {
info->pli->acct[info->th->hit[i]->pass_idx].n_output++;
- info->pli->acct[info->th->hit[i]->pass_idx].pos_output += abs(info->th->hit[i]->stop - info->th->hit[i]->start) + 1;
+ info->pli->acct[info->th->hit[i]->pass_idx].pos_output += llabs(info->th->hit[i]->stop - info->th->hit[i]->start) + 1;
}
}
@@ -1372,8 +1364,8 @@ mpi_master(ESL_GETOPTS *go, struct cfg_s *cfg)
}
}
if (tblfp != NULL) {
- if(info->pli->do_trm_F3) cm_tophits_F3TabularTargets(tblfp, info->th, info->pli, (cm_idx == 1));
- else cm_tophits_TabularTargets(tblfp, info->cm->name, info->cm->acc, info->th, info->pli, (cm_idx == 1));
+ if(info->pli->do_trm_F3) cm_tophits_F3TabularTargets1(tblfp, info->th, info->pli, (cm_idx == 1));
+ else cm_tophits_TabularTargets1(tblfp, info->cm->name, info->cm->acc, info->th, info->pli, (cm_idx == 1));
fflush(tblfp);
}
esl_stopwatch_Stop(w);
@@ -1734,15 +1726,17 @@ process_commandline(int argc, char **argv, ESL_GETOPTS **ret_go, char **ret_cmfi
esl_opt_DisplayHelp(stdout, go, 104, 2, 80);
puts("\nOptions for precise control of the final stage:");
esl_opt_DisplayHelp(stdout, go, 105, 2, 80);
- puts("\nOptions for timing pipeline stages:");
+ puts("\nOptions for terminating after individual pipeline stages:");
esl_opt_DisplayHelp(stdout, go, 106, 2, 80);
+ puts("\nOptions for timing pipeline stages:");
+ esl_opt_DisplayHelp(stdout, go, 107, 2, 80);
}
printf("\nOther options%s:\n", do_dev ? "" : devmsg);
esl_opt_DisplayHelp(stdout, go, 7, 2, 80);
if(do_dev) {
printf("\nOther expert options%s:\n", do_dev ? "" : devmsg);
- esl_opt_DisplayHelp(stdout, go, 107, 2, 80);
+ esl_opt_DisplayHelp(stdout, go, 108, 2, 80);
}
else {
puts("\n*Use --devhelp to show additional expert options.");
diff --git a/src/cp9_modelmaker.c b/src/cp9_modelmaker.c
index 1ffbcf71..1b760fd1 100644
--- a/src/cp9_modelmaker.c
+++ b/src/cp9_modelmaker.c
@@ -1199,7 +1199,6 @@ cm2hmm_trans_probs_cp9(CM_t *cm, CP9_t *hmm, CP9Map_t *cp9map, int k, double *ps
int *bp; /* CM states b' that map to HMM state b,
* bp[1] is -1 if only 1 CM state maps to b*/
- int n; /* CM node that maps to HMM node k */
int k_state; /*either HMMMATCH, HMMINSERT, or HMMDELETE*/
int hmm_trans_idx; /*0-8; CTMM, CTMI, CTMD, CTIM, CTII, CTID, CTDM, CTDI, or CTDD*/
@@ -1209,7 +1208,7 @@ cm2hmm_trans_probs_cp9(CM_t *cm, CP9_t *hmm, CP9Map_t *cp9map, int k, double *ps
ESL_ALLOC(ap, sizeof (int) * 2);
ESL_ALLOC(bp, sizeof (int) * 2);
- n = cp9map->pos2nd[k];
+
/* Fill all 9 transitions with virtual counts, later normalize these into
* probabilities.
*
@@ -1599,8 +1598,6 @@ cm_sum_subpaths_cp9(CM_t *cm, CP9Map_t *cp9map, int start, int end, char ***tmap
int k, double *psi)
{
int status;
- int s_n; /* CM node that maps to HMM node with start state */
- int e_n; /* CM node that maps to HMM node with end state */
int v; /* state index in CM */
double *sub_psi; /*sub_psi[v] is the expected number of times state v is
@@ -1612,7 +1609,6 @@ cm_sum_subpaths_cp9(CM_t *cm, CP9Map_t *cp9map, int start, int end, char ***tmap
int y;
int x;
char tmap_val;
- int n_v; /* CM node containing state v*/
int is_insert; /* 1 if v is insert, 0 if not */
float insert_to_start; /* is start is not an insert and the insert state of
* HMM node k < start, this is the
@@ -1654,8 +1650,6 @@ cm_sum_subpaths_cp9(CM_t *cm, CP9Map_t *cp9map, int start, int end, char ***tmap
return cm->t[start][0];
}
to_return = 0.;
- s_n = cm->ndidx[start];
- e_n = cm->ndidx[end];
ESL_ALLOC(sub_psi, sizeof(double) * (end - start + 1));
/* Initialize sub_psi[0]. Need to check if we need to ignore the probability
@@ -1686,7 +1680,6 @@ cm_sum_subpaths_cp9(CM_t *cm, CP9Map_t *cp9map, int start, int end, char ***tmap
{
/*printf("\t\t\tv: %d\n", v);*/
sub_psi[v-start] = 0.;
- n_v = cm->ndidx[v];
if(cm->sttype[v] == IL_st || cm->sttype[v] == IR_st)
is_insert = 1;
else
diff --git a/src/cp9_trace.c b/src/cp9_trace.c
index bd5ac2ab..f444c2cf 100644
--- a/src/cp9_trace.c
+++ b/src/cp9_trace.c
@@ -100,16 +100,16 @@ CP9_fake_tracebacks(ESL_MSA *msa, int *matassign, CP9trace_t ***ret_tr)
int apos; /* position in alignment columns */
int tpos; /* position in traceback */
int first_match; /* first match column */
- int last_match; /* last match column */
+ /*int last_match;*/ /* last match column, not used */
ESL_ALLOC(tr, sizeof(CP9trace_t *) * msa->nseq);
first_match = -1;
- last_match = -1;
+ /*last_match = -1;*/
for (apos = 0; apos < msa->alen; apos++)
{
if(matassign[apos+1] && first_match == -1) first_match = apos;
- if(matassign[apos+1]) last_match = apos;
+ /*if(matassign[apos+1]) last_match = apos;*/
}
for (idx = 0; idx < msa->nseq; idx++)
diff --git a/src/hmmband.c b/src/hmmband.c
index 9e59d063..7fcd662b 100644
--- a/src/hmmband.c
+++ b/src/hmmband.c
@@ -1533,12 +1533,6 @@ cp9_HMM2ijBands(CM_t *cm, char *errbuf, CP9_t *cp9, CP9Bands_t *cp9b, CP9Map_t *
int v;
/* ptrs to cp9b data, for convenience */
- int *pn_min_m; /* pn_min_m[k] = first position in HMM band for match state of HMM node k */
- int *pn_max_m; /* pn_max_m[k] = last position in HMM band for match state of HMM node k */
- int *pn_min_i; /* pn_min_i[k] = first position in HMM band for insert state of HMM node k */
- int *pn_max_i; /* pn_max_i[k] = last position in HMM band for insert state of HMM node k */
- int *pn_min_d; /* pn_min_d[k] = first position in HMM band for delete state of HMM node k */
- int *pn_max_d; /* pn_max_d[k] = last position in HMM band for delete state of HMM node k */
int *imin; /* imin[v] = first position in band on i for state v to be filled in this function. [1..M] */
int *imax; /* imax[v] = last position in band on i for state v to be filled in this function. [1..M] */
int *jmin; /* jmin[v] = first position in band on j for state v to be filled in this function. [1..M] */
@@ -1552,7 +1546,7 @@ cp9_HMM2ijBands(CM_t *cm, char *errbuf, CP9_t *cp9, CP9Bands_t *cp9b, CP9Map_t *
int on_right; /* TRUE if we're on the right for current node during our CM traversal */
int w; /* a state index */
int lpos, rpos; /* left/right border of subtree for current node */
- int k; /* counter of HMM nodes */
+ /*int k;*/ /* counter of HMM nodes, for debugging print statements, currently not used */
int hmm_is_localized; /* TRUE if HMM has local begins, ends or ELs on */
int cm_is_fully_localized; /* TRUE if CM has local begins and ends on */
@@ -1590,12 +1584,6 @@ cp9_HMM2ijBands(CM_t *cm, char *errbuf, CP9_t *cp9, CP9Bands_t *cp9b, CP9Map_t *
cm_is_fully_localized = ((cm->flags & CMH_LOCAL_BEGIN) && (cm->flags & CMH_LOCAL_END)) ? TRUE : FALSE;
/* ptrs to cp9b arrays, for convenience */
- pn_min_m = cp9b->pn_min_m;
- pn_max_m = cp9b->pn_max_m;
- pn_min_i = cp9b->pn_min_i;
- pn_max_i = cp9b->pn_max_i;
- pn_min_d = cp9b->pn_min_d;
- pn_max_d = cp9b->pn_max_d;
imin = cp9b->imin;
imax = cp9b->imax;
jmin = cp9b->jmin;
@@ -1642,7 +1630,6 @@ cp9_HMM2ijBands(CM_t *cm, char *errbuf, CP9_t *cp9, CP9Bands_t *cp9b, CP9Map_t *
if(!hmm_is_localized) assert(r_mx[hmm_M] == j0 || r_ix[hmm_M] == j0 || r_dx[hmm_M] == j0);
}
nd = 0;
- k = 0;
lpos = 0;
rpos = 0;
@@ -2287,7 +2274,7 @@ HMMBandsEnforceValidParse(CP9_t *cp9, CP9Bands_t *cp9b, CP9Map_t *cp9map, char *
int c; /* counter */
int sd; /* state delta, number of emissions for each state */
int local_begins_ends_on; /* TRUE if HMM has local begins (M_0(B) -> M_k for k = 1..M and local ends (M_k -> E) for k = 1..M-1 */
- int j0_is_reachable = FALSE; /* TRUE if we can reach j0 for some node */
+ /*int j0_is_reachable = FALSE; */ /* TRUE if we can reach j0 for some node */
/* ptrs to cp9b data, for convenience */
int *pn_min_m; /* pn_min_m[k] = first position in HMM band for match state of HMM node k */
int *pn_max_m; /* pn_max_m[k] = final position in HMM band for match state of HMM node k */
@@ -2758,7 +2745,7 @@ HMMBandsEnforceValidParse(CP9_t *cp9, CP9Bands_t *cp9b, CP9Map_t *cp9map, char *
*/
k -= 1;
}
- else if(r_nx_hmm[k] == j0) j0_is_reachable = TRUE;
+ /*else if(r_nx_hmm[k] == j0) j0_is_reachable = TRUE;*/
}
/* final check, if we're doing alignment, the first residue i0, must be first emitted
* residue, and the final residue, j0 must be final emittable residue. Enforce it.
diff --git a/src/impl_sse/sse_cm_dpsearch.c b/src/impl_sse/sse_cm_dpsearch.c
index f0904887..c6d935e2 100644
--- a/src/impl_sse/sse_cm_dpsearch.c
+++ b/src/impl_sse/sse_cm_dpsearch.c
@@ -80,8 +80,7 @@ SSE_CYKScan(CM_t *cm, char *errbuf, CM_SCAN_MX *smx, ESL_DSQ *dsq, int i0, int j
int W; /* max d; max size of a hit, this is min(L, smx->W) */
int sd; /* StateDelta(cm->sttype[v]), # emissions from v */
int *dnA, *dxA; /* tmp ptr to 1 row of dnAA, dxAA */
- int dn, dx; /* minimum/maximum valid d for current state */
- int cnum; /* number of children for current state */
+ /*int dn, dx; */ /* minimum/maximum valid d for current state */
int *jp_wA; /* rolling pointer index for B states, gets precalc'ed */
float **init_scAA; /* [0..v..cm->M-1][0..d..W] initial score for each v, d for all j */
double **act; /* [0..j..W-1][0..a..abc->K-1], alphabet count, count of residue a in dsq from 1..jp where j = jp%(W+1) */
@@ -387,9 +386,8 @@ SSE_CYKScan(CM_t *cm, char *errbuf, CM_SCAN_MX *smx, ESL_DSQ *dsq, int i0, int j
jp_v = (cm->stid[v] == BEGL_S) ? (j % (W+1)) : cur;
jp_y = (StateRightDelta(cm->sttype[v]) > 0) ? prv : cur;
sd = StateDelta(cm->sttype[v]);
- cnum = cm->cnum[v];
- dn = dnA[v];
- dx = dxA[v];
+ /*dn = dnA[v];*/
+ /*dx = dxA[v];*/
if(cm->sttype[v] == B_st) {
float *vec_access;
diff --git a/src/impl_sse/sse_cm_dpsmall.c b/src/impl_sse/sse_cm_dpsmall.c
index 4ea19980..35e0c881 100644
--- a/src/impl_sse/sse_cm_dpsmall.c
+++ b/src/impl_sse/sse_cm_dpsmall.c
@@ -388,7 +388,7 @@ SSE_CYKDemands(CM_t *cm, int L, int be_quiet)
float bifcalcs; /* # of inner loops executed for bifurcation calculations */
float dpcalcs; /* # of inner loops executed for non-bif calculations */
int j;
- float avg_Mb_per_banded_deck; /* average megabytes per deck in mem efficient big mode */
+ /*float avg_Mb_per_banded_deck;*/ /* average megabytes per deck in mem efficient big mode */
const int vecwidth = 4;
Mb_per_deck = sse_size_vjd_deck(L, 1, L, vecwidth);
@@ -404,7 +404,7 @@ SSE_CYKDemands(CM_t *cm, int L, int be_quiet)
dpcalcs = (float) (L+2)*(float)(L+1)*0.5*(float) (cm->M - bif_decks - nends +1);
bigmemory = (float) (cm->M - nends +1) * Mb_per_deck;
dpcells = (float) (L+2)*(float)(L+1)*0.5*(float) (cm->M - nends +1);
- avg_Mb_per_banded_deck = 0.; /* irrelevant */
+ /*avg_Mb_per_banded_deck = 0.; */ /* irrelevant */
if(!be_quiet)
{
@@ -3915,7 +3915,7 @@ SSE_CYKFilter_epi16(CM_OPTIMIZED *ocm, ESL_DSQ *dsq, int L, int vroot, int vend,
int nends; /* counter that tracks when we can release end deck to the pool */
int *touch; /* keeps track of how many higher decks still need this deck */
int v,y,z; /* indices for states */
- int j,d,i,k; /* indices in sequence dimensions */
+ int j,d,i,k; /* indices in sequence dimensions */
int16_t sc; /* a temporary variable holding a score */
int yoffset; /* y=base+offset -- counter in child states that v can transit to */
int W; /* subsequence length */
@@ -4950,11 +4950,11 @@ sse_insideT_size(CM_t *cm, int L, int r, int z, int i0, int j0, int x)
{
float Mb;
int maxdecks;
- int nends;
- int nbif;
+ /*int nends;*/
+ /*int nbif;*/
- nends = CMSegmentCountStatetype(cm, r, z, E_st);
- nbif = CMSegmentCountStatetype(cm, r, z, B_st);
+ /*nends = CMSegmentCountStatetype(cm, r, z, E_st);*/
+ /*nbif = CMSegmentCountStatetype(cm, r, z, B_st);*/
maxdecks = cyk_deck_count(cm, r, z);
Mb = (float) (sizeof(sse_deck_t *) * cm->M) / 1000000.; /* the score matrix */
diff --git a/src/impl_sse/sse_cmcons_hitmx.c b/src/impl_sse/sse_cmcons_hitmx.c
index 79f66411..f7570e43 100644
--- a/src/impl_sse/sse_cmcons_hitmx.c
+++ b/src/impl_sse/sse_cmcons_hitmx.c
@@ -127,7 +127,7 @@ UpdateGammaHitMx_epu8(CM_CONSENSUS *ccm, char *errbuf, GammaHitMx_epu8 *gamma, i
CM_TOPHITS *hitlist, int W, int sW)
{
int i, d;
- int bestd;
+ /*int bestd;*/
int ip, jp;
int do_report_hit;
uint8_t hit_sc, bestd_sc;
@@ -186,7 +186,7 @@ UpdateGammaHitMx_epu8(CM_CONSENSUS *ccm, char *errbuf, GammaHitMx_epu8 *gamma, i
hit->hmmonly = FALSE;
}
}
- bestd = 0;
+ /*bestd = 0;*/
bestd_sc = hit_sc;
/* Now, if current score is greater than maximum seen previous, report
* it if >= cutoff and set new max */
@@ -210,7 +210,7 @@ UpdateGammaHitMx_epu8(CM_CONSENSUS *ccm, char *errbuf, GammaHitMx_epu8 *gamma, i
hit->hmmonly = FALSE;
}
}
- bestd = d;
+ /*bestd = d;*/
bestd_sc = hit_sc;
}
}
diff --git a/src/infernal.h b/src/infernal.h
index ec4dff8d..d13ebee1 100644
--- a/src/infernal.h
+++ b/src/infernal.h
@@ -3003,7 +3003,7 @@ extern int cm_tophits_Grow(CM_TOPHITS *h);
extern int cm_tophits_CreateNextHit(CM_TOPHITS *h, CM_HIT **ret_hit);
extern int cm_tophits_SortByEvalue(CM_TOPHITS *h);
extern int cm_tophits_SortForOverlapRemoval(CM_TOPHITS *h);
-extern int cm_tophits_SortForOverlapMarkup(CM_TOPHITS *h);
+extern int cm_tophits_SortForOverlapMarkup(CM_TOPHITS *h, int do_clans_only);
extern int cm_tophits_SortByPosition(CM_TOPHITS *h);
extern int cm_tophits_Merge(CM_TOPHITS *h1, CM_TOPHITS *h2);
extern int cm_tophits_GetMaxPositionLength(CM_TOPHITS *h);
@@ -3017,7 +3017,7 @@ extern int cm_tophits_Reuse(CM_TOPHITS *h);
extern void cm_tophits_Destroy(CM_TOPHITS *h);
extern int cm_tophits_CloneHitMostly(CM_TOPHITS *src_th, int h, CM_TOPHITS *dest_th);
extern int cm_tophits_ComputeEvalues(CM_TOPHITS *th, double eZ, int istart);
-extern int cm_tophits_RemoveOrMarkOverlaps(CM_TOPHITS *th, int do_clans, char *errbuf);
+extern int cm_tophits_RemoveOrMarkOverlaps(CM_TOPHITS *th, int do_clans_only, char *errbuf);
extern int cm_tophits_UpdateHitPositions(CM_TOPHITS *th, int hit_start, int64_t seq_start, int in_revcomp);
extern int cm_tophits_SetSourceLengths(CM_TOPHITS *th, int64_t *srcL, uint64_t nseqs);
diff --git a/src/trcyk.c b/src/trcyk.c
index 9af50915..6aae8514 100644
--- a/src/trcyk.c
+++ b/src/trcyk.c
@@ -27,7 +27,6 @@ main(int argc, char **argv)
Parsetree_t *tr;
Fancyali_t *fali;
Fancyali_t *rev_fali;
- CMConsensus_t *cons;
int do_local;
@@ -48,7 +47,6 @@ main(int argc, char **argv)
tr = NULL;
fali = NULL;
rev_fali = NULL;
- cons = NULL;
format = eslSQFILE_UNKNOWN;
do_local = TRUE;
diff --git a/testsuite/5.c.cm b/testsuite/5.c.cm
new file mode 100644
index 00000000..04188b23
--- /dev/null
+++ b/testsuite/5.c.cm
@@ -0,0 +1,4815 @@
+INFERNAL1/a [1.1 | April 2012]
+NAME tRNA
+ACC RF00005
+DESC tRNA
+STATES 227
+NODES 60
+CLEN 71
+W 218
+ALPH RNA
+RF no
+CONS yes
+MAP yes
+DATE Mon Apr 30 08:54:53 2012
+COM [1] /groups/eddy/home/nawrockie/notebook/12_0423_inf_final_stress_tests/wd-infernal/src/cmbuild -F tRNA.cm tRNA.sto
+COM [2] /groups/eddy/home/nawrockie/notebook/12_0423_inf_final_stress_tests/wd-infernal/src/cmcalibrate --mpi tRNA.cm
+PBEGIN 0.05
+PEND 0.05
+WBETA 1e-07
+QDBBETA1 1e-07
+QDBBETA2 1e-15
+N2OMEGA 1.52588e-05
+N3OMEGA 1.52588e-05
+ELSELF -0.08926734
+NSEQ 967
+EFFN 64.453232
+CKSUM 1685224748
+NULL 0.000 0.000 0.000 0.000
+GA 24.00
+TC 24.04
+EFP7GF -6.5772 0.73469
+ECMLC 0.79302 -4.21089 2.90112 1600000 337752 0.003553
+ECMGC 0.38490 -15.21245 -3.62397 1600000 34609 0.011558
+ECMLI 0.64537 -4.35897 4.09652 1600000 281252 0.004267
+ECMGI 0.41538 -11.77572 -1.10020 1600000 33721 0.011862
+CM
+ [ ROOT 0 ] - - - - - -
+ S 0 -1 0 1 4 0 1 218 410 -10.978 -12.223 -0.031 -5.613
+ IL 1 1 2 1 4 11 38 219 411 -2.817 -4.319 -0.613 -2.698 0.000 0.000 0.000 0.000
+ IR 2 2 3 2 3 12 39 220 411 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000
+ [ MATR 1 ] - 119 - A - -
+ MR 3 2 3 5 5 16 42 219 410 -11.011 -0.003 -10.827 -11.039 -11.930 1.085 -1.826 -0.113 -0.575
+ D 4 2 3 5 5 8 34 217 408 -3.401 -0.736 -4.225 -2.539 -3.651
+ IR 5 5 3 5 5 11 37 218 410 -2.562 -0.438 -6.073 -4.241 -5.347 0.000 0.000 0.000 0.000
+ [ MATP 2 ] 1 117 G C - -
+ MP 6 5 3 10 6 16 42 218 409 -12.060 -11.999 -0.003 -10.776 -11.056 -11.451 -5.257 -3.238 -3.838 1.469 -3.960 -4.395 0.510 -5.473 -6.181 3.049 -5.251 0.654 0.496 -5.677 -3.994 -3.530
+ ML 7 5 3 10 6 9 34 215 407 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094
+ MR 8 5 3 10 6 10 35 215 407 -7.466 -6.195 -0.958 -6.173 -1.307 -4.386 0.234 -0.467 -0.604 0.529
+ D 9 5 3 10 6 6 30 209 401 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319
+ IL 10 10 5 10 6 10 36 216 408 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000
+ IR 11 11 6 11 5 10 36 216 408 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 3 ] 2 116 g c - -
+ MP 12 11 6 16 6 16 41 216 407 -12.066 -12.006 -0.003 -10.782 -11.062 -11.457 -5.460 -4.628 -5.529 1.461 -3.223 -4.845 2.206 -4.664 -5.578 2.317 -6.079 -0.480 1.207 -5.364 -1.993 -4.350
+ ML 13 11 6 16 6 9 34 213 405 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094
+ MR 14 11 6 16 6 9 34 213 404 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094
+ D 15 11 6 16 6 6 30 208 399 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319
+ IL 16 16 5 16 6 10 35 215 406 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000
+ IR 17 17 6 17 5 10 35 214 406 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 4 ] 3 115 g c - -
+ MP 18 17 6 22 6 15 39 214 405 -12.066 -12.006 -0.003 -10.782 -11.062 -11.457 -2.991 -3.252 -3.304 1.529 -2.993 -4.063 1.911 -3.457 -3.750 1.994 -3.635 -0.550 1.687 -3.577 -1.152 -2.580
+ ML 19 17 6 22 6 9 34 211 403 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094
+ MR 20 17 6 22 6 9 33 211 402 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094
+ D 21 17 6 22 6 6 29 206 398 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319
+ IL 22 22 5 22 6 10 35 213 404 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000
+ IR 23 23 6 23 5 10 35 212 404 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 5 ] 4 114 g c - -
+ MP 24 23 6 28 6 14 37 212 403 -9.013 -12.006 -0.005 -10.782 -11.062 -11.457 -2.318 -3.248 -3.520 1.564 -2.588 -3.607 1.704 -3.816 -3.523 2.096 -4.340 -0.292 1.495 -3.841 -0.309 -2.742
+ ML 25 23 6 28 6 9 33 209 401 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094
+ MR 26 23 6 28 6 8 33 209 401 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094
+ D 27 23 6 28 6 5 29 205 397 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319
+ IL 28 28 5 28 6 10 34 211 402 -2.756 -3.018 -0.649 -4.674 -5.450 -5.110 0.000 0.000 0.000 0.000
+ IR 29 29 6 29 5 10 34 210 402 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 6 ] 6 113 a u - -
+ MP 30 29 6 34 6 12 35 210 401 -12.066 -12.006 -0.003 -10.782 -11.062 -11.457 -2.802 -2.929 -3.236 2.045 -2.639 -3.980 1.703 -3.541 -3.409 1.608 -3.571 -0.269 1.483 -3.685 -0.323 -2.349
+ ML 31 29 6 34 6 8 32 208 399 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094
+ MR 32 29 6 34 6 8 32 207 399 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094
+ D 33 29 6 34 6 5 29 204 396 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319
+ IL 34 34 5 34 6 9 33 209 400 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000
+ IR 35 35 6 35 5 9 33 209 400 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 7 ] 7 112 u a - -
+ MP 36 35 6 40 6 10 33 208 399 -12.066 -12.006 -0.004 -9.123 -11.062 -11.457 -3.175 -3.172 -3.309 1.654 -2.791 -4.151 1.551 -3.938 -3.781 1.406 -4.354 -0.768 2.109 -3.857 0.237 -1.273
+ ML 37 35 6 40 6 8 31 206 398 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094
+ MR 38 35 6 40 6 7 30 206 397 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094
+ D 39 35 6 40 6 5 28 203 395 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319
+ IL 40 40 5 40 6 8 32 207 398 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000
+ IR 41 41 6 41 5 8 32 207 398 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 8 ] 8 111 g c - -
+ MP 42 41 6 46 4 8 31 206 397 -11.175 -8.859 -0.009 -8.063 -6.121 -4.131 -5.942 2.409 -7.033 -6.542 -0.625 -6.618 -5.229 2.583 -6.623 -0.535 1.615 -5.801 -4.123 -3.910
+ ML 43 41 6 46 4 7 30 205 396 -3.888 -4.071 -0.455 -2.800 0.157 -0.368 -0.428 0.451
+ MR 44 41 6 46 4 6 29 204 396 -4.809 -3.838 -1.706 -0.766 0.368 -0.385 -0.191 0.094
+ D 45 41 6 46 4 5 28 203 394 -4.568 -4.250 -2.265 -0.520
+ IL 46 46 5 46 4 7 31 205 397 -1.686 -2.369 -1.117 -4.855 0.000 0.000 0.000 0.000
+ IR 47 47 6 47 3 7 30 205 397 -1.542 -0.728 -4.242 0.000 0.000 0.000 0.000
+ [ MATL 9 ] 9 - U - - -
+ ML 48 47 6 50 3 6 29 204 395 -7.007 -0.023 -6.990 -2.076 -4.312 -3.010 1.843
+ D 49 47 6 50 3 5 28 202 394 -6.681 -0.958 -1.072
+ IL 50 50 3 50 3 6 29 204 396 -1.826 -0.568 -4.527 0.000 0.000 0.000 0.000
+ [ MATL 10 ] 11 - A - - -
+ ML 51 50 3 53 2 5 28 203 394 -7.010 -0.011 1.376 -2.669 0.178 -3.109
+ D 52 50 3 53 2 4 27 202 393 -8.544 -0.004
+ IL 53 53 3 53 2 5 28 203 394 -2.436 -0.295 0.000 0.000 0.000 0.000
+ [ BIF 11 ] - - - - - -
+ B 54 53 3 121 55 4 27 202 393
+ [ BEGR 42 ] - - - - - -
+ S 55 54 1 56 3 0 1 168 360 -12.092 -0.001 -10.746
+ IL 56 56 2 56 3 1 2 172 364 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000
+ [ MATL 43 ] 56 - a - - -
+ ML 57 56 2 59 3 1 1 168 360 -12.092 -0.217 -2.840 0.929 -0.896 -1.145 0.146
+ D 58 56 2 59 3 0 0 182 374 -6.174 -1.687 -0.566
+ IL 59 59 3 59 3 1 2 165 357 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000
+ [ MATL 44 ] 57 - g - - -
+ ML 60 59 3 62 3 1 1 147 339 -5.640 -0.035 -7.889 0.193 -2.464 0.978 -0.503
+ D 61 59 3 62 3 0 0 186 378 -0.120 -4.288 -5.120
+ IL 62 62 3 62 3 1 1 187 379 -0.139 -3.869 -5.430 0.000 0.000 0.000 0.000
+ [ MATL 45 ] 82 - g - - -
+ ML 63 62 3 65 3 1 1 31 49 -1.124 -0.892 -8.860 0.551 -2.766 0.852 -0.781
+ D 64 62 3 65 3 0 0 30 48 -4.985 -0.177 -3.578
+ IL 65 65 3 65 3 1 1 31 49 -4.976 -0.051 -8.398 0.000 0.000 0.000 0.000
+ [ MATL 46 ] 86 - c - - -
+ ML 66 65 3 68 5 1 1 30 48 -11.035 -0.003 -10.850 -11.063 -11.954 -1.666 0.881 -2.788 0.764
+ D 67 65 3 68 5 0 0 28 46 -5.141 -0.681 -4.402 -2.777 -2.690
+ IL 68 68 3 68 5 1 1 30 48 -2.408 -0.496 -4.087 -5.920 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 47 ] 87 109 g c - -
+ MP 69 68 3 73 6 2 2 29 47 -12.066 -7.900 -0.008 -10.782 -11.062 -11.457 -4.338 -4.271 -5.753 2.128 -4.947 -6.390 1.123 -6.352 -6.113 2.587 -6.424 0.870 -0.003 -3.099 -2.196 -3.666
+ ML 70 68 3 73 6 1 1 27 45 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094
+ MR 71 68 3 73 6 1 1 27 45 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094
+ D 72 68 3 73 6 0 0 25 43 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319
+ IL 73 73 5 73 6 1 1 28 46 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000
+ IR 74 74 6 74 5 1 1 28 46 -2.650 -0.408 -6.162 -4.329 -5.435 0.000 0.000 0.000 0.000
+ [ MATP 48 ] 88 107 c g - -
+ MP 75 74 6 79 6 2 2 27 45 -12.066 -12.006 -0.003 -10.782 -11.062 -11.457 -4.797 -4.148 -4.946 1.610 -4.313 -5.795 2.143 -5.044 -4.961 1.243 -5.516 -0.370 2.039 -4.022 -0.495 -2.107
+ ML 76 74 6 79 6 1 1 26 44 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094
+ MR 77 74 6 79 6 1 1 25 44 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094
+ D 78 74 6 79 6 0 0 23 42 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319
+ IL 79 79 5 79 6 1 1 27 44 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000
+ IR 80 80 6 80 5 1 1 26 44 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 49 ] 89 106 g c - -
+ MP 81 80 6 85 6 2 2 25 43 -6.997 -12.006 -0.026 -10.782 -11.062 -6.807 -5.441 -3.017 -5.435 2.200 -5.771 -6.144 1.104 -5.192 -5.345 2.488 -5.099 -0.755 1.132 -5.418 -1.315 -2.689
+ ML 82 80 6 85 6 1 1 24 43 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094
+ MR 83 80 6 85 6 1 1 24 43 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094
+ D 84 80 6 85 6 0 0 22 41 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319
+ IL 85 85 5 85 6 1 1 24 42 -3.239 -3.502 -0.433 -5.157 -5.933 -5.594 0.000 0.000 0.000 0.000
+ IR 86 86 6 86 5 1 1 24 42 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 50 ] 91 105 G C - -
+ MP 87 86 6 91 6 2 2 23 41 -12.054 -11.993 -0.088 -9.124 -9.700 -4.168 -6.104 -2.525 -5.923 1.744 -4.412 -6.518 -0.885 -5.441 -4.365 3.360 -6.607 -1.450 -0.228 -5.777 -2.310 -4.135
+ ML 88 86 6 91 6 1 1 24 42 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094
+ MR 89 86 6 91 6 1 1 23 42 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094
+ D 90 86 6 91 6 0 0 21 40 -10.139 -8.837 -4.634 -5.316 -2.943 -0.319
+ IL 91 91 5 91 6 1 1 23 42 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000
+ IR 92 92 6 92 5 1 1 23 41 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 51 ] 92 104 G C - -
+ MP 93 92 6 97 4 2 2 21 38 -11.071 -11.278 -0.039 -5.270 -6.025 -2.560 -5.843 0.080 -2.638 -4.094 -1.944 -4.527 -6.282 3.730 -5.566 -1.805 -1.436 -3.445 -3.431 -3.751
+ ML 94 92 6 97 4 1 1 23 42 -3.886 -4.069 -0.456 -2.798 0.168 0.082 -0.504 0.153
+ MR 95 92 6 97 4 1 1 23 41 -5.133 -4.162 -1.713 -0.712 0.189 -0.363 0.109 0.005
+ D 96 92 6 97 4 0 0 20 38 -7.671 -7.352 -1.134 -0.907
+ IL 97 97 5 97 4 1 1 25 43 -1.686 -2.369 -1.117 -4.855 0.000 0.000 0.000 0.000
+ IR 98 98 6 98 3 1 1 24 42 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000
+ [ MATL 52 ] 93 - U - - -
+ ML 99 98 6 101 3 1 1 18 36 -10.261 -0.002 -10.659 -1.981 -2.560 -3.724 1.808
+ D 100 98 6 101 3 0 0 17 35 -9.568 -0.142 -3.440
+ IL 101 101 3 101 3 1 1 22 41 -1.473 -0.775 -4.173 0.000 0.000 0.000 0.000
+ [ MATL 53 ] 95 - U - - -
+ ML 102 101 3 104 3 1 1 17 34 -12.090 -0.006 -7.982 -2.089 -3.017 -2.077 1.767
+ D 103 101 3 104 3 0 0 17 36 -6.545 -1.099 -0.937
+ IL 104 104 3 104 3 1 1 22 40 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000
+ [ MATL 54 ] 96 - C - - -
+ ML 105 104 3 107 3 1 1 16 33 -12.088 -0.003 -9.081 -0.857 1.537 -3.289 -1.172
+ D 106 104 3 107 3 0 0 16 34 -6.801 -1.079 -0.950
+ IL 107 107 3 107 3 1 1 21 39 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000
+ [ MATL 55 ] 97 - g - - -
+ ML 108 107 3 110 3 1 1 15 32 -7.365 -0.019 -7.158 0.735 -2.516 0.939 -2.045
+ D 109 107 3 110 3 0 0 14 32 -6.582 -1.057 -0.974
+ IL 110 110 3 110 3 1 1 17 33 -1.748 -0.607 -4.448 0.000 0.000 0.000 0.000
+ [ MATL 56 ] 99 - A - - -
+ ML 111 110 3 113 3 1 1 14 30 -12.083 -0.049 -4.915 1.834 -3.125 -3.688 -2.037
+ D 112 110 3 113 3 0 0 14 32 -7.200 -2.713 -0.250
+ IL 113 113 3 113 3 1 1 19 37 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000
+ [ MATL 57 ] 100 - a - - -
+ ML 114 113 3 116 3 1 1 13 29 -6.117 -0.139 -3.691 0.744 -1.208 -0.297 0.110
+ D 115 113 3 116 3 0 0 12 28 -5.138 -3.853 -0.148
+ IL 116 116 3 116 3 1 1 16 32 -1.657 -0.618 -4.994 0.000 0.000 0.000 0.000
+ [ MATL 58 ] 103 - U - - -
+ ML 117 116 3 119 2 1 1 1 1 * 0.000 -2.222 -0.662 -3.835 1.625
+ D 118 116 3 119 2 0 0 0 0 * 0.000
+ IL 119 119 3 119 2 1 1 13 28 -1.823 -0.479 0.000 0.000 0.000 0.000
+ [ END 59 ] - - - - - -
+ E 120 119 3 -1 0 0 0 0 0
+ [ BEGL 12 ] - - - - - -
+ S 121 54 1 122 1 0 8 47 65 0.000
+ [ BIF 13 ] - - - - - -
+ B 122 121 1 123 170 0 8 47 65
+ [ BEGL 14 ] - - - - - -
+ S 123 122 1 124 4 0 0 28 46 -0.004 -10.151 -9.558 -10.198
+ [ MATP 15 ] 13 33 G C - -
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+ ML 125 123 1 128 6 1 1 27 45 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094
+ MR 126 123 1 128 6 1 1 27 45 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094
+ D 127 123 1 128 6 0 0 25 43 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319
+ IL 128 128 5 128 6 1 1 28 46 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000
+ IR 129 129 6 129 5 1 1 28 45 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 16 ] 14 32 C G - -
+ MP 130 129 6 134 6 2 2 26 44 -12.066 -12.006 -0.004 -9.288 -11.062 -11.457 -6.391 -4.319 -5.973 -0.507 -5.273 -7.239 3.055 -5.923 -6.255 0.169 -6.770 -3.355 2.348 -3.545 -1.361 -4.289
+ ML 131 129 6 134 6 1 1 26 44 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094
+ MR 132 129 6 134 6 1 1 26 44 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094
+ D 133 129 6 134 6 0 0 24 43 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319
+ IL 134 134 5 134 6 1 1 26 44 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000
+ IR 135 135 6 135 5 1 1 26 44 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 17 ] 15 31 u a - -
+ MP 136 135 6 140 6 2 2 24 42 -12.065 -12.004 -0.003 -10.781 -11.060 -11.456 -3.197 -3.903 -5.383 0.955 -2.911 -6.231 1.594 -5.342 -4.046 1.426 -5.910 -2.702 2.857 -5.539 -1.190 -4.334
+ ML 137 135 6 140 6 1 1 25 44 -6.396 -6.742 -1.118 -1.151 -6.592 -4.122 0.192 0.038 -0.475 0.153
+ MR 138 135 6 140 6 1 1 25 44 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094
+ D 139 135 6 140 6 0 0 24 42 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319
+ IL 140 140 5 140 6 1 1 25 43 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000
+ IR 141 141 6 141 5 1 1 24 43 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 18 ] 16 30 c g - -
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+ ML 143 141 6 146 4 1 1 25 44 -3.758 -3.940 -0.507 -2.670 0.368 -0.385 -0.191 0.094
+ MR 144 141 6 146 4 1 1 25 43 -4.809 -3.838 -1.706 -0.766 0.368 -0.385 -0.191 0.094
+ D 145 141 6 146 4 0 0 24 42 -4.568 -4.250 -2.265 -0.520
+ IL 146 146 5 146 4 1 1 26 45 -1.686 -2.369 -1.117 -4.855 0.000 0.000 0.000 0.000
+ IR 147 147 6 147 3 1 1 25 44 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000
+ [ MATL 19 ] 17 - A - - -
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+ D 149 147 6 150 3 0 0 20 38 -6.658 -2.171 -0.381
+ IL 150 150 3 150 3 1 1 24 43 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000
+ [ MATL 20 ] 18 - g - - -
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+ D 152 150 3 153 3 0 0 18 37 -7.682 -3.195 -0.175
+ IL 153 153 3 153 3 1 1 23 42 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000
+ [ MATL 21 ] 19 - U - - -
+ ML 154 153 3 156 3 1 1 17 34 -1.178 -0.948 -4.648 -0.779 -0.356 -2.426 1.293
+ D 155 153 3 156 3 0 0 15 32 -10.935 -0.301 -2.413
+ IL 156 156 3 156 3 1 1 17 34 -2.344 -0.381 -4.840 0.000 0.000 0.000 0.000
+ [ MATL 22 ] 23 - G - - -
+ ML 157 156 3 159 3 1 1 15 32 -11.979 -0.001 -10.633 -1.165 -2.582 1.649 -1.996
+ D 158 156 3 159 3 0 0 14 32 -9.899 -5.412 -0.036
+ IL 159 159 3 159 3 1 1 21 39 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000
+ [ MATL 23 ] 24 - G - - -
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+ D 161 159 3 162 3 0 0 13 31 -9.899 -5.412 -0.036
+ IL 162 162 3 162 3 1 1 20 38 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000
+ [ MATL 24 ] 25 - U - - -
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+ D 164 162 3 165 3 0 0 10 22 -5.788 -0.077 -4.875
+ IL 165 165 3 165 3 1 1 12 25 -2.149 -0.388 -6.606 0.000 0.000 0.000 0.000
+ [ MATL 25 ] 29 - A - - -
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+ D 167 165 3 168 2 0 0 0 0 * 0.000
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+ [ END 26 ] - - - - - -
+ E 169 168 3 -1 0 0 0 0 0
+ [ BEGR 27 ] - - - - - -
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+ IL 171 171 2 171 3 1 1 35 53 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000
+ [ MATL 28 ] 34 - a - - -
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+ D 173 171 2 174 5 0 0 28 46 -5.414 -0.538 -4.676 -3.051 -2.963
+ IL 174 174 3 174 5 1 1 29 48 -2.743 -0.379 -4.422 -6.254 -5.527 0.000 0.000 0.000 0.000
+ [ MATP 29 ] 36 55 u a - -
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+ ML 176 174 3 179 6 1 1 27 45 -6.348 -6.694 -1.177 -1.103 -6.544 -4.073 0.243 -0.066 -0.407 0.147
+ MR 177 174 3 179 6 1 1 27 45 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094
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+ IR 180 180 6 180 5 1 1 27 46 -2.480 -0.468 -5.991 -4.159 -5.265 0.000 0.000 0.000 0.000
+ [ MATP 30 ] 38 53 c g - -
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+ ML 182 180 6 185 6 1 1 25 44 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094
+ MR 183 180 6 185 6 1 1 25 44 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094
+ D 184 180 6 185 6 0 0 23 42 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319
+ IL 185 185 5 185 6 1 1 26 44 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000
+ IR 186 186 6 186 5 1 1 26 44 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 31 ] 39 52 g c - -
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+ ML 188 186 6 191 6 1 1 24 43 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094
+ MR 189 186 6 191 6 1 1 24 43 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094
+ D 190 186 6 191 6 0 0 22 41 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319
+ IL 191 191 5 191 6 1 1 24 43 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000
+ IR 192 192 6 192 5 1 1 24 42 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 32 ] 40 51 G C - -
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+ ML 194 192 6 197 6 1 1 24 42 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094
+ MR 195 192 6 197 6 1 1 23 42 -7.103 -5.832 -1.410 -5.811 -0.945 -4.024 0.199 -0.364 -0.381 0.387
+ D 196 192 6 197 6 0 0 22 41 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319
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+ IR 198 198 6 198 5 1 1 23 41 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 33 ] 41 50 a u - -
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+ ML 200 198 6 203 4 1 1 23 42 -3.758 -3.940 -0.507 -2.670 0.368 -0.385 -0.191 0.094
+ MR 201 198 6 203 4 1 1 23 41 -4.901 -3.930 -1.518 -0.858 0.251 -0.082 -0.397 0.145
+ D 202 198 6 203 4 0 0 22 40 -4.568 -4.250 -2.265 -0.520
+ IL 203 203 5 203 4 1 1 25 43 -1.686 -2.369 -1.117 -4.855 0.000 0.000 0.000 0.000
+ IR 204 204 6 204 3 1 1 24 42 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000
+ [ MATL 34 ] 42 - C - - -
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+ D 206 204 6 207 3 0 0 18 36 -6.174 -1.687 -0.566
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+ [ MATL 35 ] 44 - U - - -
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+ D 209 207 3 210 3 0 0 18 36 -6.174 -1.687 -0.566
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+ [ MATL 36 ] 45 - u - - -
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+ D 212 210 3 213 3 0 0 17 35 -6.174 -1.687 -0.566
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+ [ MATL 37 ] 46 - u - - -
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+ [ MATL 38 ] 47 - u - - -
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+ D 218 216 3 219 3 0 0 15 33 -6.174 -1.687 -0.566
+ IL 219 219 3 219 3 1 1 19 37 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000
+ [ MATL 39 ] 48 - A - - -
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+ D 221 219 3 222 3 0 0 13 32 -6.174 -1.687 -0.566
+ IL 222 222 3 222 3 1 1 18 36 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000
+ [ MATL 40 ] 49 - A - - -
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+ D 224 222 3 225 2 0 0 0 0 * 0.000
+ IL 225 225 3 225 2 1 1 13 28 -1.823 -0.479 0.000 0.000 0.000 0.000
+ [ END 41 ] - - - - - -
+ E 226 225 3 -1 0 0 0 0 0
+//
+HMMER3/f [i1.1 | April 2012]
+NAME tRNA
+ACC RF00005
+DESC tRNA
+LENG 71
+MAXL 253
+ALPH RNA
+RF no
+MM no
+CONS yes
+CS yes
+MAP yes
+DATE Mon Apr 30 08:54:53 2012
+COM [1] /groups/eddy/home/nawrockie/notebook/12_0423_inf_final_stress_tests/wd-infernal/src/cmbuild -F tRNA.cm tRNA.sto
+NSEQ 967
+EFFN 186.722610
+CKSUM 1685224748
+STATS LOCAL MSV -8.9378 0.73469
+STATS LOCAL VITERBI -9.6821 0.73469
+STATS LOCAL FORWARD -2.5854 0.73469
+HMM A C G U
+ m->m m->i m->d i->m i->i d->m d->d
+ COMPO 1.35282 1.54883 1.34468 1.31539
+ 1.38629 1.38629 1.38629 1.38629
+ 0.01069 9.17906 4.55379 1.46634 0.26236 0.00000 *
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+ 0.00011 9.15565 * 1.46634 0.26236 0.00000 *
+//
+INFERNAL1/a [1.1 | April 2012]
+NAME Vault
+ACC RF00006
+DESC Vault RNA
+STATES 304
+NODES 83
+CLEN 100
+W 181
+ALPH RNA
+RF yes
+CONS yes
+MAP yes
+DATE Mon Apr 30 08:54:54 2012
+COM [1] /groups/eddy/home/nawrockie/notebook/12_0423_inf_final_stress_tests/wd-infernal/src/cmbuild -F Vault.cm Vault.sto
+COM [2] /groups/eddy/home/nawrockie/notebook/12_0423_inf_final_stress_tests/wd-infernal/src/cmcalibrate --mpi Vault.cm
+PBEGIN 0.05
+PEND 0.05
+WBETA 1e-07
+QDBBETA1 1e-07
+QDBBETA2 1e-15
+N2OMEGA 1.52588e-05
+N3OMEGA 1.52588e-05
+ELSELF -0.08926734
+NSEQ 75
+EFFN 4.368496
+CKSUM 2397722235
+NULL 0.000 0.000 0.000 0.000
+GA 29.00
+TC 29.39
+NC 28.20
+EFP7GF -10.4482 0.71855
+ECMLC 0.69230 -6.00388 2.28041 1600000 371500 0.003230
+ECMGC 0.43256 -15.96507 -4.24742 1600000 63581 0.006291
+ECMLI 0.63611 -4.87878 3.73222 1600000 287121 0.004179
+ECMGI 0.45930 -10.59291 -0.39663 1600000 43242 0.009250
+CM
+ [ ROOT 0 ] - - - - - -
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+ IL 1 1 2 1 4 6 44 183 280 -1.686 -2.369 -1.117 -4.855 0.000 0.000 0.000 0.000
+ IR 2 2 3 2 3 5 44 183 280 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000
+ [ MATL 1 ] 1 - G - G -
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+ D 4 2 3 5 3 1 39 180 276 -6.507 -0.590 -1.623
+ IL 5 5 3 5 3 4 43 182 278 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000
+ [ MATR 2 ] - 164 - U - U
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+ IR 8 8 3 8 3 4 42 181 277 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000
+ [ MATR 3 ] - 163 - U - U
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+ [ MATR 4 ] - 162 - U - U
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+ [ MATR 5 ] - 161 - U - U
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+ D 16 14 3 17 3 0 34 175 271 -6.776 -1.954 -0.448
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+ [ MATR 6 ] - 160 - c - c
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+ [ MATP 7 ] 2 159 g c g c
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+ ML 22 20 3 25 6 1 35 173 270 -6.399 -6.745 -1.459 -0.869 -6.595 -4.124 0.181 -0.365 -0.401 0.414
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+ IR 26 26 6 26 5 2 37 175 271 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 8 ] 3 158 G C G C
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+ D 30 26 6 31 6 0 29 167 264 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319
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+ IR 32 32 6 32 5 2 35 173 269 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 9 ] 4 157 c g C G
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+ ML 34 32 6 37 6 1 32 170 266 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094
+ MR 35 32 6 37 6 1 32 169 266 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094
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+ IR 38 38 6 38 5 1 34 171 267 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 10 ] 5 156 c g c g
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+ D 42 38 6 43 6 0 28 164 261 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319
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+ IR 44 44 6 44 5 1 32 169 265 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 11 ] 6 155 G C G C
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+ ML 46 44 6 49 6 1 30 166 263 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094
+ MR 47 44 6 49 6 1 30 166 262 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094
+ D 48 44 6 49 6 0 27 164 260 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319
+ IL 49 49 5 49 6 1 31 167 264 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000
+ IR 50 50 6 50 5 1 31 167 263 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 12 ] 7 154 G C G C
+ MP 51 50 6 55 4 2 30 166 262 -7.707 -7.914 -0.322 -2.386 -5.770 -3.635 -6.023 -0.526 -6.940 -5.158 -1.941 -6.379 -5.006 3.797 -5.287 -0.760 -2.230 -5.155 -4.050 -4.891
+ ML 52 50 6 55 4 1 29 165 262 -3.758 -3.940 -0.507 -2.670 0.368 -0.385 -0.191 0.094
+ MR 53 50 6 55 4 1 28 164 261 -4.809 -3.838 -1.706 -0.766 0.368 -0.385 -0.191 0.094
+ D 54 50 6 55 4 0 27 163 260 -4.568 -4.250 -2.265 -0.520
+ IL 55 55 5 55 4 1 30 166 262 -1.686 -2.369 -1.117 -4.855 0.000 0.000 0.000 0.000
+ IR 56 56 6 56 3 1 29 165 262 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000
+ [ MATL 13 ] 8 - C - C -
+ ML 57 56 6 59 3 1 28 164 260 -4.834 -0.281 -2.818 -1.425 1.612 -2.679 -1.273
+ D 58 56 6 59 3 0 27 163 259 -8.021 -0.401 -2.065
+ IL 59 59 3 59 3 1 29 164 261 -1.581 -0.703 -4.281 0.000 0.000 0.000 0.000
+ [ MATL 14 ] 10 - U - U -
+ ML 60 59 3 62 3 1 28 163 260 -8.491 -0.014 -7.145 -0.818 -0.895 -1.524 1.349
+ D 61 59 3 62 3 0 25 161 258 -7.698 -0.395 -2.090
+ IL 62 62 3 62 3 1 27 163 260 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000
+ [ MATL 15 ] 11 - U - U -
+ ML 63 62 3 65 3 1 27 162 259 -8.681 -0.013 -7.335 -0.786 -1.323 -1.305 1.387
+ D 64 62 3 65 3 0 22 160 256 -6.174 -1.687 -0.566
+ IL 65 65 3 65 3 1 26 162 259 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000
+ [ MATL 16 ] 12 - U - U -
+ ML 66 65 3 68 3 1 26 161 258 -8.681 -0.013 -7.335 -1.336 -1.294 -2.358 1.585
+ D 67 65 3 68 3 0 21 159 255 -6.174 -1.687 -0.566
+ IL 68 68 3 68 3 1 25 161 258 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000
+ [ MATL 17 ] 13 - A - A -
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+ D 70 68 3 71 3 0 20 158 255 -5.620 -0.734 -1.403
+ IL 71 71 3 71 3 1 24 160 257 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000
+ [ MATR 18 ] - 153 - U - U
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+ D 73 71 3 74 3 0 17 157 253 -6.390 -1.568 -0.620
+ IR 74 74 3 74 3 1 23 159 256 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000
+ [ MATR 19 ] - 152 - g - u
+ MR 75 74 3 77 3 1 23 158 255 -9.034 -0.028 -5.878 -0.259 0.009 0.157 0.061
+ D 76 74 3 77 3 0 16 156 252 -6.390 -1.568 -0.620
+ IR 77 77 3 77 3 1 22 158 255 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000
+ [ MATR 20 ] - 151 - U - U
+ MR 78 77 3 80 3 1 23 157 254 -9.018 -0.012 -7.336 -1.027 -0.467 -1.547 1.289
+ D 79 77 3 80 3 0 15 155 251 -6.586 -1.247 -0.815
+ IR 80 80 3 80 3 1 21 157 254 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000
+ [ MATR 21 ] - 150 - C - C
+ MR 81 80 3 83 3 1 22 156 253 -9.034 -0.012 -7.352 -2.398 1.773 -3.412 -1.743
+ D 82 80 3 83 3 0 14 154 250 -6.390 -1.568 -0.620
+ IR 83 83 3 83 3 1 20 156 253 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000
+ [ MATR 22 ] - 149 - G - G
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+ D 85 83 3 86 5 0 13 153 250 -5.352 -0.707 -2.978 -4.409 -2.404
+ IR 86 86 3 86 5 1 18 155 252 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 23 ] 14 148 G C G C
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+ ML 88 86 3 91 6 1 14 152 248 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094
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+ IL 91 91 5 91 6 1 16 153 250 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000
+ IR 92 92 6 92 5 1 17 153 250 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 24 ] 15 147 C G C G
+ MP 93 92 6 97 6 2 19 152 249 -9.446 -9.385 -0.017 -8.162 -8.441 -8.836 -7.061 -7.108 -6.386 -3.321 -4.912 -4.389 3.925 -6.159 -6.763 -3.157 -6.485 -5.176 -1.831 -7.090 -3.013 -5.588
+ ML 94 92 6 97 6 1 14 150 247 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094
+ MR 95 92 6 97 6 1 12 150 246 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094
+ D 96 92 6 97 6 0 8 146 243 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319
+ IL 97 97 5 97 6 1 16 151 248 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000
+ IR 98 98 6 98 5 1 16 151 248 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 25 ] 16 146 u g u g
+ MP 99 98 6 103 6 2 18 150 247 -9.446 -9.385 -0.017 -8.162 -8.441 -8.836 -2.844 -1.557 -2.958 0.481 -2.529 -3.749 1.822 -3.033 -2.991 0.548 -2.443 -1.199 1.081 -3.123 2.436 -2.043
+ ML 100 98 6 103 6 1 13 148 245 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094
+ MR 101 98 6 103 6 1 11 148 244 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094
+ D 102 98 6 103 6 0 8 145 242 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319
+ IL 103 103 5 103 6 1 14 149 246 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000
+ IR 104 104 6 104 5 1 14 149 246 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 26 ] 17 145 c g c g
+ MP 105 104 6 109 4 2 16 148 245 -3.306 -7.914 -0.181 -6.328 -2.899 -2.949 -3.022 0.526 -1.297 -3.845 2.842 -3.039 -1.555 0.610 -3.564 -0.842 1.211 -3.183 0.293 -2.041
+ ML 106 104 6 109 4 1 12 147 243 -3.758 -3.940 -0.507 -2.670 0.368 -0.385 -0.191 0.094
+ MR 107 104 6 109 4 1 9 146 243 -4.809 -3.838 -1.706 -0.766 0.368 -0.385 -0.191 0.094
+ D 108 104 6 109 4 0 8 145 241 -4.568 -4.250 -2.265 -0.520
+ IL 109 109 5 109 4 1 15 147 244 -2.463 -3.146 -0.545 -5.632 0.000 0.000 0.000 0.000
+ IR 110 110 6 110 3 1 13 147 244 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000
+ [ MATL 27 ] 19 - A - A -
+ ML 111 110 6 113 5 1 15 146 243 -7.736 -0.025 -7.552 -7.764 -8.655 1.787 -2.787 -2.640 -2.036
+ D 112 110 6 113 5 0 7 144 240 -4.959 -0.803 -4.221 -2.596 -2.508
+ IL 113 113 3 113 5 1 11 146 242 -2.408 -0.496 -4.087 -5.920 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 28 ] 20 144 G C G C
+ MP 114 113 3 118 6 2 14 145 242 -9.446 -9.385 -0.017 -8.162 -8.441 -8.836 -4.892 -3.253 -4.907 0.078 -5.709 -4.819 -0.939 -5.420 -2.919 3.667 -2.940 -0.898 -1.225 -4.478 -2.960 -3.861
+ ML 115 113 3 118 6 1 9 143 239 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094
+ MR 116 113 3 118 6 1 8 142 239 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094
+ D 117 113 3 118 6 0 5 138 235 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319
+ IL 118 118 5 118 6 1 10 144 241 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000
+ IR 119 119 6 119 5 1 11 144 240 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 29 ] 21 143 c g C G
+ MP 120 119 6 124 6 2 13 143 240 -9.446 -9.385 -0.017 -8.162 -8.441 -8.836 -3.901 -3.816 -3.873 0.042 -1.998 -4.574 2.856 -3.551 -3.835 0.380 -4.296 -1.695 2.122 -4.092 -0.237 -2.688
+ ML 121 119 6 124 6 1 8 141 237 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094
+ MR 122 119 6 124 6 1 8 140 237 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094
+ D 123 119 6 124 6 0 5 137 233 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319
+ IL 124 124 5 124 6 1 10 142 239 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000
+ IR 125 125 6 125 5 1 10 142 239 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 30 ] 22 142 G C G C
+ MP 126 125 6 130 6 2 11 141 238 -9.446 -9.385 -0.017 -8.162 -8.441 -8.836 -5.089 -3.338 -5.151 0.141 -6.188 -5.052 -1.291 -5.596 -4.729 3.634 -5.046 0.321 -1.556 -4.754 -3.337 -4.033
+ ML 127 125 6 130 6 1 8 139 235 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094
+ MR 128 125 6 130 6 1 7 138 235 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094
+ D 129 125 6 130 6 0 4 135 232 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319
+ IL 130 130 5 130 6 1 9 140 237 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000
+ IR 131 131 6 131 5 1 9 140 237 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 31 ] 23 141 G C G C
+ MP 132 131 6 136 4 2 9 139 236 -7.707 -2.696 -0.272 -6.328 -5.928 -3.679 -6.164 -0.666 -6.761 -3.229 -1.795 -6.618 -5.088 3.816 -5.307 -1.505 -2.140 -5.050 -3.910 -5.135
+ ML 133 131 6 136 4 1 7 137 233 -3.758 -3.940 -0.507 -2.670 0.368 -0.385 -0.191 0.094
+ MR 134 131 6 136 4 1 5 136 232 -4.809 -3.838 -1.706 -0.766 0.368 -0.385 -0.191 0.094
+ D 135 131 6 136 4 0 4 134 231 -4.568 -4.250 -2.265 -0.520
+ IL 136 136 5 136 4 1 8 140 237 -1.686 -2.369 -1.117 -4.855 0.000 0.000 0.000 0.000
+ IR 137 137 6 137 3 1 9 144 240 -0.322 -2.392 -6.702 0.000 0.000 0.000 0.000
+ [ MATL 32 ] 24 - U - U -
+ ML 138 137 6 140 3 1 7 133 230 -6.359 -0.027 -7.335 -1.067 -1.538 -2.305 1.573
+ D 139 137 6 140 3 0 3 131 228 -6.174 -1.687 -0.566
+ IL 140 140 3 140 3 1 7 134 230 -1.494 -0.760 -4.195 0.000 0.000 0.000 0.000
+ [ MATL 33 ] 26 - U - U -
+ ML 141 140 3 143 3 1 6 132 229 -8.681 -0.026 -6.004 -2.054 -2.140 -2.976 1.768
+ D 142 140 3 143 3 0 3 130 227 -6.174 -1.687 -0.566
+ IL 143 143 3 143 3 1 6 133 229 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000
+ [ MATL 34 ] 27 - A - A -
+ ML 144 143 3 146 3 1 5 131 228 -8.667 -0.013 -7.321 1.179 -0.329 -1.603 -0.711
+ D 145 143 3 146 3 0 2 129 226 -6.366 -1.879 -0.482
+ IL 146 146 3 146 3 1 5 132 229 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000
+ [ MATL 35 ] 28 - C - C -
+ ML 147 146 3 149 3 1 4 131 227 -9.021 -0.254 -2.648 -2.177 1.710 -3.179 -1.336
+ D 148 146 3 149 3 0 2 129 225 -5.740 -0.854 -1.225
+ IL 149 149 3 149 3 1 6 131 228 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000
+ [ MATR 36 ] - 123 - C - C
+ MR 150 149 3 152 3 1 7 130 226 -8.781 -0.033 -5.625 -2.382 1.729 -3.220 -1.376
+ D 151 149 3 152 3 0 0 127 224 -8.044 -2.698 -0.248
+ IR 152 152 3 152 3 1 5 130 227 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000
+ [ MATR 37 ] - 122 - a - A
+ MR 153 152 3 155 5 1 7 129 225 -7.495 -0.029 -7.310 -7.523 -8.414 0.997 -0.745 -0.910 -0.191
+ D 154 152 3 155 5 0 0 127 223 -6.491 -0.770 -1.918 -5.548 -3.103
+ IR 155 155 3 155 5 1 3 129 225 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 38 ] 29 121 u a u a
+ MP 156 155 3 160 6 2 8 128 224 -9.389 -9.328 -0.017 -8.104 -8.384 -8.779 -2.409 -2.530 -2.559 0.677 -2.271 -3.381 1.556 -2.728 -2.601 0.712 -3.148 -0.940 1.819 -1.940 1.816 -0.456
+ ML 157 155 3 160 6 1 2 126 223 -6.901 -7.247 -0.820 -1.431 -7.097 -4.627 -0.247 -0.532 -0.874 0.941
+ MR 158 155 3 160 6 1 2 125 222 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094
+ D 159 155 3 160 6 0 0 121 217 -9.196 -7.894 -3.691 -4.373 -4.391 -0.285
+ IL 160 160 5 160 6 1 3 127 223 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000
+ IR 161 161 6 161 5 1 3 127 223 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 39 ] 30 120 U A u a
+ MP 162 161 6 166 6 2 7 126 222 -9.431 -9.371 -0.017 -8.147 -8.427 -8.822 -4.153 -4.253 -4.294 -0.958 -3.417 -5.112 -0.013 -4.410 -4.313 -0.909 -4.866 -2.594 3.674 -2.944 -1.521 -2.817
+ ML 163 161 6 166 6 1 2 124 220 -6.367 -6.713 -1.153 -1.122 -6.563 -4.092 0.217 -0.364 -0.362 0.359
+ MR 164 161 6 166 6 1 1 123 220 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094
+ D 165 161 6 166 6 0 0 119 216 -9.196 -7.894 -3.691 -4.373 -4.391 -0.285
+ IL 166 166 5 166 6 1 2 125 221 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000
+ IR 167 167 6 167 5 1 3 125 221 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 40 ] 31 119 C G C G
+ MP 168 167 6 172 6 2 6 124 220 -9.439 -9.378 -0.017 -8.154 -8.434 -8.829 -5.643 -5.729 -5.457 -2.226 -1.769 -3.327 3.839 -5.409 -5.642 -2.143 -5.784 -3.958 -1.192 -5.849 -2.507 -4.606
+ ML 169 167 6 172 6 1 1 122 218 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094
+ MR 170 167 6 172 6 1 1 121 218 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094
+ D 171 167 6 172 6 0 0 118 214 -9.196 -7.894 -3.691 -4.373 -4.391 -0.285
+ IL 172 172 5 172 6 1 2 123 220 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000
+ IR 173 173 6 173 5 1 2 123 219 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 41 ] 32 118 g c g c
+ MP 174 173 6 178 6 2 5 122 218 -9.439 -9.378 -0.017 -8.154 -8.434 -8.829 -2.037 -0.375 -2.204 1.092 -1.921 -1.342 1.044 -2.579 -2.295 2.207 -2.826 -0.183 0.969 -0.253 -0.442 -1.430
+ ML 175 173 6 178 6 1 1 120 217 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094
+ MR 176 173 6 178 6 1 1 120 216 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094
+ D 177 173 6 178 6 0 0 117 213 -9.196 -7.894 -3.691 -4.373 -4.391 -0.285
+ IL 178 178 5 178 6 1 2 121 218 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000
+ IR 179 179 6 179 5 1 2 121 217 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 42 ] 33 117 a u a u
+ MP 180 179 6 184 4 2 4 120 216 -7.693 -7.900 -0.031 -6.314 -1.816 -1.873 -2.016 1.612 -2.014 -2.340 1.242 0.029 -2.064 1.184 -2.604 0.321 1.092 -2.135 -0.222 0.224
+ ML 181 179 6 184 4 1 1 119 215 -3.758 -3.940 -0.507 -2.670 0.368 -0.385 -0.191 0.094
+ MR 182 179 6 184 4 1 1 118 214 -4.809 -3.838 -1.706 -0.766 0.368 -0.385 -0.191 0.094
+ D 183 179 6 184 4 0 0 116 213 -4.706 -4.387 -2.403 -0.464
+ IL 184 184 5 184 4 1 1 120 216 -1.686 -2.369 -1.117 -4.855 0.000 0.000 0.000 0.000
+ IR 185 185 6 185 3 1 1 119 216 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000
+ [ MATL 43 ] 34 - c - a -
+ ML 186 185 6 188 3 1 3 118 214 -8.667 -0.013 -7.321 0.088 0.206 -0.562 0.146
+ D 187 185 6 188 3 0 0 115 212 -6.366 -1.879 -0.482
+ IL 188 188 3 188 3 1 1 118 215 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000
+ [ MATL 44 ] 35 - u - a -
+ ML 189 188 3 191 3 1 2 117 213 -8.667 -0.013 -7.321 0.324 -0.462 -0.457 0.371
+ D 190 188 3 191 3 0 0 114 211 -6.366 -1.879 -0.482
+ IL 191 191 3 191 3 1 1 117 214 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000
+ [ MATL 45 ] 36 - a - a -
+ ML 192 191 3 194 3 1 2 116 212 -8.667 -0.013 -7.321 0.476 -0.269 -0.412 0.039
+ D 193 191 3 194 3 0 0 113 210 -6.366 -1.879 -0.482
+ IL 194 194 3 194 3 1 1 116 213 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000
+ [ MATL 46 ] 37 - u - a -
+ ML 195 194 3 197 3 1 2 115 211 -8.667 -0.013 -7.321 0.327 -0.498 -0.406 0.359
+ D 196 194 3 197 3 0 0 112 209 -6.366 -1.879 -0.482
+ IL 197 197 3 197 3 1 1 115 212 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000
+ [ MATL 47 ] 38 - u - u -
+ ML 198 197 3 200 3 1 1 114 210 -8.667 -0.013 -7.321 0.115 0.014 -0.900 0.456
+ D 199 197 3 200 3 0 0 111 208 -6.366 -1.879 -0.482
+ IL 200 200 3 200 3 1 1 114 211 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000
+ [ MATL 48 ] 39 - a - a -
+ ML 201 200 3 203 3 1 1 113 209 -8.667 -0.013 -7.321 0.165 -0.170 -0.132 0.107
+ D 202 200 3 203 3 0 0 110 207 -6.366 -1.879 -0.482
+ IL 203 203 3 203 3 1 1 113 210 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000
+ [ MATL 49 ] 40 - u - a -
+ ML 204 203 3 206 3 1 1 112 208 -8.667 -0.013 -7.321 0.298 -0.282 -0.564 0.347
+ D 205 203 3 206 3 0 0 109 206 -6.366 -1.879 -0.482
+ IL 206 206 3 206 3 1 1 113 209 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000
+ [ MATL 50 ] 41 - a - a -
+ ML 207 206 3 209 3 1 1 111 207 -8.667 -0.013 -7.321 0.275 -0.218 -0.250 0.124
+ D 208 206 3 209 3 0 0 108 205 -6.366 -1.879 -0.482
+ IL 209 209 3 209 3 1 1 112 208 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000
+ [ MATL 51 ] 42 - a - a -
+ ML 210 209 3 212 3 1 1 110 206 -8.667 -0.013 -7.321 0.566 -0.320 -0.700 0.141
+ D 211 209 3 212 3 0 0 107 204 -6.366 -1.879 -0.482
+ IL 212 212 3 212 3 1 1 111 207 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000
+ [ MATL 52 ] 43 - u - a -
+ ML 213 212 3 215 3 1 1 109 205 -8.667 -0.013 -7.321 0.254 -0.169 -0.632 0.348
+ D 214 212 3 215 3 0 0 106 203 -6.366 -1.879 -0.482
+ IL 215 215 3 215 3 1 1 110 206 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000
+ [ MATL 53 ] 44 - u - u -
+ ML 216 215 3 218 3 1 1 108 205 -8.667 -0.013 -7.321 0.199 -0.217 -0.533 0.380
+ D 217 215 3 218 3 0 0 105 202 -6.366 -1.879 -0.482
+ IL 218 218 3 218 3 1 1 109 205 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000
+ [ MATL 54 ] 45 - u - u -
+ ML 219 218 3 221 3 1 1 107 204 -8.667 -0.013 -7.321 -0.041 -0.331 -0.320 0.517
+ D 220 218 3 221 3 0 0 104 201 -6.366 -1.879 -0.482
+ IL 221 221 3 221 3 1 1 108 204 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000
+ [ MATL 55 ] 46 - u - u -
+ ML 222 221 3 224 3 1 1 106 203 -8.667 -0.013 -7.321 0.103 0.047 -0.633 0.320
+ D 223 221 3 224 3 0 0 103 200 -6.366 -1.879 -0.482
+ IL 224 224 3 224 3 1 1 107 203 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000
+ [ MATL 56 ] 47 - a - a -
+ ML 225 224 3 227 3 1 1 105 202 -8.667 -0.013 -7.321 0.430 -0.549 -0.632 0.406
+ D 226 224 3 227 3 0 0 102 199 -6.366 -1.879 -0.482
+ IL 227 227 3 227 3 1 1 106 202 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000
+ [ MATL 57 ] 48 - u - u -
+ ML 228 227 3 230 3 1 1 104 201 -8.667 -0.013 -7.321 0.157 -0.190 -0.539 0.401
+ D 229 227 3 230 3 0 0 101 198 -6.366 -1.879 -0.482
+ IL 230 230 3 230 3 1 1 105 201 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000
+ [ MATL 58 ] 49 - u - u -
+ ML 231 230 3 233 3 1 1 103 200 -8.667 -0.013 -7.321 0.062 -0.033 -0.736 0.463
+ D 232 230 3 233 3 0 0 100 197 -6.366 -1.879 -0.482
+ IL 233 233 3 233 3 1 1 104 200 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000
+ [ MATL 59 ] 50 - u - u -
+ ML 234 233 3 236 3 1 1 102 199 -8.667 -0.013 -7.321 0.111 -0.501 -0.744 0.693
+ D 235 233 3 236 3 0 0 99 196 -6.366 -1.879 -0.482
+ IL 236 236 3 236 3 1 1 103 199 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000
+ [ MATL 60 ] 51 - u - a -
+ ML 237 236 3 239 3 1 1 101 198 -8.667 -0.013 -7.321 0.164 0.140 -0.988 0.348
+ D 238 236 3 239 3 0 0 98 195 -6.366 -1.879 -0.482
+ IL 239 239 3 239 3 1 1 102 198 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000
+ [ MATL 61 ] 52 - u - a -
+ ML 240 239 3 242 3 1 1 100 197 -8.667 -0.013 -7.321 0.081 0.123 -0.754 0.333
+ D 241 239 3 242 3 0 0 97 193 -6.366 -1.879 -0.482
+ IL 242 242 3 242 3 1 1 101 197 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000
+ [ MATL 62 ] 53 - u - a -
+ ML 243 242 3 245 3 1 1 99 196 -8.667 -0.024 -6.167 0.059 0.054 -0.244 0.105
+ D 244 242 3 245 3 0 0 96 192 -6.366 -1.879 -0.482
+ IL 245 245 3 245 3 1 1 100 196 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000
+ [ MATL 63 ] 54 - u - u -
+ ML 246 245 3 248 3 1 1 98 195 -8.656 -0.074 -4.401 0.169 -0.325 -0.536 0.473
+ D 247 245 3 248 3 0 0 94 191 -6.505 -2.018 -0.430
+ IL 248 248 3 248 3 1 1 99 195 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000
+ [ MATL 64 ] 55 - a - a -
+ ML 249 248 3 251 3 1 1 97 194 -8.596 -0.067 -4.551 0.235 -0.081 -0.340 0.120
+ D 250 248 3 251 3 0 0 92 189 -7.078 -2.591 -0.275
+ IL 251 251 3 251 3 1 1 98 194 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000
+ [ MATL 65 ] 56 - u - u -
+ ML 252 251 3 254 3 1 1 96 193 -8.543 -0.014 -7.197 0.066 0.041 -0.515 0.293
+ D 253 251 3 254 3 0 0 91 187 -7.430 -2.943 -0.211
+ IL 254 254 3 254 3 1 1 97 193 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000
+ [ MATL 66 ] 57 - a - a -
+ ML 255 254 3 257 3 1 1 95 192 -8.543 -0.057 -4.801 0.192 -0.028 -0.416 0.172
+ D 256 254 3 257 3 0 0 90 186 -7.430 -2.943 -0.211
+ IL 257 257 3 257 3 1 1 96 192 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000
+ [ MATL 67 ] 58 - u - a -
+ ML 258 257 3 260 3 1 1 95 191 -8.500 -0.043 -5.241 0.018 0.144 -0.439 0.195
+ D 259 257 3 260 3 0 0 88 185 -7.654 -3.167 -0.178
+ IL 260 260 3 260 3 1 1 95 191 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000
+ [ MATL 68 ] 59 - u - u -
+ ML 261 260 3 263 3 1 1 94 190 -8.472 -0.035 -5.562 0.013 0.036 -0.509 0.337
+ D 262 260 3 263 3 0 0 87 183 -7.783 -3.296 -0.162
+ IL 263 263 3 263 3 1 1 94 191 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000
+ [ MATL 69 ] 60 - u - u -
+ ML 264 263 3 266 3 1 1 93 189 -8.451 -0.055 -4.863 -0.088 -0.264 -0.190 0.433
+ D 265 263 3 266 3 0 0 85 182 -7.867 -3.380 -0.153
+ IL 266 266 3 266 3 1 1 93 190 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000
+ [ MATL 70 ] 61 - u - u -
+ ML 267 266 3 269 3 1 1 92 188 -8.412 -0.146 -3.424 -0.066 -0.061 -0.497 0.462
+ D 268 266 3 269 3 0 0 83 180 -8.016 -3.529 -0.137
+ IL 269 269 3 269 3 1 1 93 189 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000
+ [ MATL 71 ] 62 - u - a -
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+ [ MATL 72 ] 63 - c - a -
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+ [ MATL 73 ] 64 - u - u -
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+ D 277 275 3 278 3 0 0 75 171 -8.687 -4.200 -0.084
+ IL 278 278 3 278 3 1 1 90 187 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000
+ [ MATL 74 ] 65 - u - u -
+ ML 279 278 3 281 3 1 1 89 186 -0.992 -1.036 -6.727 -0.236 -0.009 -0.317 0.439
+ D 280 278 3 281 3 0 0 60 156 -8.812 -0.169 -3.204
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+ [ MATL 75 ] 110 - u - u -
+ ML 282 281 3 284 3 1 1 19 38 -8.681 -0.013 -7.335 -0.050 -0.085 -0.342 0.381
+ D 283 281 3 284 3 0 0 19 38 -6.174 -1.687 -0.566
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+ [ MATL 76 ] 111 - u - g -
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+ D 286 284 3 287 3 0 0 18 37 -6.174 -1.687 -0.566
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+ [ MATL 77 ] 112 - g - g -
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+ [ MATL 79 ] 114 - G - G -
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+ D 295 293 3 296 3 0 0 15 33 -6.174 -1.687 -0.566
+ IL 296 296 3 296 3 1 1 19 37 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000
+ [ MATL 80 ] 115 - G - G -
+ ML 297 296 3 299 3 1 1 13 31 -8.681 -0.013 -7.335 -2.020 -3.750 1.835 -3.177
+ D 298 296 3 299 3 0 0 13 32 -6.174 -1.687 -0.566
+ IL 299 299 3 299 3 1 1 18 36 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000
+ [ MATL 81 ] 116 - U - U -
+ ML 300 299 3 302 2 1 1 1 1 * 0.000 -0.669 -0.946 -1.933 1.373
+ D 301 299 3 302 2 0 0 0 0 * 0.000
+ IL 302 302 3 302 2 1 1 13 28 -1.823 -0.479 0.000 0.000 0.000 0.000
+ [ END 82 ] - - - - - -
+ E 303 302 3 -1 0 0 0 0 0
+//
+HMMER3/f [i1.1 | April 2012]
+NAME Vault
+ACC RF00006
+DESC Vault RNA
+LENG 100
+MAXL 365
+ALPH RNA
+RF yes
+MM no
+CONS yes
+CS yes
+MAP yes
+DATE Mon Apr 30 08:54:54 2012
+COM [1] /groups/eddy/home/nawrockie/notebook/12_0423_inf_final_stress_tests/wd-infernal/src/cmbuild -F Vault.cm Vault.sto
+NSEQ 75
+EFFN 6.824398
+CKSUM 2397722235
+STATS LOCAL MSV -9.1834 0.71855
+STATS LOCAL VITERBI -10.0399 0.71855
+STATS LOCAL FORWARD -3.5401 0.71855
+HMM A C G U
+ m->m m->i m->d i->m i->i d->m d->d
+ COMPO 1.60500 1.33501 1.37221 1.26440
+ 1.38629 1.38629 1.38629 1.38629
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+ 0.01103 4.51294 * 1.46634 0.26236 0.00000 *
+//
+INFERNAL1/a [1.1 | April 2012]
+NAME snR75
+ACC RF01185
+DESC Small nucleolar RNA snR75
+STATES 268
+NODES 90
+CLEN 88
+W 177
+ALPH RNA
+RF yes
+CONS yes
+MAP yes
+DATE Mon Apr 30 08:55:03 2012
+COM [1] /groups/eddy/home/nawrockie/notebook/12_0423_inf_final_stress_tests/wd-infernal/src/cmbuild -F snR75.cm snR75.sto
+COM [2] /groups/eddy/home/nawrockie/notebook/12_0423_inf_final_stress_tests/wd-infernal/src/cmcalibrate --mpi snR75.cm
+PBEGIN 0.05
+PEND 0.05
+WBETA 1e-07
+QDBBETA1 1e-07
+QDBBETA2 1e-15
+N2OMEGA 1.52588e-05
+N3OMEGA 1.52588e-05
+ELSELF -0.08926734
+NSEQ 62
+EFFN 4.939774
+CKSUM 83182668
+NULL 0.000 0.000 0.000 0.000
+GA 35.00
+TC 38.64
+NC 33.63
+EFP7GF -9.5719 0.71844
+ECMLC 0.71904 -9.37221 -0.69475 1600000 615097 0.001951
+ECMGC 0.38387 -15.89791 -4.70763 1600000 29352 0.013628
+ECMLI 0.57223 -8.93105 0.94674 1600000 341971 0.003509
+ECMGI 0.42933 -8.01800 1.88721 1600000 28115 0.014227
+CM
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+ [ END 89 ] - - - - - -
+ E 267 266 3 -1 0 0 0 0 0
+//
+HMMER3/f [i1.1 | April 2012]
+NAME snR75
+ACC RF01185
+DESC Small nucleolar RNA snR75
+LENG 88
+MAXL 177
+ALPH RNA
+RF yes
+MM no
+CONS yes
+CS yes
+MAP no
+DATE Mon Apr 30 08:55:03 2012
+COM [1] /groups/eddy/home/nawrockie/notebook/12_0423_inf_final_stress_tests/wd-infernal/src/cmbuild -F snR75.cm snR75.sto
+COM [2] /groups/eddy/home/nawrockie/notebook/12_0423_inf_final_stress_tests/wd-infernal/src/cmbuild -F snR75.cm snR75.sto
+NSEQ 62
+EFFN 4.939774
+STATS LOCAL MSV -8.8346 0.71844
+STATS LOCAL VITERBI -9.8187 0.71844
+STATS LOCAL FORWARD -3.5583 0.71844
+HMM A C G U
+ m->m m->i m->d i->m i->i d->m d->d
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+ * 0.00000 * 0.45905 0.99936 0.00000 *
+//
+INFERNAL1/a [1.1 | April 2012]
+NAME Plant_SRP
+ACC RF01855
+DESC Plant signal recognition particle RNA
+STATES 939
+NODES 200
+CLEN 305
+W 336
+ALPH RNA
+RF yes
+CONS yes
+MAP yes
+DATE Mon Apr 30 08:55:04 2012
+COM [1] /groups/eddy/home/nawrockie/notebook/12_0423_inf_final_stress_tests/wd-infernal/src/cmbuild -F Plant_SRP.cm Plant_SRP.sto
+COM [2] /groups/eddy/home/nawrockie/notebook/12_0423_inf_final_stress_tests/wd-infernal/src/cmcalibrate --mpi Plant_SRP.cm
+PBEGIN 0.05
+PEND 0.05
+WBETA 1e-07
+QDBBETA1 1e-07
+QDBBETA2 1e-15
+N2OMEGA 1.52588e-05
+N3OMEGA 1.52588e-05
+ELSELF -0.08926734
+NSEQ 64
+EFFN 2.234863
+CKSUM 2513792503
+NULL 0.000 0.000 0.000 0.000
+GA 95.00
+TC 95.05
+NC 94.99
+EFP7GF -12.1478 0.70581
+ECMLC 0.72286 -9.32098 -0.83588 1600000 553286 0.002169
+ECMGC 0.26831 -51.71669 -41.24636 1600000 6639 0.060250
+ECMLI 0.70748 -9.17856 -0.59906 1600000 519142 0.002312
+ECMGI 0.32510 -31.66828 -23.01468 1600000 6666 0.060006
+CM
+ [ ROOT 0 ] - - - - - -
+ S 0 -1 0 1 3 0 1 336 379 -5.363 -15.832 -0.036
+ IL 1 1 2 1 3 129 202 345 390 -0.610 -4.491 -1.736 0.000 0.000 0.000 0.000
+ IR 2 2 3 2 2 127 201 338 381 -1.823 -0.479 0.000 0.000 0.000 0.000
+ [ BIF 1 ] - - - - - -
+ B 3 2 3 4 131 126 200 336 379
+ [ BEGL 2 ] - - - - - -
+ S 4 3 1 5 4 0 2 70 113 -0.171 -6.895 -3.572 -5.693
+ [ MATP 3 ] 1 42 G C G C
+ MP 5 4 1 9 6 2 5 70 113 -9.060 -9.000 -0.022 -7.776 -8.056 -8.451 -3.372 -2.153 -3.378 1.001 -3.766 -3.221 0.508 -3.832 -3.510 3.162 -3.886 -0.135 0.233 -2.801 -1.381 -2.421
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+ MR 7 4 1 9 6 1 2 71 114 -7.711 -6.440 -2.103 -6.418 -0.517 -4.632 -0.321 0.786 -1.051 -0.011
+ D 8 4 1 9 6 0 0 70 113 -9.250 -7.948 -3.745 -4.427 -4.445 -0.273
+ IL 9 9 5 9 6 1 2 70 113 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000
+ IR 10 10 6 10 5 1 2 70 113 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 4 ] 2 41 c g c g
+ MP 11 10 6 15 6 2 4 68 111 -9.068 -9.007 -0.022 -7.784 -8.064 -8.459 -3.085 -3.032 -2.855 0.592 -2.145 -3.851 2.721 -2.987 -2.795 0.840 -3.606 -1.076 1.722 -3.305 -0.044 -2.061
+ ML 12 10 6 15 6 1 2 70 114 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094
+ MR 13 10 6 15 6 1 2 71 114 -7.657 -6.386 -2.295 -6.364 -0.463 -4.578 -0.047 -1.053 0.869 -0.465
+ D 14 10 6 15 6 0 0 69 113 -9.250 -7.948 -3.745 -4.427 -4.445 -0.273
+ IL 15 15 5 15 6 1 2 69 112 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000
+ IR 16 16 6 16 5 1 2 68 111 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 5 ] 3 40 C G C G
+ MP 17 16 6 21 3 2 2 66 109 -5.043 -15.513 -0.044 -3.886 -3.830 -3.689 -0.100 -2.533 -4.183 3.213 -3.287 -3.719 0.158 -4.058 -1.836 1.069 -3.987 0.470 -2.580
+ ML 18 16 6 21 3 1 1 71 114 -1.585 -1.585 -1.585 0.368 -0.385 -0.191 0.094
+ MR 19 16 6 21 3 1 1 70 113 -1.785 -1.796 -1.245 0.225 -0.929 0.599 -0.338
+ D 20 16 6 21 3 0 0 70 113 -1.624 -1.624 -1.511
+ IL 21 21 5 21 3 1 1 72 115 -0.617 -4.499 -1.719 0.000 0.000 0.000 0.000
+ IR 22 22 6 22 2 1 1 51 70 -1.823 -0.479 0.000 0.000 0.000 0.000
+ [ BIF 6 ] - - - - - -
+ B 23 22 6 24 86 0 0 49 68
+ [ BEGL 7 ] - - - - - -
+ S 24 23 1 25 4 0 0 34 52 -0.133 -6.895 -4.173 -5.384
+ [ MATP 8 ] 5 24 g u g u
+ MP 25 24 1 29 6 2 2 34 52 -9.088 -9.028 -0.021 -7.804 -8.084 -8.479 -3.529 -2.328 -3.694 1.183 -4.408 -5.040 -0.021 -3.755 -3.386 1.644 -3.901 2.937 -0.343 -4.255 -1.961 -2.419
+ ML 26 24 1 29 6 1 1 32 51 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094
+ MR 27 24 1 29 6 1 1 32 51 -7.462 -6.191 -1.736 -6.169 -0.798 -3.454 -0.156 -0.480 -0.773 0.848
+ D 28 24 1 29 6 0 0 29 48 -9.325 -8.024 -3.821 -4.503 -4.520 -0.258
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+ IR 30 30 6 30 5 1 1 33 52 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 9 ] 6 23 a u a u
+ MP 31 30 6 35 6 2 2 32 50 -9.100 -9.039 -0.021 -7.816 -8.096 -8.491 -2.896 -1.353 -2.974 2.301 -3.214 -3.844 0.911 -3.287 -3.050 2.133 -3.537 0.399 0.565 -3.100 -0.999 -1.998
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+ MR 33 30 6 35 6 1 1 30 49 -7.294 -6.023 -1.931 -6.001 -0.629 -4.214 0.022 -0.101 -0.645 0.499
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+ IR 36 36 6 36 5 1 1 31 50 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 10 ] 7 22 g c G C
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+ MR 39 36 6 41 6 1 1 28 47 -7.294 -6.023 -1.931 -6.001 -0.629 -4.214 0.016 0.347 -0.677 0.126
+ D 40 36 6 41 6 0 0 25 44 -9.427 -8.125 -3.922 -4.604 -4.622 -0.239
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+ IR 42 42 6 42 5 1 1 29 48 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 11 ] 8 21 c g C G
+ MP 43 42 6 47 6 2 2 28 46 -9.100 -9.039 -0.021 -7.816 -8.096 -8.491 -3.294 -3.215 -3.289 0.588 -2.453 -3.979 2.815 -2.410 -3.288 0.719 -3.745 -1.216 1.657 -3.491 -0.001 -2.197
+ ML 44 42 6 47 6 1 1 26 45 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094
+ MR 45 42 6 47 6 1 1 26 45 -7.294 -6.023 -1.931 -6.001 -0.629 -4.214 0.125 -0.751 0.544 -0.222
+ D 46 42 6 47 6 0 0 23 42 -9.427 -8.125 -3.922 -4.604 -4.622 -0.239
+ IL 47 47 5 47 6 1 1 27 46 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000
+ IR 48 48 6 48 5 1 1 27 46 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 12 ] 9 20 u a u a
+ MP 49 48 6 53 6 2 2 26 44 -9.100 -9.039 -0.050 -7.816 -5.866 -6.795 -2.738 -2.696 -2.839 0.891 -2.334 -3.645 1.951 -2.847 -2.585 1.218 -3.376 -0.802 2.063 -2.991 0.742 -1.837
+ ML 50 48 6 53 6 1 1 24 43 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094
+ MR 51 48 6 53 6 1 1 24 43 -7.294 -6.023 -1.484 -6.001 -0.977 -3.365 0.611 -0.685 -0.069 -0.156
+ D 52 48 6 53 6 0 0 22 40 -9.427 -8.125 -3.922 -4.604 -4.622 -0.239
+ IL 53 53 5 53 6 1 1 25 44 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000
+ IR 54 54 6 54 5 1 1 25 44 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 13 ] 10 19 c g c g
+ MP 55 54 6 59 6 2 2 24 42 -9.086 -9.026 -0.021 -7.802 -8.082 -8.477 -2.280 -2.262 -1.955 1.137 -2.201 -3.253 1.984 -2.616 -2.475 1.541 -3.016 -0.275 1.381 -2.551 0.553 -1.308
+ ML 56 54 6 59 6 1 1 22 41 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094
+ MR 57 54 6 59 6 1 1 22 41 -7.275 -6.004 -1.165 -5.982 -1.116 -4.195 0.142 -0.733 0.516 -0.209
+ D 58 54 6 59 6 0 0 20 39 -9.617 -8.315 -4.112 -4.794 -4.812 -0.207
+ IL 59 59 5 59 6 1 1 23 42 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000
+ IR 60 60 6 60 5 1 1 23 42 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 14 ] 11 18 a u a u
+ MP 61 60 6 65 6 2 2 22 40 -9.114 -9.053 -0.030 -7.830 -6.732 -8.505 -0.500 -1.052 -1.336 1.528 -1.762 -2.601 1.421 -2.111 -1.625 1.308 -2.394 -0.248 1.295 -1.893 0.091 -0.887
+ ML 62 60 6 65 6 1 1 21 40 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094
+ MR 63 60 6 65 6 1 1 21 40 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094
+ D 64 60 6 65 6 0 0 19 38 -9.617 -8.315 -4.112 -4.794 -4.812 -0.207
+ IL 65 65 5 65 6 1 1 22 40 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000
+ IR 66 66 6 66 5 1 1 21 40 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 15 ] 12 17 c g g c
+ MP 67 66 6 71 4 2 2 20 38 -6.943 -7.150 -0.053 -5.564 -1.755 -1.694 -2.118 1.115 -2.075 -2.824 1.400 -2.372 -1.087 1.249 1.046 0.051 1.224 -2.219 -0.190 -1.280
+ ML 68 66 6 71 4 1 1 21 39 -3.758 -3.940 -0.507 -2.670 0.368 -0.385 -0.191 0.094
+ MR 69 66 6 71 4 1 1 20 39 -4.917 -3.946 -1.813 -0.696 0.330 -0.561 0.174 -0.094
+ D 70 66 6 71 4 0 0 19 37 -5.106 -4.787 -2.802 -0.338
+ IL 71 71 5 71 4 1 1 22 41 -1.686 -2.369 -1.117 -4.855 0.000 0.000 0.000 0.000
+ IR 72 72 6 72 3 1 1 21 40 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000
+ [ MATL 16 ] 13 - U - U -
+ ML 73 72 6 75 3 1 1 16 35 -7.960 -0.021 -6.614 -0.847 -0.314 -1.590 1.206
+ D 74 72 6 75 3 0 0 15 34 -7.000 -2.005 -0.428
+ IL 75 75 3 75 3 1 1 20 38 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000
+ [ MATL 17 ] 14 - A - A -
+ ML 76 75 3 78 3 1 1 15 33 -7.980 -0.020 -6.634 1.071 -0.684 -1.113 -0.298
+ D 77 75 3 78 3 0 0 14 33 -6.889 -2.402 -0.318
+ IL 78 78 3 78 3 1 1 19 37 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000
+ [ MATL 18 ] 15 - A - A -
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+ D 80 78 3 81 3 0 0 13 31 -6.889 -2.402 -0.318
+ IL 81 81 3 81 3 1 1 18 36 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000
+ [ MATL 19 ] 16 - C - C -
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+ D 83 81 3 84 2 0 0 0 0 * 0.000
+ IL 84 84 3 84 2 1 1 13 28 -1.823 -0.479 0.000 0.000 0.000 0.000
+ [ END 20 ] - - - - - -
+ E 85 84 3 -1 0 0 0 0 0
+ [ BEGR 21 ] - - - - - -
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+ IL 87 87 2 87 3 1 1 31 50 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000
+ [ MATL 22 ] 25 - G - G -
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+ D 89 87 2 90 3 0 0 26 45 -6.531 -2.044 -0.421
+ IL 90 90 3 90 3 1 1 30 49 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000
+ [ MATL 23 ] 26 - U - U -
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+ D 92 90 3 93 3 0 0 25 44 -6.531 -2.044 -0.421
+ IL 93 93 3 93 3 1 1 29 48 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000
+ [ MATL 24 ] 27 - a - A -
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+ D 95 93 3 96 3 0 0 24 43 -6.531 -1.856 -0.488
+ IL 96 96 3 96 3 1 1 28 47 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000
+ [ MATL 25 ] 28 - A - A -
+ ML 97 96 3 99 5 1 1 24 43 -7.161 -0.056 -6.976 -5.687 -8.080 1.663 -2.208 -1.635 -1.760
+ D 98 96 3 99 5 0 0 23 41 -5.140 -0.984 -4.402 -2.598 -1.979
+ IL 99 99 3 99 5 1 1 25 43 -2.408 -0.496 -4.087 -5.920 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 26 ] 29 39 C G C G
+ MP 100 99 3 104 6 2 2 23 42 -9.131 -9.070 -0.021 -7.847 -8.126 -8.521 -4.252 -4.190 -3.988 -0.406 -2.735 -4.433 3.384 -3.521 -4.021 -0.169 -4.324 -2.159 1.133 -4.325 -0.417 -2.860
+ ML 101 99 3 104 6 1 1 22 40 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094
+ MR 102 99 3 104 6 1 1 22 40 -7.114 -5.843 -1.464 -5.821 -0.905 -4.035 0.295 -0.590 0.242 -0.112
+ D 103 99 3 104 6 0 0 19 38 -9.250 -7.948 -3.745 -4.427 -4.445 -0.273
+ IL 104 104 5 104 6 1 1 23 41 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000
+ IR 105 105 6 105 5 1 1 23 41 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 27 ] 30 38 C G C G
+ MP 106 105 6 110 6 2 2 21 40 -9.140 -9.079 -0.021 -7.855 -8.135 -8.530 -4.526 -4.464 -4.215 -0.677 -2.916 -4.623 3.522 -3.728 -4.261 -0.452 -4.529 -2.430 0.742 -4.585 -0.612 -3.096
+ ML 107 105 6 110 6 1 1 20 38 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094
+ MR 108 105 6 110 6 1 1 20 38 -7.016 -5.745 -1.568 -5.723 -0.857 -3.937 0.395 -0.487 -0.004 -0.037
+ D 109 105 6 110 6 0 0 18 36 -9.250 -7.948 -3.745 -4.427 -4.445 -0.273
+ IL 110 110 5 110 6 1 1 21 39 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000
+ IR 111 111 6 111 5 1 1 21 39 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 28 ] 31 37 C G C G
+ MP 112 111 6 116 6 2 2 19 38 -9.142 -9.081 -0.021 -7.858 -8.138 -8.533 -4.200 -4.163 -3.954 -0.382 -2.714 -4.408 3.359 -3.497 -3.986 -0.154 -4.299 -2.155 1.016 -4.277 0.076 -2.828
+ ML 113 111 6 116 6 1 1 19 37 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094
+ MR 114 111 6 116 6 1 1 19 37 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094
+ D 115 111 6 116 6 0 0 17 35 -9.250 -7.948 -3.745 -4.427 -4.445 -0.273
+ IL 116 116 5 116 6 1 1 19 37 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000
+ IR 117 117 6 117 5 1 1 19 37 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 29 ] 32 36 a u a u
+ MP 118 117 6 122 4 2 2 17 35 -7.037 -5.685 -0.069 -5.658 -3.025 -1.009 -3.099 2.343 -3.473 -3.997 0.577 -3.436 -3.164 2.219 -3.647 0.660 0.335 -3.240 -1.235 -2.104
+ ML 119 117 6 122 4 1 1 18 36 -3.758 -3.940 -0.507 -2.670 0.368 -0.385 -0.191 0.094
+ MR 120 117 6 122 4 1 1 18 36 -4.809 -3.838 -1.706 -0.766 0.368 -0.385 -0.191 0.094
+ D 121 117 6 122 4 0 0 17 35 -4.757 -4.438 -2.454 -0.445
+ IL 122 122 5 122 4 1 1 19 38 -1.686 -2.369 -1.117 -4.855 0.000 0.000 0.000 0.000
+ IR 123 123 6 123 3 1 1 18 36 -1.484 -0.768 -4.184 0.000 0.000 0.000 0.000
+ [ MATL 30 ] 33 - A - A -
+ ML 124 123 6 126 3 1 1 13 31 -8.047 -0.037 -5.534 1.146 -1.166 -1.221 -0.131
+ D 125 123 6 126 3 0 0 13 32 -6.436 -1.949 -0.455
+ IL 126 126 3 126 3 1 1 18 36 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000
+ [ MATL 31 ] 34 - G - G -
+ ML 127 126 3 129 2 1 1 1 1 * 0.000 -1.056 -2.477 1.617 -1.883
+ D 128 126 3 129 2 0 0 0 0 * 0.000
+ IL 129 129 3 129 2 1 1 13 28 -1.823 -0.479 0.000 0.000 0.000 0.000
+ [ END 32 ] - - - - - -
+ E 130 129 3 -1 0 0 0 0 0
+ [ BEGR 33 ] - - - - - -
+ S 131 3 1 132 3 93 164 291 320 -8.076 -0.099 -3.999
+ IL 132 132 2 132 3 94 165 293 322 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000
+ [ MATL 34 ] 43 - A - A -
+ ML 133 132 2 135 3 95 166 291 320 -7.997 -0.020 -6.651 1.621 -2.071 -1.478 -1.610
+ D 134 132 2 135 3 86 156 289 318 -6.789 -2.302 -0.344
+ IL 135 135 3 135 3 93 164 292 321 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000
+ [ MATL 35 ] 44 - u - u -
+ ML 136 135 3 138 5 95 165 290 319 -3.997 -0.285 -3.240 -7.150 -8.041 0.042 -0.342 -1.117 0.783
+ D 137 135 3 138 5 85 155 288 317 -5.337 -1.180 -4.598 -2.794 -1.520
+ IL 138 138 3 138 5 93 164 290 319 -2.621 -0.486 -3.545 -6.132 -5.406 0.000 0.000 0.000 0.000
+ [ MATP 36 ] 46 366 c g a u
+ MP 139 138 3 143 6 97 166 289 318 -9.042 -8.981 -0.031 -7.758 -6.637 -8.433 -1.674 -1.710 -1.875 1.306 -1.842 -2.283 1.503 -0.954 -1.912 1.287 -2.446 -0.045 1.324 -1.993 -0.016 0.262
+ ML 140 138 3 143 6 90 160 287 316 -7.028 -7.374 -1.239 -0.947 -7.224 -4.753 0.079 -0.129 -0.571 0.440
+ MR 141 138 3 143 6 88 158 287 316 -7.016 -5.745 -1.654 -5.723 -0.807 -3.937 0.321 -0.373 -0.244 0.182
+ D 142 138 3 143 6 82 151 284 313 -9.503 -8.202 -3.999 -2.175 -4.698 -0.572
+ IL 143 143 5 143 6 91 162 288 318 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000
+ IR 144 144 6 144 5 92 162 288 317 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 37 ] 47 365 a u a u
+ MP 145 144 6 149 6 96 164 287 316 -9.070 -9.009 -0.022 -7.785 -8.065 -8.460 -3.119 -2.523 -3.191 2.901 -3.376 -4.231 0.680 -3.395 -3.217 1.463 -3.746 -0.053 0.388 -3.459 -1.172 -0.895
+ ML 146 144 6 149 6 89 158 285 314 -6.917 -7.263 -1.315 -0.900 -7.113 -4.642 0.550 -0.230 -0.644 0.061
+ MR 147 144 6 149 6 88 157 285 314 -7.110 -5.839 -1.470 -5.818 -0.901 -4.031 0.190 -0.365 -0.391 0.400
+ D 148 144 6 149 6 81 149 282 311 -9.213 -7.911 -3.708 -4.390 -4.408 -0.281
+ IL 149 149 5 149 6 90 160 286 316 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000
+ IR 150 150 6 150 5 91 161 286 315 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 38 ] 48 364 a u a u
+ MP 151 150 6 155 6 95 162 285 314 -9.104 -9.043 -0.021 -7.820 -8.100 -8.495 -3.377 -2.459 -3.464 2.914 -3.964 -4.718 0.281 -3.651 -3.376 1.710 -3.921 0.732 0.014 -3.853 -1.621 -2.329
+ ML 152 150 6 155 6 88 157 283 312 -6.686 -7.032 -1.746 -0.669 -6.881 -4.411 0.738 -0.740 -0.213 -0.200
+ MR 153 150 6 155 6 87 156 283 312 -7.016 -5.745 -1.654 -5.723 -0.807 -3.937 0.321 -0.373 -0.244 0.182
+ D 154 150 6 155 6 80 149 280 309 -9.213 -7.911 -3.708 -4.390 -4.408 -0.281
+ IL 155 155 5 155 6 90 159 284 314 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000
+ IR 156 156 6 156 5 90 159 284 313 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 39 ] 49 363 g c g c
+ MP 157 156 6 161 6 93 161 283 312 -9.104 -9.043 -0.021 -7.820 -8.100 -8.495 -2.729 -1.847 -2.807 1.402 -3.034 -3.532 0.958 -3.179 -2.668 2.492 -3.373 0.860 0.759 -2.839 -0.839 -1.192
+ ML 158 156 6 161 6 87 156 281 310 -6.686 -7.032 -1.541 -0.777 -6.881 -4.411 0.214 -0.775 0.486 -0.226
+ MR 159 156 6 161 6 86 155 281 310 -7.016 -5.745 -1.654 -5.723 -0.807 -3.937 0.323 -0.253 -0.283 0.121
+ D 160 156 6 161 6 80 148 278 307 -9.213 -7.911 -3.708 -4.390 -4.408 -0.281
+ IL 161 161 5 161 6 89 158 282 312 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000
+ IR 162 162 6 162 5 89 158 282 311 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 40 ] 50 362 g c g c
+ MP 163 162 6 167 6 92 159 281 310 -9.111 -9.050 -0.021 -7.827 -8.106 -8.502 -3.105 -2.283 -3.130 1.505 -3.451 -3.908 0.825 -3.484 -3.266 2.569 -3.694 1.093 0.659 -3.180 -1.083 -1.744
+ ML 164 162 6 167 6 86 154 279 308 -6.618 -6.965 -1.373 -0.896 -6.814 -4.344 0.140 -0.570 0.219 0.084
+ MR 165 162 6 167 6 85 154 279 308 -7.016 -5.745 -1.654 -5.723 -0.807 -3.937 0.323 -0.253 -0.283 0.121
+ D 166 162 6 167 6 79 147 276 305 -9.213 -7.911 -3.708 -4.390 -4.408 -0.281
+ IL 167 167 5 167 6 88 156 280 310 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000
+ IR 168 168 6 168 5 88 157 280 309 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 41 ] 51 361 u a u a
+ MP 169 168 6 173 6 90 157 279 308 -9.121 -9.060 -0.021 -7.837 -8.117 -8.512 -2.157 -2.247 -2.318 1.086 -1.730 -3.159 1.784 -2.510 -1.708 1.151 -2.913 -0.614 2.122 -2.208 -0.057 -1.453
+ ML 170 168 6 173 6 85 153 277 306 -6.508 -6.854 -1.277 -0.986 -6.704 -4.233 0.422 -0.575 0.007 -0.022
+ MR 171 168 6 173 6 84 152 277 306 -7.016 -5.745 -1.654 -5.723 -0.807 -3.937 0.471 -0.457 -0.189 0.012
+ D 172 168 6 173 6 79 146 274 303 -9.213 -7.911 -3.708 -4.390 -4.408 -0.281
+ IL 173 173 5 173 6 87 155 278 308 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000
+ IR 174 174 6 174 5 87 155 278 307 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 42 ] 52 360 G C G C
+ MP 175 174 6 179 6 88 155 277 306 -9.131 -9.070 -0.021 -7.847 -8.126 -8.521 -3.516 -1.894 -3.499 1.126 -3.957 -4.090 0.455 -3.932 -2.965 3.157 -4.014 -0.225 0.285 -3.434 -1.483 -2.490
+ ML 176 174 6 179 6 84 152 275 304 -6.394 -6.741 -1.455 -0.873 -6.590 -4.120 0.554 -0.585 -0.093 -0.108
+ MR 177 174 6 179 6 83 151 275 304 -7.016 -5.745 -1.654 -5.723 -0.807 -3.937 0.323 -0.253 -0.283 0.121
+ D 178 174 6 179 6 78 146 272 301 -9.213 -7.911 -3.708 -4.390 -4.408 -0.281
+ IL 179 179 5 179 6 86 153 276 306 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000
+ IR 180 180 6 180 5 86 153 276 305 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 43 ] 53 359 g c g c
+ MP 181 180 6 185 6 87 153 275 304 -9.131 -9.070 -0.021 -7.847 -8.126 -8.521 -3.046 -2.267 -3.045 1.555 -3.393 -3.759 0.838 -3.477 -3.265 2.733 -3.673 0.297 0.655 -2.346 -1.041 -2.003
+ ML 182 180 6 185 6 83 150 273 302 -6.394 -6.741 -1.455 -0.873 -6.590 -4.120 0.655 -0.581 -0.285 -0.095
+ MR 183 180 6 185 6 82 150 273 302 -7.016 -5.745 -1.654 -5.723 -0.807 -3.937 0.323 -0.253 -0.283 0.121
+ D 184 180 6 185 6 78 145 270 299 -9.213 -7.911 -3.708 -4.390 -4.408 -0.281
+ IL 185 185 5 185 6 85 152 274 304 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000
+ IR 186 186 6 186 5 85 152 274 303 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 44 ] 54 358 u a u a
+ MP 187 186 6 191 6 85 151 273 302 -9.131 -9.070 -0.021 -7.847 -8.126 -8.521 -1.250 -1.889 -1.904 1.104 -1.444 -2.753 1.577 -2.208 -1.691 1.094 -2.531 -0.363 2.001 -1.648 0.005 -1.133
+ ML 188 186 6 191 6 82 149 271 300 -6.394 -6.741 -1.455 -0.873 -6.590 -4.120 0.186 -0.365 -0.396 0.407
+ MR 189 186 6 191 6 81 148 271 300 -7.016 -5.745 -1.654 -5.723 -0.807 -3.937 0.471 -0.457 -0.189 0.012
+ D 190 186 6 191 6 77 145 268 297 -9.213 -7.911 -3.708 -4.390 -4.408 -0.281
+ IL 191 191 5 191 6 83 150 272 302 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000
+ IR 192 192 6 192 5 83 150 272 301 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 45 ] 55 357 g c g c
+ MP 193 192 6 197 6 83 150 271 300 -6.988 -9.070 -0.030 -7.847 -8.126 -8.521 -2.110 -2.006 -2.254 1.180 -1.899 -3.061 1.290 -2.596 -2.246 2.236 -2.882 -0.069 1.208 -1.208 -0.338 -0.999
+ ML 194 192 6 197 6 80 147 269 299 -6.394 -6.741 -1.455 -0.873 -6.590 -4.120 0.295 -0.590 0.242 -0.112
+ MR 195 192 6 197 6 79 147 269 298 -7.016 -5.745 -1.654 -5.723 -0.807 -3.937 0.471 -0.457 -0.189 0.012
+ D 196 192 6 197 6 77 144 267 296 -9.213 -7.911 -3.708 -4.390 -4.408 -0.281
+ IL 197 197 5 197 6 81 148 270 300 -2.665 -2.927 -0.704 -4.583 -5.359 -5.019 0.000 0.000 0.000 0.000
+ IR 198 198 6 198 5 81 148 270 299 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 46 ] 57 356 g c G C
+ MP 199 198 6 203 4 81 148 269 298 -2.992 -7.215 -0.239 -5.630 -2.477 -2.112 -2.586 1.146 -2.756 -2.726 0.927 -2.986 -1.864 2.727 -3.192 -0.206 0.721 -1.113 -0.731 -1.746
+ ML 200 198 6 203 4 79 146 268 297 -3.867 -4.049 -0.463 -2.779 0.554 -0.585 -0.093 -0.108
+ MR 201 198 6 203 4 78 145 267 296 -4.842 -3.871 -1.738 -0.744 0.323 -0.253 -0.283 0.121
+ D 202 198 6 203 4 77 144 266 295 -4.722 -4.403 -2.419 -0.458
+ IL 203 203 5 203 4 80 147 269 298 -1.774 -3.164 -0.796 -5.649 0.000 0.000 0.000 0.000
+ IR 204 204 6 204 3 80 147 268 298 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000
+ [ MATL 47 ] 60 - a - a -
+ ML 205 204 6 207 3 79 145 266 296 -8.432 -0.086 -4.189 0.644 -1.487 0.627 -0.899
+ D 206 204 6 207 3 76 143 265 294 -5.784 -0.686 -1.472
+ IL 207 207 3 207 3 79 146 267 296 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000
+ [ MATR 48 ] - 355 - A - A
+ MR 208 207 3 210 5 78 145 265 295 -7.124 -0.060 -6.939 -5.541 -8.043 1.661 -2.036 -1.837 -1.671
+ D 209 207 3 210 5 74 141 264 293 -5.667 -0.725 -2.560 -4.725 -2.574
+ IR 210 210 3 210 5 77 144 266 295 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 49 ] 61 354 c g u a
+ MP 211 210 3 215 6 77 144 264 294 -9.131 -9.070 -0.021 -7.847 -8.126 -8.521 0.915 -2.027 0.962 1.060 -2.105 -3.021 1.308 -2.441 -2.203 1.107 -2.761 -0.388 1.073 -2.323 -0.247 -1.355
+ ML 212 210 3 215 6 74 141 263 292 -6.394 -6.741 -1.455 -0.873 -6.590 -4.120 0.655 -0.581 -0.285 -0.095
+ MR 213 210 3 215 6 74 141 263 292 -7.099 -5.828 -1.737 -5.806 -0.748 -4.020 0.633 -0.566 -0.268 -0.084
+ D 214 210 3 215 6 70 137 260 289 -9.094 -7.792 -3.589 -4.272 -4.289 -0.308
+ IL 215 215 5 215 6 76 143 264 293 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000
+ IR 216 216 6 216 5 76 143 264 293 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 50 ] 62 353 c g c g
+ MP 217 216 6 221 6 76 142 262 292 -9.131 -9.070 -0.021 -7.847 -8.126 -8.521 -2.813 -2.785 -2.913 0.778 -1.813 -3.722 2.323 -2.886 -2.915 1.187 -3.440 -0.873 1.968 -3.070 -0.111 -1.463
+ ML 218 216 6 221 6 73 139 261 290 -6.394 -6.741 -1.455 -0.873 -6.590 -4.120 0.193 0.035 -0.473 0.153
+ MR 219 216 6 221 6 73 140 261 290 -7.099 -5.828 -1.490 -5.806 -0.890 -4.020 0.633 -0.566 -0.268 -0.084
+ D 220 216 6 221 6 70 136 258 288 -9.094 -7.792 -3.589 -4.272 -4.289 -0.308
+ IL 221 221 5 221 6 74 141 262 291 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000
+ IR 222 222 6 222 5 74 141 262 291 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 51 ] 63 352 g c a u
+ MP 223 222 6 227 4 74 140 260 290 -2.411 -8.183 -0.502 -3.287 -2.113 -1.827 -2.552 1.567 -2.740 -3.080 0.999 -2.949 -2.687 2.393 -3.154 0.524 0.876 -2.118 -0.683 -1.694
+ ML 224 222 6 227 4 71 138 259 288 -2.273 -4.823 -1.584 -1.238 0.357 -0.419 -0.330 0.234
+ MR 225 222 6 227 4 72 139 259 288 -4.164 -12.591 -0.453 -2.227 0.321 -0.373 -0.244 0.182
+ D 226 222 6 227 4 69 136 258 287 -12.938 -14.208 -2.236 -0.344
+ IL 227 227 5 227 4 72 139 259 288 -3.568 -5.071 -0.581 -2.200 0.000 0.000 0.000 0.000
+ IR 228 228 6 228 3 73 139 260 289 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000
+ [ MATR 52 ] - 351 - u - a
+ MR 229 228 6 231 5 72 138 258 287 -4.445 -0.140 -6.819 -5.646 -5.798 0.151 -0.358 -0.477 0.476
+ D 230 228 6 231 5 69 135 257 286 -2.537 -0.905 -2.970 -4.662 -2.984
+ IR 231 231 3 231 5 72 138 258 288 -2.726 -0.384 -6.238 -4.405 -5.511 0.000 0.000 0.000 0.000
+ [ MATP 53 ] 65 349 u a u a
+ MP 232 231 3 236 6 72 138 257 286 -9.122 -9.061 -0.034 -6.241 -8.117 -8.512 -2.273 -2.305 -1.577 0.996 -2.168 -3.258 1.837 -2.599 -2.292 1.358 -3.013 -0.464 2.018 -2.558 0.020 -1.533
+ ML 233 231 3 236 6 68 134 256 285 -6.394 -6.741 -1.455 -0.873 -6.590 -4.120 0.277 -0.431 -0.131 0.181
+ MR 234 231 3 236 6 69 135 256 285 -7.103 -5.832 -1.484 -5.810 -0.893 -4.023 0.638 -0.570 -0.272 -0.087
+ D 235 231 3 236 6 64 130 253 282 -9.232 -7.931 -2.583 -4.410 -4.427 -0.446
+ IL 236 236 5 236 6 70 136 257 286 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000
+ IR 237 237 6 237 5 70 136 256 286 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 54 ] 66 348 u a u a
+ MP 238 237 6 242 6 70 136 255 284 -9.126 -9.065 -0.032 -7.841 -6.471 -8.516 -1.679 -1.839 -1.358 1.143 -1.815 -2.712 1.541 -1.897 -1.700 1.312 -2.497 -0.282 1.803 -1.775 0.085 -0.834
+ ML 239 237 6 242 6 67 133 254 283 -6.542 -6.888 -1.230 -1.020 -6.738 -4.267 0.254 -0.428 -0.284 0.314
+ MR 240 237 6 242 6 68 134 254 283 -7.016 -5.745 -1.654 -5.723 -0.807 -3.937 0.471 -0.457 -0.189 0.012
+ D 241 237 6 242 6 63 129 251 280 -9.094 -7.792 -3.589 -4.272 -4.289 -0.308
+ IL 242 242 5 242 6 69 135 255 284 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000
+ IR 243 243 6 243 5 69 135 255 284 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 55 ] 67 347 g c g c
+ MP 244 243 6 248 4 68 134 253 282 -2.918 -8.157 -0.370 -3.470 -1.601 -1.710 -1.551 1.196 -1.800 -2.342 1.464 -1.698 -1.529 1.531 -2.411 0.374 1.349 -1.452 -0.029 -0.816
+ ML 245 243 6 248 4 65 131 252 281 -2.699 -4.823 -1.584 -1.068 0.300 -0.407 0.031 -0.010
+ MR 246 243 6 248 4 67 133 252 281 -4.418 -12.845 -0.305 -2.801 0.160 -0.260 -0.460 0.402
+ D 247 243 6 248 4 63 129 250 279 -12.938 -14.208 -2.236 -0.344
+ IL 248 248 5 248 4 67 133 253 282 -2.137 -5.078 -0.679 -3.079 0.000 0.000 0.000 0.000
+ IR 249 249 6 249 3 68 133 253 282 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000
+ [ MATR 56 ] - 346 - c - c
+ MR 250 249 6 252 5 67 133 251 280 -3.611 -0.181 -6.899 -6.517 -5.907 -0.088 0.481 -1.175 0.288
+ D 251 249 6 252 5 62 128 250 279 -4.073 -0.728 -2.716 -4.881 -2.730
+ IR 252 252 3 252 5 67 132 251 280 -2.719 -0.386 -6.230 -4.398 -5.503 0.000 0.000 0.000 0.000
+ [ MATP 57 ] 72 344 g c g c
+ MP 253 252 3 257 6 68 133 250 279 -9.130 -9.069 -0.021 -7.846 -8.125 -8.520 -1.880 -1.948 -1.772 1.242 -1.762 -2.885 1.576 -1.987 -2.122 1.633 -2.674 0.363 1.340 -2.178 0.103 -0.870
+ ML 254 252 3 257 6 63 128 248 277 -6.394 -6.741 -1.455 -0.873 -6.590 -4.120 0.293 -0.514 0.090 0.014
+ MR 255 252 3 257 6 63 128 248 277 -7.016 -5.745 -1.654 -5.723 -0.807 -3.937 0.321 -0.373 -0.244 0.182
+ D 256 252 3 257 6 57 122 246 275 -9.229 -7.927 -2.601 -4.406 -4.424 -0.443
+ IL 257 257 5 257 6 65 130 249 279 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000
+ IR 258 258 6 258 5 65 130 249 278 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 58 ] 73 343 g c g c
+ MP 259 258 6 263 6 66 131 248 277 -9.138 -9.078 -0.021 -7.854 -8.134 -8.529 -1.626 -1.909 -2.035 1.208 -1.995 -2.857 1.493 -1.990 -1.988 1.759 -2.649 -0.135 1.445 -2.059 0.132 -0.653
+ ML 260 258 6 263 6 62 127 246 275 -6.394 -6.741 -1.455 -0.873 -6.590 -4.120 0.295 -0.590 0.242 -0.112
+ MR 261 258 6 263 6 62 126 246 275 -7.016 -5.745 -1.654 -5.723 -0.807 -3.937 0.323 -0.253 -0.283 0.121
+ D 262 258 6 263 6 57 121 243 272 -9.094 -7.792 -3.589 -4.272 -4.289 -0.308
+ IL 263 263 5 263 6 64 129 247 277 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000
+ IR 264 264 6 264 5 64 129 247 276 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 59 ] 74 342 c g u a
+ MP 265 264 6 269 6 65 129 246 275 -9.138 -9.078 -0.067 -5.109 -6.614 -8.529 -1.722 -1.885 -1.909 1.300 -1.316 -2.755 1.762 -2.211 -1.968 1.140 -2.534 -0.345 1.487 -1.320 0.289 -0.524
+ ML 266 264 6 269 6 61 126 244 273 -6.394 -6.741 -1.455 -0.873 -6.590 -4.120 0.190 -0.063 -0.466 0.236
+ MR 267 264 6 269 6 60 125 244 273 -7.016 -5.745 -1.654 -5.723 -0.807 -3.937 0.395 -0.487 -0.004 -0.037
+ D 268 264 6 269 6 56 120 241 271 -9.094 -7.792 -3.589 -4.272 -4.289 -0.308
+ IL 269 269 5 269 6 63 127 245 275 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000
+ IR 270 270 6 270 5 63 127 245 274 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 60 ] 75 341 c g g c
+ MP 271 270 6 275 6 63 127 244 273 -9.092 -9.032 -0.021 -7.808 -8.088 -8.483 -1.578 -1.381 -1.794 1.250 -1.796 -1.159 1.521 -1.852 -1.819 1.477 -2.343 -0.160 1.277 -1.072 -0.020 -0.541
+ ML 272 270 6 275 6 60 125 243 272 -6.776 -7.122 -0.965 -1.254 -6.972 -4.502 0.013 0.052 -0.596 0.370
+ MR 273 270 6 275 6 59 123 242 271 -7.123 -5.852 -1.448 -5.830 -0.914 -4.044 0.181 -0.017 -0.482 0.217
+ D 274 270 6 275 6 56 120 240 269 -9.094 -7.792 -3.589 -4.272 -4.289 -0.308
+ IL 275 275 5 275 6 61 126 244 273 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000
+ IR 276 276 6 276 5 61 125 243 272 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 61 ] 76 340 g c g c
+ MP 277 276 6 281 6 61 125 242 271 -9.138 -9.078 -0.103 -4.298 -8.134 -6.479 -2.113 -1.684 -2.098 1.325 -2.373 -2.529 1.105 -2.212 -2.369 2.370 -2.883 0.053 0.936 -1.305 -0.456 -1.314
+ ML 278 276 6 281 6 59 123 241 270 -6.394 -6.741 -1.455 -0.948 -6.590 -3.554 0.423 -0.512 -0.075 0.013
+ MR 279 276 6 281 6 58 122 240 270 -7.016 -5.745 -1.654 -5.723 -0.807 -3.937 0.321 -0.373 -0.244 0.182
+ D 280 276 6 281 6 55 119 238 268 -9.094 -7.792 -3.589 -4.272 -4.289 -0.308
+ IL 281 281 5 281 6 60 124 242 271 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000
+ IR 282 282 6 282 5 60 124 241 270 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 62 ] 77 339 c g g c
+ MP 283 282 6 287 4 59 123 240 269 -6.811 -3.468 -0.239 -4.232 -1.504 -1.429 -1.347 1.218 -1.697 -2.069 1.514 -2.049 -1.170 1.353 -2.043 -0.000 1.344 -1.835 0.313 -0.712
+ ML 284 282 6 287 4 58 122 239 269 -4.368 -1.881 -0.884 -2.853 0.168 -0.068 -0.479 0.269
+ MR 285 282 6 287 4 56 120 239 268 -4.842 -3.871 -1.738 -0.744 0.395 -0.487 -0.004 -0.037
+ D 286 282 6 287 4 55 119 238 267 -4.836 -2.663 -2.533 -0.657
+ IL 287 287 5 287 4 59 123 240 269 -1.686 -2.369 -1.117 -4.855 0.000 0.000 0.000 0.000
+ IR 288 288 6 288 3 58 122 239 268 -1.900 -0.734 -2.933 0.000 0.000 0.000 0.000
+ [ MATL 63 ] 78 - u - u -
+ ML 289 288 6 291 5 58 122 238 267 -4.106 -0.270 -5.588 -5.227 -3.936 -0.129 0.024 -0.499 0.445
+ D 290 288 6 291 5 54 117 236 266 -5.607 -0.748 -3.397 -3.065 -2.560
+ IL 291 291 3 291 5 59 123 238 267 -2.209 -0.517 -4.365 -6.197 -5.471 0.000 0.000 0.000 0.000
+ [ MATP 64 ] 82 336 c g c g
+ MP 292 291 3 296 6 62 125 237 266 -9.070 -9.009 -0.022 -7.785 -8.065 -8.460 -1.769 -1.922 -1.952 1.217 -1.194 -2.584 1.919 -2.232 -1.794 1.148 -2.292 -0.366 1.543 -2.092 0.173 -1.000
+ ML 293 291 3 296 6 55 118 235 264 -6.482 -6.828 -1.314 -0.960 -6.678 -4.208 0.111 0.186 -0.571 0.149
+ MR 294 291 3 296 6 55 118 235 264 -7.154 -5.883 -1.660 -5.861 -0.778 -4.075 0.250 -0.456 -0.057 0.164
+ D 295 291 3 296 6 49 111 233 262 -9.725 -8.423 -1.993 -4.902 -4.920 -0.560
+ IL 296 296 5 296 6 57 121 236 266 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000
+ IR 297 297 6 297 5 58 121 236 265 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 65 ] 83 335 c g c g
+ MP 298 297 6 302 6 61 123 235 264 -9.108 -9.048 -0.021 -7.824 -8.104 -8.499 -1.918 -2.069 -1.335 1.032 -1.565 -2.934 2.034 -2.334 -2.141 1.009 -2.172 -0.566 1.525 -2.237 0.726 -1.279
+ ML 299 297 6 302 6 54 117 233 262 -6.394 -6.741 -1.209 -1.064 -6.590 -4.120 0.190 -0.063 -0.466 0.236
+ MR 300 297 6 302 6 54 117 233 262 -7.114 -5.843 -1.464 -5.821 -0.905 -4.035 0.295 -0.590 0.242 -0.112
+ D 301 297 6 302 6 48 110 230 259 -9.407 -8.105 -3.902 -4.585 -2.082 -0.621
+ IL 302 302 5 302 6 56 119 234 264 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000
+ IR 303 303 6 303 5 57 120 234 263 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 66 ] 84 334 a u a u
+ MP 304 303 6 308 6 60 121 233 262 -9.125 -9.065 -0.021 -7.841 -8.121 -8.516 -1.805 -1.929 -1.986 1.560 -1.647 -2.826 1.559 -1.153 -2.045 1.221 -2.605 -0.211 1.540 -2.121 -0.031 -0.567
+ ML 305 303 6 308 6 54 116 231 260 -6.293 -6.640 -1.354 -0.962 -6.489 -4.019 0.306 -0.370 -0.261 0.208
+ MR 306 303 6 308 6 53 115 231 260 -7.239 -5.968 -1.877 -5.946 -0.660 -4.160 0.067 0.204 -0.620 0.201
+ D 307 303 6 308 6 47 109 228 257 -9.094 -7.792 -3.589 -4.272 -4.289 -0.308
+ IL 308 308 5 308 6 56 118 232 262 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000
+ IR 309 309 6 309 5 56 118 232 261 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 67 ] 85 333 c g g c
+ MP 310 309 6 314 6 59 119 231 260 -9.125 -9.065 -0.021 -7.841 -8.121 -8.516 -1.493 -1.509 -1.258 1.218 -1.682 -2.079 1.586 -2.039 -0.572 1.201 -1.915 -0.359 1.418 -1.602 0.287 -0.957
+ ML 311 309 6 314 6 53 115 229 258 -6.293 -6.640 -1.354 -0.962 -6.489 -4.019 0.495 -0.474 -0.195 -0.005
+ MR 312 309 6 314 6 53 114 229 258 -7.239 -5.968 -1.877 -5.946 -0.660 -4.160 0.180 0.135 -0.564 0.128
+ D 313 309 6 314 6 47 108 226 255 -9.094 -7.792 -3.589 -4.272 -4.289 -0.308
+ IL 314 314 5 314 6 55 117 230 260 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000
+ IR 315 315 6 315 5 55 117 230 259 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 68 ] 86 332 c g u a
+ MP 316 315 6 320 6 57 118 229 258 -9.125 -9.065 -0.070 -5.978 -5.715 -6.820 -1.164 -1.686 -0.636 1.187 -0.912 -2.162 1.530 -2.020 -1.646 1.040 -2.152 -0.377 1.520 -1.256 0.328 -0.940
+ ML 317 315 6 320 6 52 114 227 257 -6.293 -6.640 -1.354 -0.962 -6.489 -4.019 0.495 -0.474 -0.195 -0.005
+ MR 318 315 6 320 6 52 113 227 256 -7.239 -5.968 -1.877 -5.946 -0.660 -4.160 0.178 -0.403 -0.485 0.483
+ D 319 315 6 320 6 46 107 224 253 -9.094 -7.792 -3.589 -4.272 -4.289 -0.308
+ IL 320 320 5 320 6 54 116 228 258 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000
+ IR 321 321 6 321 5 55 116 228 257 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 69 ] 87 331 c g a u
+ MP 322 321 6 326 6 56 116 227 256 -4.085 -6.137 -0.127 -7.793 -8.072 -8.467 -1.617 -1.571 -1.821 1.341 -1.814 -2.613 1.467 -1.445 -1.730 1.441 -2.400 -0.005 1.323 -1.257 -0.023 -0.262
+ ML 323 321 6 326 6 52 112 226 255 -2.578 -6.842 -1.556 -1.250 -6.691 -4.221 0.228 -0.488 0.204 -0.053
+ MR 324 321 6 326 6 52 112 225 255 -7.443 -3.486 -1.261 -6.150 -1.234 -4.364 0.095 -0.257 -0.118 0.231
+ D 325 321 6 326 6 46 106 223 252 -9.234 -7.932 -2.576 -4.411 -4.429 -0.448
+ IL 326 326 5 326 6 54 114 226 255 -3.332 -2.720 -0.568 -4.656 -6.027 -5.687 0.000 0.000 0.000 0.000
+ IR 327 327 6 327 5 53 114 226 255 -2.666 -0.490 -6.177 -3.415 -5.451 0.000 0.000 0.000 0.000
+ [ MATP 70 ] 89 329 g c G C
+ MP 328 327 6 332 6 55 114 225 254 -9.134 -9.073 -0.028 -6.747 -8.129 -8.524 -3.290 -2.368 -3.252 1.196 -3.635 -3.908 0.837 -3.690 -3.486 2.960 -3.861 0.097 0.468 -2.561 -0.927 -2.258
+ ML 329 327 6 332 6 50 111 223 252 -6.293 -6.640 -1.354 -0.962 -6.489 -4.019 0.388 -0.502 0.028 -0.051
+ MR 330 327 6 332 6 50 111 223 252 -7.155 -5.884 -1.394 -5.862 -0.946 -4.076 0.148 0.120 -0.528 0.153
+ D 331 327 6 332 6 45 105 220 249 -9.094 -7.792 -3.589 -4.272 -4.289 -0.308
+ IL 332 332 5 332 6 52 113 224 253 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000
+ IR 333 333 6 333 5 52 113 224 253 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 71 ] 90 328 g c g c
+ MP 334 333 6 338 6 53 112 223 252 -9.139 -9.078 -0.028 -6.731 -8.135 -8.530 -1.898 -1.674 -2.375 1.258 -2.485 -2.627 1.215 -2.252 -2.492 2.434 -2.992 0.016 0.926 -2.447 -0.349 -1.420
+ ML 335 333 6 338 6 49 109 221 250 -6.385 -6.731 -1.222 -1.054 -6.581 -4.110 0.541 -0.579 -0.081 -0.105
+ MR 336 333 6 338 6 49 109 221 250 -7.016 -5.745 -1.654 -5.723 -0.807 -3.937 0.323 -0.253 -0.283 0.121
+ D 337 333 6 338 6 45 105 218 247 -9.094 -7.792 -3.589 -4.272 -4.289 -0.308
+ IL 338 338 5 338 6 51 111 222 251 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000
+ IR 339 339 6 339 5 51 111 222 251 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 72 ] 91 327 c g c g
+ MP 340 339 6 344 6 51 111 221 250 -9.139 -9.078 -0.030 -7.855 -6.671 -8.529 -2.404 -2.478 -2.545 0.874 -1.688 -3.372 2.201 -2.561 -2.569 0.956 -3.114 -0.742 1.516 -2.310 1.144 -1.468
+ ML 341 339 6 344 6 48 108 219 248 -6.387 -6.733 -1.219 -1.056 -6.583 -4.113 0.198 -0.079 -0.456 0.236
+ MR 342 339 6 344 6 48 108 219 248 -7.016 -5.745 -1.654 -5.723 -0.807 -3.937 0.395 -0.487 -0.004 -0.037
+ D 343 339 6 344 6 44 104 217 246 -9.094 -7.792 -3.589 -4.272 -4.289 -0.308
+ IL 344 344 5 344 6 49 109 220 249 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000
+ IR 345 345 6 345 5 49 109 220 249 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 73 ] 92 326 c g c g
+ MP 346 345 6 350 4 49 109 219 248 -2.610 -8.180 -0.336 -4.634 -1.829 -1.646 -2.014 1.120 -1.908 -2.844 1.957 -2.292 -2.062 1.122 -2.617 -0.450 1.483 -1.066 0.392 -0.763
+ ML 347 345 6 350 4 46 106 218 247 -2.499 -4.623 -1.383 -1.325 0.306 -0.370 -0.261 0.208
+ MR 348 345 6 350 4 47 107 218 247 -4.376 -12.803 -0.315 -2.759 0.564 -0.436 -0.329 -0.020
+ D 349 345 6 350 4 44 104 215 245 -12.938 -14.208 -2.236 -0.344
+ IL 350 350 5 350 4 48 107 218 247 -3.470 -4.973 -0.358 -3.352 0.000 0.000 0.000 0.000
+ IR 351 351 6 351 3 48 108 218 247 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000
+ [ MATR 74 ] - 325 - a - a
+ MR 352 351 6 354 3 47 107 217 246 -8.447 -0.148 -3.397 0.403 -0.672 -0.391 0.365
+ D 353 351 6 354 3 43 103 215 244 -6.500 -1.678 -0.564
+ IR 354 354 3 354 3 48 107 217 246 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000
+ [ MATR 75 ] - 324 - a - a
+ MR 355 354 3 357 3 48 106 216 245 -2.287 -0.349 -6.635 0.709 -0.330 -0.831 0.011
+ D 356 354 3 357 3 42 102 214 243 -2.657 -1.094 -1.423
+ IR 357 357 3 357 3 47 106 216 245 -2.734 -0.290 -4.972 0.000 0.000 0.000 0.000
+ [ MATR 76 ] - 322 - u - u
+ MR 358 357 3 360 3 47 105 214 244 -8.454 -0.017 -6.771 -0.105 0.154 -1.189 0.603
+ D 359 357 3 360 3 40 99 213 242 -6.441 -1.618 -0.593
+ IR 360 360 3 360 3 46 105 215 244 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000
+ [ MATR 77 ] - 321 - c - a
+ MR 361 360 3 363 3 46 105 213 243 -8.454 -0.033 -5.650 0.195 0.285 -0.745 0.057
+ D 362 360 3 363 3 39 98 212 241 -6.441 -1.618 -0.593
+ IR 363 363 3 363 3 45 104 214 243 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000
+ [ MATR 78 ] - 320 - A - A
+ MR 364 363 3 366 5 46 104 212 242 -7.171 -0.077 -6.987 -4.891 -8.091 1.033 -0.972 -0.417 -0.524
+ D 365 363 3 366 5 38 97 211 240 -5.455 -0.688 -3.081 -4.512 -2.361
+ IR 366 366 3 366 5 43 102 213 242 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 79 ] 94 319 G C G C
+ MP 367 366 3 371 6 47 104 211 241 -9.133 -9.072 -0.021 -7.849 -8.129 -8.524 -4.103 -2.820 -4.141 0.586 -4.607 -4.432 -0.115 -4.511 -2.340 3.464 -4.368 -0.431 -0.419 -3.959 -2.089 -3.090
+ ML 368 366 3 371 6 40 98 210 239 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094
+ MR 369 366 3 371 6 40 98 210 239 -7.195 -5.924 -1.332 -5.902 -0.986 -4.116 0.108 0.193 -0.575 0.148
+ D 370 366 3 371 6 34 91 207 236 -9.094 -7.792 -3.589 -4.272 -4.289 -0.308
+ IL 371 371 5 371 6 42 100 211 240 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000
+ IR 372 372 6 372 5 42 101 211 240 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 80 ] 95 318 G C G C
+ MP 373 372 6 377 6 45 102 209 239 -9.149 -6.890 -0.030 -7.865 -8.145 -8.540 -4.002 -2.746 -3.994 0.656 -4.516 -3.038 -0.019 -4.477 -3.995 3.392 -4.318 0.118 -0.309 -3.751 -1.977 -2.999
+ ML 374 372 6 377 6 40 97 208 237 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094
+ MR 375 372 6 377 6 39 97 208 237 -7.016 -5.745 -1.654 -5.723 -0.807 -3.937 0.321 -0.373 -0.244 0.182
+ D 376 372 6 377 6 34 91 205 234 -9.094 -7.792 -3.589 -4.272 -4.289 -0.308
+ IL 377 377 5 377 6 41 99 209 238 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000
+ IR 378 378 6 378 5 42 99 209 238 -2.466 -0.473 -5.977 -4.145 -5.250 0.000 0.000 0.000 0.000
+ [ MATP 81 ] 96 316 g c g c
+ MP 379 378 6 383 6 44 100 207 237 -9.149 -9.089 -0.059 -7.865 -5.079 -8.540 -1.685 -1.336 -1.612 1.252 -1.899 -2.039 1.332 -2.228 -1.942 1.705 -2.086 0.369 1.297 -1.759 0.046 -0.968
+ ML 380 378 6 383 6 39 96 206 235 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094
+ MR 381 378 6 383 6 39 96 206 235 -7.016 -5.745 -1.654 -5.723 -0.807 -3.937 0.321 -0.373 -0.244 0.182
+ D 382 378 6 383 6 33 90 203 232 -9.094 -7.792 -3.589 -4.272 -4.289 -0.308
+ IL 383 383 5 383 6 41 98 207 236 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000
+ IR 384 384 6 384 5 41 98 207 236 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 82 ] 97 315 c g C G
+ MP 385 384 6 389 6 43 98 205 235 -9.111 -9.051 -0.021 -7.827 -8.107 -8.502 -2.593 -2.616 -2.605 0.808 -2.251 -3.515 2.413 -2.756 -2.728 0.974 -2.324 -0.822 1.694 -2.867 0.490 -1.605
+ ML 386 384 6 389 6 38 95 204 233 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094
+ MR 387 384 6 389 6 38 95 204 233 -7.399 -6.128 -1.069 -6.106 -1.190 -4.320 0.034 -0.853 0.688 -0.303
+ D 388 384 6 389 6 33 89 201 230 -9.094 -7.792 -3.589 -4.272 -4.289 -0.308
+ IL 389 389 5 389 6 40 96 205 234 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000
+ IR 390 390 6 390 5 40 96 205 234 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 83 ] 98 314 c g c g
+ MP 391 390 6 395 6 41 96 203 233 -9.149 -9.089 -0.020 -7.865 -8.145 -8.540 -2.134 -2.253 -2.299 0.966 -0.723 -3.143 1.990 -2.484 -2.334 1.037 -2.413 -0.497 1.736 -2.445 0.589 -1.438
+ ML 392 390 6 395 6 37 93 202 231 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094
+ MR 393 390 6 395 6 37 93 202 231 -7.016 -5.745 -1.654 -5.723 -0.807 -3.937 0.471 -0.457 -0.189 0.012
+ D 394 390 6 395 6 32 88 199 228 -9.094 -7.792 -3.589 -4.272 -4.289 -0.308
+ IL 395 395 5 395 6 39 95 203 232 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000
+ IR 396 396 6 396 5 39 95 203 232 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 84 ] 99 313 c g u a
+ MP 397 396 6 401 6 39 94 201 231 -6.864 -9.089 -0.031 -7.865 -8.145 -8.540 -1.638 -1.792 -1.833 1.134 -1.785 -2.219 1.711 -1.878 -1.888 1.129 -2.449 -0.214 1.640 -1.205 0.257 -0.701
+ ML 398 396 6 401 6 36 92 200 229 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094
+ MR 399 396 6 401 6 35 91 200 229 -7.016 -5.745 -1.654 -5.723 -0.807 -3.937 0.471 -0.457 -0.189 0.012
+ D 400 396 6 401 6 32 88 197 226 -9.094 -7.792 -3.589 -4.272 -4.289 -0.308
+ IL 401 401 5 401 6 37 93 201 230 -2.676 -2.938 -0.697 -4.594 -5.370 -5.030 0.000 0.000 0.000 0.000
+ IR 402 402 6 402 5 37 93 201 230 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 85 ] 101 312 g c g c
+ MP 403 402 6 407 6 37 93 199 229 -9.149 -9.089 -0.041 -7.865 -5.855 -8.540 -2.889 -2.205 -2.923 1.459 -3.231 -3.637 0.857 -3.347 -3.115 2.639 -3.536 0.660 0.658 -2.347 -0.967 -1.423
+ ML 404 402 6 407 6 35 91 198 227 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094
+ MR 405 402 6 407 6 34 90 198 227 -7.016 -5.745 -1.654 -5.723 -0.807 -3.937 0.323 -0.253 -0.283 0.121
+ D 406 402 6 407 6 32 87 196 225 -9.094 -7.792 -3.589 -4.272 -4.289 -0.308
+ IL 407 407 5 407 6 36 92 199 228 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000
+ IR 408 408 6 408 5 36 91 199 228 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 86 ] 102 311 c g g c
+ MP 409 408 6 413 4 35 91 197 227 -7.005 -4.996 -0.351 -2.501 -1.348 -1.464 -1.507 1.311 -1.746 -2.576 1.443 -1.879 -1.808 1.385 -2.111 0.114 1.372 -1.091 0.006 -0.551
+ ML 410 408 6 413 4 34 90 197 226 -3.758 -3.940 -0.507 -2.670 0.368 -0.385 -0.191 0.094
+ MR 411 408 6 413 4 33 88 196 226 -5.086 -3.706 -1.688 -0.777 0.522 -0.600 -0.088 -0.055
+ D 412 408 6 413 4 31 87 195 224 -4.611 -4.292 -2.308 -0.502
+ IL 413 413 5 413 4 35 91 198 227 -1.686 -2.369 -1.117 -4.855 0.000 0.000 0.000 0.000
+ IR 414 414 6 414 3 35 90 197 227 -1.532 -0.756 -4.004 0.000 0.000 0.000 0.000
+ [ MATL 87 ] 103 - u - u -
+ ML 415 414 6 417 5 34 89 196 225 -6.960 -0.169 -5.224 -4.258 -5.426 0.078 -0.612 -0.367 0.599
+ D 416 414 6 417 5 31 86 194 223 -5.919 -1.580 -5.181 -2.952 -1.023
+ IL 417 417 3 417 5 35 90 196 225 -2.408 -0.496 -4.087 -5.920 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 88 ] 104 309 g c g c
+ MP 418 417 3 422 4 34 89 195 224 -6.655 -4.158 -0.213 -3.807 -2.215 -1.623 -2.347 1.379 -2.424 -3.110 1.340 -2.697 -1.985 2.266 -2.942 0.059 1.030 -1.737 -0.419 -1.503
+ ML 419 417 3 422 4 32 87 194 223 -3.862 -4.045 -0.465 -2.774 0.193 -0.365 -0.388 0.397
+ MR 420 417 3 422 4 30 86 193 223 -3.678 -4.265 -1.760 -0.800 -0.035 -0.190 -0.697 0.614
+ D 421 417 3 422 4 30 85 193 222 -5.643 -1.501 -2.184 -1.298
+ IL 422 422 5 422 4 34 88 195 224 -1.769 -2.453 -1.025 -4.938 0.000 0.000 0.000 0.000
+ IR 423 423 6 423 3 33 88 194 223 -1.854 -0.570 -4.325 0.000 0.000 0.000 0.000
+ [ MATL 89 ] 106 - u - u -
+ ML 424 423 6 426 5 33 87 192 222 -5.623 -0.059 -6.888 -7.100 -7.992 -0.212 -0.639 0.030 0.559
+ D 425 423 6 426 5 28 83 191 220 -5.548 -0.544 -4.810 -3.006 -2.914
+ IL 426 426 3 426 5 31 86 193 222 -2.459 -0.476 -4.138 -5.970 -5.244 0.000 0.000 0.000 0.000
+ [ MATP 90 ] 108 307 c g g c
+ MP 427 426 3 431 6 33 86 191 221 -9.149 -9.089 -0.020 -7.865 -8.145 -8.540 -1.573 -1.221 -1.778 1.168 -1.568 -2.322 1.500 -2.115 -1.825 1.397 -1.775 0.244 1.406 -1.261 0.201 -1.027
+ ML 428 426 3 431 6 29 83 190 219 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094
+ MR 429 426 3 431 6 28 82 190 219 -7.016 -5.745 -1.654 -5.723 -0.807 -3.937 0.321 -0.373 -0.244 0.182
+ D 430 426 3 431 6 24 78 187 216 -9.094 -7.792 -3.589 -4.272 -4.289 -0.308
+ IL 431 431 5 431 6 30 85 191 220 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000
+ IR 432 432 6 432 5 30 85 191 220 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 91 ] 109 306 u a u a
+ MP 433 432 6 437 6 31 84 189 219 -9.149 -9.089 -0.020 -7.865 -8.145 -8.540 -1.893 -2.004 -1.900 1.188 -1.379 -2.910 1.565 -2.350 -1.863 1.440 -2.688 0.099 1.738 -2.202 0.027 -1.070
+ ML 434 432 6 437 6 28 82 188 217 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094
+ MR 435 432 6 437 6 26 80 188 217 -7.016 -5.745 -1.654 -5.723 -0.807 -3.937 0.323 -0.253 -0.283 0.121
+ D 436 432 6 437 6 24 78 185 215 -9.094 -7.792 -3.589 -4.272 -4.289 -0.308
+ IL 437 437 5 437 6 29 83 189 218 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000
+ IR 438 438 6 438 5 29 83 189 218 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 92 ] 110 305 g c g c
+ MP 439 438 6 443 4 29 82 187 217 -7.055 -3.030 -0.234 -5.676 -2.367 -1.533 -2.482 1.340 -2.674 -2.406 1.021 -2.888 -2.613 2.498 -3.088 0.243 0.833 -1.345 -0.663 -1.642
+ ML 440 438 6 443 4 27 81 187 216 -3.758 -3.940 -0.507 -2.670 0.368 -0.385 -0.191 0.094
+ MR 441 438 6 443 4 25 79 186 215 -4.842 -3.871 -1.738 -0.744 0.321 -0.373 -0.244 0.182
+ D 442 438 6 443 4 23 77 185 214 -4.611 -4.292 -2.308 -0.502
+ IL 443 443 5 443 4 28 82 188 217 -1.686 -2.369 -1.117 -4.855 0.000 0.000 0.000 0.000
+ IR 444 444 6 444 3 28 81 187 216 -1.786 -0.588 -4.486 0.000 0.000 0.000 0.000
+ [ MATL 93 ] 111 - c - c -
+ ML 445 444 6 447 5 27 80 185 214 -7.181 -0.037 -6.997 -7.209 -8.100 -0.530 0.941 -1.251 -0.048
+ D 446 444 6 447 5 23 76 184 213 -5.024 -0.814 -4.285 -2.660 -2.389
+ IL 447 447 3 447 5 26 80 185 214 -2.408 -0.496 -4.087 -5.920 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 94 ] 112 303 c g c g
+ MP 448 447 3 452 6 26 80 184 213 -9.152 -9.091 -0.033 -6.270 -8.147 -8.542 -2.146 -2.245 0.165 0.927 -2.079 -3.124 1.861 -2.509 -2.352 1.046 -2.899 -0.436 1.317 -2.446 1.142 -1.462
+ ML 449 447 3 452 6 24 77 183 212 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094
+ MR 450 447 3 452 6 22 76 182 211 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094
+ D 451 447 3 452 6 20 73 180 209 -9.094 -7.792 -3.589 -4.272 -4.289 -0.308
+ IL 452 452 5 452 6 25 78 184 213 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000
+ IR 453 453 6 453 5 25 78 183 212 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 95 ] 113 302 a u a u
+ MP 454 453 6 458 4 24 78 182 211 -2.681 -7.237 -0.443 -3.295 -1.540 -1.480 -1.742 1.636 -1.621 -2.569 1.441 -1.334 -1.347 1.080 -2.355 -0.091 1.374 -1.419 0.023 -0.600
+ ML 455 453 6 458 4 23 76 181 210 -2.744 -4.063 -0.629 -2.792 0.167 -0.367 -0.416 0.435
+ MR 456 453 6 458 4 21 74 179 208 -4.809 -3.838 -1.706 -0.766 0.368 -0.385 -0.191 0.094
+ D 457 453 6 458 4 19 72 178 207 -4.611 -4.292 -2.308 -0.502
+ IL 458 458 5 458 4 23 76 183 212 -0.912 -4.027 -1.930 -2.787 0.000 0.000 0.000 0.000
+ IR 459 459 6 459 3 24 77 177 198 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000
+ [ MATL 96 ] 126 - u - u -
+ ML 460 459 6 462 3 24 77 174 195 -7.822 -0.030 -5.978 0.180 -0.330 -0.674 0.531
+ D 461 459 6 462 3 19 71 173 193 -7.561 -0.753 -1.317
+ IL 462 462 3 462 3 23 76 176 197 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000
+ [ MATL 97 ] 127 - u - u -
+ ML 463 462 3 465 3 24 76 173 194 -8.015 -0.020 -6.669 0.189 -0.543 -0.759 0.663
+ D 464 462 3 465 3 17 68 172 192 -6.673 -2.017 -0.428
+ IL 465 465 3 465 3 22 75 175 196 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000
+ [ MATL 98 ] 128 - u - u -
+ ML 466 465 3 468 3 23 75 172 193 -8.021 -0.020 -6.675 -0.025 -0.736 -0.886 0.907
+ D 467 465 3 468 3 16 67 171 191 -6.633 -1.097 -0.937
+ IL 468 468 3 468 3 21 74 174 195 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000
+ [ MATL 99 ] 129 - u - u -
+ ML 469 468 3 471 5 23 75 171 192 -7.186 -0.050 -7.001 -5.971 -8.105 -0.128 -0.904 0.199 0.488
+ D 470 468 3 471 5 15 65 170 190 -4.993 -0.837 -4.255 -2.630 -2.359
+ IL 471 471 3 471 5 20 71 172 192 -2.408 -0.496 -4.087 -5.920 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 100 ] 130 301 c g c g
+ MP 472 471 3 476 6 24 75 170 191 -9.145 -9.085 -0.021 -7.861 -8.141 -8.536 -1.522 -1.508 -1.289 1.168 -1.365 -0.710 1.812 -1.769 -1.784 1.113 -2.355 -0.390 1.337 -1.470 0.047 -0.982
+ ML 473 471 3 476 6 17 67 169 189 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094
+ MR 474 471 3 476 6 17 67 169 189 -7.063 -5.792 -1.480 -5.770 -0.904 -3.983 0.257 -0.095 -0.389 0.144
+ D 475 471 3 476 6 13 60 166 187 -9.094 -7.792 -3.589 -4.272 -4.289 -0.308
+ IL 476 476 5 476 6 19 70 170 190 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000
+ IR 477 477 6 477 5 19 70 170 190 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 101 ] 131 300 c g c g
+ MP 478 477 6 482 6 24 73 168 189 -9.152 -9.091 -0.020 -7.868 -8.147 -8.542 -2.963 -2.982 -3.017 0.499 -2.377 -3.747 2.012 -2.954 -3.040 0.683 -3.527 -1.161 1.686 -3.203 1.877 -0.947
+ ML 479 477 6 482 6 17 66 167 187 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094
+ MR 480 477 6 482 6 17 66 167 187 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094
+ D 481 477 6 482 6 12 59 164 185 -9.094 -7.792 -3.589 -4.272 -4.289 -0.308
+ IL 482 482 5 482 6 18 69 168 188 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000
+ IR 483 483 6 483 5 19 69 168 188 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 102 ] 132 299 g c g c
+ MP 484 483 6 488 6 23 72 166 187 -9.152 -9.091 -0.020 -7.868 -8.147 -8.542 -2.855 -2.172 -2.894 1.323 -3.224 -3.085 0.823 -3.333 -3.087 2.730 -2.684 0.644 0.574 -2.888 -0.978 -1.692
+ ML 485 483 6 488 6 16 65 165 185 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094
+ MR 486 483 6 488 6 16 65 165 185 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094
+ D 487 483 6 488 6 12 58 162 183 -9.094 -7.792 -3.589 -4.272 -4.289 -0.308
+ IL 488 488 5 488 6 18 68 166 186 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000
+ IR 489 489 6 489 5 18 68 166 186 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 103 ] 133 298 G C G C
+ MP 490 489 6 494 6 23 70 164 185 -9.152 -9.091 -0.020 -7.868 -8.147 -8.542 -3.757 -1.853 -3.739 1.122 -4.410 -4.308 0.110 -4.190 -3.811 3.208 -4.185 0.476 -0.161 -3.671 -1.842 -2.692
+ ML 491 489 6 494 6 16 64 163 183 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094
+ MR 492 489 6 494 6 16 64 163 183 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094
+ D 493 489 6 494 6 12 58 160 181 -9.094 -7.792 -3.589 -4.272 -4.289 -0.308
+ IL 494 494 5 494 6 18 67 164 184 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000
+ IR 495 495 6 495 5 18 67 164 184 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 104 ] 134 297 c g C G
+ MP 496 495 6 500 6 22 69 162 183 -9.152 -9.091 -0.020 -7.868 -8.147 -8.542 -1.813 -2.257 -2.309 0.897 -1.527 -3.147 2.510 -2.527 -2.350 0.913 -2.144 -0.436 1.315 -2.452 0.053 -1.472
+ ML 497 495 6 500 6 16 63 161 181 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094
+ MR 498 495 6 500 6 15 63 161 181 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094
+ D 499 495 6 500 6 11 57 158 179 -9.094 -7.792 -3.589 -4.272 -4.289 -0.308
+ IL 500 500 5 500 6 17 66 162 182 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000
+ IR 501 501 6 501 5 17 66 162 182 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 105 ] 135 296 c g C G
+ MP 502 501 6 506 6 21 67 160 181 -9.152 -9.091 -0.020 -7.868 -8.147 -8.542 -3.041 -2.994 -3.114 0.645 -1.895 -3.897 2.694 -3.009 -3.103 0.849 -3.612 -0.504 1.496 -3.284 0.351 -2.045
+ ML 503 501 6 506 6 15 62 159 179 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094
+ MR 504 501 6 506 6 15 62 159 179 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094
+ D 505 501 6 506 6 11 57 156 177 -9.094 -7.792 -3.589 -4.272 -4.289 -0.308
+ IL 506 506 5 506 6 17 64 160 180 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000
+ IR 507 507 6 507 5 17 64 160 180 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 106 ] 136 295 c g c g
+ MP 508 507 6 512 6 19 65 158 179 -7.149 -9.091 -0.028 -7.868 -8.147 -8.542 -3.028 -3.018 -3.085 0.557 -2.406 -3.836 2.240 -2.987 -3.090 0.742 -3.585 -1.116 2.048 -3.267 1.086 -1.472
+ ML 509 507 6 512 6 14 61 157 177 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094
+ MR 510 507 6 512 6 15 61 157 177 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094
+ D 511 507 6 512 6 11 56 154 175 -9.094 -7.792 -3.589 -4.272 -3.607 -0.364
+ IL 512 512 5 512 6 16 63 158 178 -2.655 -2.917 -0.710 -4.573 -5.349 -5.009 0.000 0.000 0.000 0.000
+ IR 513 513 6 513 5 16 63 157 178 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 107 ] 138 294 G C G C
+ MP 514 513 6 518 6 18 63 156 177 -9.152 -9.091 -0.020 -7.868 -8.147 -8.542 -4.556 -2.988 -4.625 0.375 -5.314 -4.690 -0.625 -4.982 -4.272 3.572 -4.621 -0.094 -0.923 -4.338 -2.649 -3.513
+ ML 515 513 6 518 6 13 59 155 175 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094
+ MR 516 513 6 518 6 14 60 155 175 -7.019 -5.748 -1.656 -5.726 -0.805 -3.939 0.319 -0.242 -0.290 0.123
+ D 517 513 6 518 6 10 55 152 173 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319
+ IL 518 518 5 518 6 15 61 156 176 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000
+ IR 519 519 6 519 5 15 61 156 176 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 108 ] 139 293 c a c a
+ MP 520 519 6 524 4 16 61 154 175 -6.969 -5.901 -0.096 -4.668 -4.158 -4.255 -3.846 -0.655 2.920 -4.226 1.687 -3.372 -3.912 -0.530 -4.188 -2.475 0.814 -4.214 0.380 -2.796
+ ML 521 519 6 524 4 12 58 153 174 -2.408 -4.532 -1.293 -1.473 0.368 -0.385 -0.191 0.094
+ MR 522 519 6 524 4 13 59 153 174 -4.170 -12.597 -0.370 -2.553 0.478 -0.462 -0.191 0.007
+ D 523 519 6 524 4 10 55 151 172 -12.737 -14.007 -2.036 -0.404
+ IL 524 524 5 524 4 13 59 153 174 -2.817 -4.319 -0.613 -2.698 0.000 0.000 0.000 0.000
+ IR 525 525 6 525 3 14 60 154 174 -1.988 -0.526 -4.226 0.000 0.000 0.000 0.000
+ [ MATR 109 ] - 291 - a - A
+ MR 526 525 6 528 3 15 60 152 172 -8.459 -0.017 -6.777 0.983 -0.514 -1.122 -0.211
+ D 527 525 6 528 3 10 54 150 171 -6.390 -1.568 -0.620
+ IR 528 528 3 528 3 14 59 153 173 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000
+ [ MATR 110 ] - 290 - U - U
+ MR 529 528 3 531 3 14 59 151 171 -8.459 -0.017 -6.777 -1.444 -1.295 -2.182 1.587
+ D 530 528 3 531 3 9 53 150 170 -6.390 -1.568 -0.620
+ IR 531 531 3 531 3 13 58 152 172 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000
+ [ MATR 111 ] - 289 - A - A
+ MR 532 531 3 534 5 14 58 150 170 -7.191 -0.042 -7.007 -6.581 -8.111 1.763 -2.598 -2.208 -2.163
+ D 533 531 3 534 5 9 52 149 169 -5.352 -0.707 -2.978 -4.409 -2.404
+ IR 534 534 3 534 5 12 56 150 171 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 112 ] 140 288 C G C G
+ MP 535 534 3 539 6 14 57 149 169 -9.152 -9.091 -0.020 -7.868 -8.147 -8.542 -4.783 -4.709 -4.433 -0.921 -3.101 -4.814 3.617 -3.935 -4.491 -0.712 -4.726 -2.660 0.388 -4.836 -0.814 -3.323
+ ML 536 534 3 539 6 10 53 148 169 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094
+ MR 537 534 3 539 6 9 51 148 168 -7.019 -5.748 -1.656 -5.726 -0.805 -3.939 0.393 -0.492 0.005 -0.041
+ D 538 534 3 539 6 7 48 146 167 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319
+ IL 539 539 5 539 6 11 55 149 169 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000
+ IR 540 540 6 540 5 11 55 148 169 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 113 ] 141 287 C G C G
+ MP 541 540 6 545 4 12 56 147 167 -7.061 -7.268 -0.049 -5.683 -4.783 -4.709 -4.433 -0.921 -3.101 -4.814 3.617 -3.935 -4.491 -0.712 -4.726 -2.660 0.388 -4.836 -0.814 -3.323
+ ML 542 540 6 545 4 9 52 147 168 -3.758 -3.940 -0.507 -2.670 0.368 -0.385 -0.191 0.094
+ MR 543 540 6 545 4 8 49 147 167 -4.845 -3.874 -1.741 -0.742 0.393 -0.492 0.005 -0.041
+ D 544 540 6 545 4 7 47 146 166 -4.568 -4.250 -2.265 -0.520
+ IL 545 545 5 545 4 11 54 148 169 -1.686 -2.369 -1.117 -4.855 0.000 0.000 0.000 0.000
+ IR 546 546 6 546 3 10 54 148 168 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000
+ [ MATL 114 ] 142 - g - a -
+ ML 547 546 6 549 5 12 54 145 165 -7.186 -0.037 -7.001 -7.214 -8.105 0.260 -0.983 0.347 0.036
+ D 548 546 6 549 5 7 46 144 164 -4.993 -0.837 -4.255 -2.435 -2.542
+ IL 549 549 3 549 5 9 51 145 165 -2.408 -0.496 -4.087 -5.920 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 115 ] 143 286 u a u a
+ MP 550 549 3 554 6 13 54 144 164 -9.152 -9.091 -0.020 -7.868 -8.147 -8.542 -1.252 -1.950 -1.965 1.079 -1.181 -2.814 1.745 -2.249 -1.285 1.136 -2.587 -0.505 1.867 -2.107 0.007 -1.181
+ ML 551 549 3 554 6 8 48 142 163 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094
+ MR 552 549 3 554 6 8 47 142 162 -7.019 -5.748 -1.656 -5.726 -0.805 -3.939 0.478 -0.462 -0.191 0.007
+ D 553 549 3 554 6 5 42 140 160 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319
+ IL 554 554 5 554 6 9 50 144 164 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000
+ IR 555 555 6 555 5 9 50 143 163 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 116 ] 144 285 U A u a
+ MP 556 555 6 560 6 12 53 142 162 -9.152 -9.091 -0.020 -7.868 -8.147 -8.542 -3.932 -3.879 -3.776 -0.154 -2.680 -4.315 1.808 -3.407 -3.798 0.092 -4.168 -1.880 3.088 -4.055 -0.143 -2.654
+ ML 557 555 6 560 6 8 47 140 161 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094
+ MR 558 555 6 560 6 8 46 140 160 -7.019 -5.748 -1.656 -5.726 -0.805 -3.939 0.478 -0.462 -0.191 0.007
+ D 559 555 6 560 6 5 41 138 158 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319
+ IL 560 560 5 560 6 9 49 142 162 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000
+ IR 561 561 6 561 5 9 49 141 161 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 117 ] 145 284 C G C G
+ MP 562 561 6 566 6 12 51 140 160 -9.152 -9.091 -0.020 -7.868 -8.147 -8.542 -4.209 -4.088 -4.004 -0.299 -2.833 -4.509 3.382 -3.588 -4.024 0.200 -4.357 -2.002 0.944 -4.316 -0.509 -2.867
+ ML 563 561 6 566 6 8 45 138 159 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094
+ MR 564 561 6 566 6 7 45 138 158 -7.019 -5.748 -1.656 -5.726 -0.805 -3.939 0.393 -0.492 0.005 -0.041
+ D 565 561 6 566 6 4 40 136 156 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319
+ IL 566 566 5 566 6 8 48 140 160 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000
+ IR 567 567 6 567 5 8 48 139 159 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 118 ] 146 283 C G C G
+ MP 568 567 6 572 6 10 49 138 158 -9.152 -9.091 -0.033 -7.868 -6.357 -8.542 -3.978 -3.923 -3.847 -0.206 -2.783 -4.403 3.351 -2.055 -3.867 0.011 -4.236 -1.923 0.987 -4.123 -0.482 -2.747
+ ML 569 567 6 572 6 7 44 137 157 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094
+ MR 570 567 6 572 6 7 44 136 157 -7.019 -5.748 -1.656 -5.726 -0.805 -3.939 0.393 -0.492 0.005 -0.041
+ D 571 567 6 572 6 4 40 134 154 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319
+ IL 572 572 5 572 6 8 47 138 158 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000
+ IR 573 573 6 573 5 8 47 137 157 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 119 ] 147 282 A U A U
+ MP 574 573 6 578 4 9 48 136 156 -6.940 -8.185 -0.077 -4.639 -3.673 -2.689 -3.732 3.200 -4.201 -5.099 0.111 -3.842 -3.613 1.530 -4.165 -0.178 -0.226 -4.237 -1.823 -2.561
+ ML 575 573 6 578 4 6 42 135 155 -2.408 -4.532 -1.293 -1.473 0.368 -0.385 -0.191 0.094
+ MR 576 573 6 578 4 6 43 135 155 -4.457 -12.884 -0.657 -1.643 0.135 -0.371 -0.452 0.483
+ D 577 573 6 578 4 4 39 133 153 -12.737 -14.007 -2.036 -0.404
+ IL 578 578 5 578 4 7 44 135 156 -2.817 -4.319 -0.613 -2.698 0.000 0.000 0.000 0.000
+ IR 579 579 6 579 3 7 46 136 156 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000
+ [ MATR 120 ] - 281 - G - G
+ MR 580 579 6 582 5 8 47 134 154 -7.166 -0.043 -6.981 -6.555 -8.085 -1.756 -3.003 1.761 -2.390
+ D 581 579 6 582 5 4 39 133 153 -5.483 -0.630 -3.109 -4.540 -2.535
+ IR 582 582 3 582 5 6 44 134 154 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 121 ] 148 280 c g a a
+ MP 583 582 3 587 6 9 47 133 153 -9.152 -9.091 -0.020 -7.868 -8.147 -8.542 1.130 -2.011 0.695 1.132 -2.120 -3.022 1.266 -2.444 -2.195 1.119 -2.757 -0.366 1.054 -2.315 -0.273 -1.350
+ ML 584 582 3 587 6 5 40 131 152 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094
+ MR 585 582 3 587 6 5 40 131 151 -7.019 -5.748 -1.656 -5.726 -0.805 -3.939 0.478 -0.462 -0.191 0.007
+ D 586 582 3 587 6 2 34 129 149 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319
+ IL 587 587 5 587 6 6 42 133 153 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000
+ IR 588 588 6 588 5 6 43 132 152 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 122 ] 149 279 G C g c
+ MP 589 588 6 593 6 9 46 131 151 -9.152 -9.091 -0.020 -7.868 -8.147 -8.542 -3.350 -1.816 -2.195 1.212 -3.872 -4.019 0.555 -3.778 -3.540 3.069 -3.919 -0.054 0.278 -3.285 -1.370 -2.296
+ ML 590 588 6 593 6 5 40 129 150 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094
+ MR 591 588 6 593 6 5 39 129 149 -7.019 -5.748 -1.656 -5.726 -0.805 -3.939 0.319 -0.242 -0.290 0.123
+ D 592 588 6 593 6 2 33 127 147 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319
+ IL 593 593 5 593 6 6 42 131 151 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000
+ IR 594 594 6 594 5 6 42 130 150 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 123 ] 150 278 c g c g
+ MP 595 594 6 599 6 9 45 129 149 -9.152 -9.091 -0.020 -7.868 -8.147 -8.542 -2.845 -2.794 -2.941 0.842 -2.396 -3.746 2.267 -2.920 -2.946 1.101 -3.468 -0.870 2.043 -3.096 -0.100 -0.998
+ ML 596 594 6 599 6 5 39 127 148 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094
+ MR 597 594 6 599 6 5 38 127 147 -7.019 -5.748 -1.656 -5.726 -0.805 -3.939 0.393 -0.492 0.005 -0.041
+ D 598 594 6 599 6 2 33 125 145 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319
+ IL 599 599 5 599 6 6 41 129 149 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000
+ IR 600 600 6 600 5 6 41 128 148 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 124 ] 151 277 c g c g
+ MP 601 600 6 605 6 9 43 127 147 -9.152 -9.091 -0.020 -7.868 -8.147 -8.542 -2.308 -2.353 -2.073 1.174 -2.177 -3.298 1.879 -2.618 -2.494 1.150 -3.045 -0.352 1.853 -2.598 0.577 -1.419
+ ML 602 600 6 605 6 5 38 125 146 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094
+ MR 603 600 6 605 6 5 38 125 145 -7.019 -5.748 -1.656 -5.726 -0.805 -3.939 0.393 -0.492 0.005 -0.041
+ D 604 600 6 605 6 2 32 123 143 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319
+ IL 605 605 5 605 6 5 40 127 147 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000
+ IR 606 606 6 606 5 6 40 126 146 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 125 ] 152 276 g c g c
+ MP 607 606 6 611 6 8 41 125 145 -4.529 -6.572 -0.096 -7.868 -8.147 -8.542 -2.853 -2.327 -2.364 1.273 -2.968 -3.652 1.384 -3.219 -3.059 2.508 -3.516 0.219 0.982 -2.936 -0.513 -1.953
+ ML 608 606 6 611 6 4 37 123 143 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094
+ MR 609 606 6 611 6 4 37 123 143 -7.019 -5.748 -1.656 -5.726 -0.805 -3.939 0.317 -0.372 -0.249 0.189
+ D 610 606 6 611 6 1 31 121 141 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319
+ IL 611 611 5 611 6 5 39 124 144 -3.086 -3.349 -0.491 -5.004 -5.780 -5.440 0.000 0.000 0.000 0.000
+ IR 612 612 6 612 5 5 39 124 144 -2.483 -0.467 -5.995 -4.162 -5.268 0.000 0.000 0.000 0.000
+ [ MATP 126 ] 154 274 g c g c
+ MP 613 612 6 617 6 8 39 123 143 -9.152 -9.091 -0.020 -7.868 -8.147 -8.542 -2.861 -0.444 -2.920 1.707 -3.215 -3.670 0.803 -3.316 -3.065 2.508 -3.508 0.357 0.715 -2.958 -0.996 -1.987
+ ML 614 612 6 617 6 4 36 121 141 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094
+ MR 615 612 6 617 6 4 35 121 141 -7.019 -5.748 -1.656 -5.726 -0.805 -3.939 0.319 -0.242 -0.290 0.123
+ D 616 612 6 617 6 1 31 119 139 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319
+ IL 617 617 5 617 6 5 37 122 143 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000
+ IR 618 618 6 618 5 5 38 122 142 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 127 ] 155 273 g c g c
+ MP 619 618 6 623 6 8 38 121 141 -9.152 -9.091 -0.020 -7.868 -8.147 -8.542 -2.929 -2.289 -2.973 1.180 -3.179 -3.738 1.076 -3.328 -3.124 2.630 -3.572 0.342 0.661 -3.018 -0.913 -0.021
+ ML 620 618 6 623 6 4 35 119 139 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094
+ MR 621 618 6 623 6 4 34 119 139 -7.019 -5.748 -1.656 -5.726 -0.805 -3.939 0.319 -0.242 -0.290 0.123
+ D 622 618 6 623 6 1 30 117 137 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319
+ IL 623 623 5 623 6 5 36 120 141 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000
+ IR 624 624 6 624 5 5 36 120 140 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 128 ] 156 272 A U A U
+ MP 625 624 6 629 6 7 36 119 139 -9.152 -9.091 -0.020 -7.868 -8.147 -8.542 -3.726 -2.990 -3.724 3.341 -4.010 -4.943 0.135 -3.853 -3.756 0.934 -4.292 -0.604 -0.208 -4.156 -1.751 -1.275
+ ML 626 624 6 629 6 4 33 117 138 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094
+ MR 627 624 6 629 6 4 33 117 137 -7.019 -5.748 -1.656 -5.726 -0.805 -3.939 0.317 -0.372 -0.249 0.189
+ D 628 624 6 629 6 1 30 115 135 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319
+ IL 629 629 5 629 6 4 34 118 139 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000
+ IR 630 630 6 630 5 5 34 118 138 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 129 ] 157 271 G C G C
+ MP 631 630 6 635 6 5 34 117 137 -9.152 -9.091 -0.020 -7.868 -8.147 -8.542 -4.223 -1.830 -4.239 0.687 -4.926 -4.500 -0.312 -4.672 -4.107 3.479 -4.454 -0.341 -0.593 -4.026 -2.301 -3.175
+ ML 632 630 6 635 6 3 32 116 136 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094
+ MR 633 630 6 635 6 3 32 115 136 -7.019 -5.748 -1.656 -5.726 -0.805 -3.939 0.319 -0.242 -0.290 0.123
+ D 634 630 6 635 6 1 30 114 134 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319
+ IL 635 635 5 635 6 4 33 116 137 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000
+ IR 636 636 6 636 5 4 33 116 136 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 130 ] 158 270 c g c g
+ MP 637 636 6 641 4 3 32 115 135 -5.474 -5.470 -0.385 -2.404 -1.795 -1.955 -1.662 1.067 -1.873 -2.819 1.673 -2.263 -2.035 1.043 -1.618 -0.507 1.419 -2.118 1.221 -0.594
+ ML 638 636 6 641 4 2 31 114 135 -3.758 -3.940 -0.507 -2.670 0.368 -0.385 -0.191 0.094
+ MR 639 636 6 641 4 2 30 114 134 -4.845 -3.874 -1.741 -0.742 0.393 -0.492 0.005 -0.041
+ D 640 636 6 641 4 1 29 113 133 -4.568 -4.250 -2.265 -0.520
+ IL 641 641 5 641 4 3 31 116 136 -1.785 -2.468 -1.216 -3.342 0.000 0.000 0.000 0.000
+ IR 642 642 6 642 3 3 31 115 135 -1.495 -0.851 -3.462 0.000 0.000 0.000 0.000
+ [ MATL 131 ] 160 - U - U -
+ ML 643 642 6 645 2 2 30 112 132 -8.121 -0.005 -0.589 -0.840 -1.179 1.223
+ D 644 642 6 645 2 1 29 111 131 -8.602 -0.004
+ IL 645 645 3 645 2 2 30 113 133 -1.823 -0.479 0.000 0.000 0.000 0.000
+ [ BIF 132 ] - - - - - -
+ B 646 645 3 794 647 1 29 111 131
+ [ BEGR 165 ] - - - - - -
+ S 647 646 1 648 5 0 5 63 83 -4.041 -0.145 -5.577 -6.581 -8.111
+ IL 648 648 2 648 5 1 4 65 84 -2.625 -0.416 -4.304 -6.136 -5.410 0.000 0.000 0.000 0.000
+ [ MATP 166 ] 220 268 c g g c
+ MP 649 648 2 653 6 2 8 63 83 -9.143 -9.082 -0.021 -7.858 -8.138 -8.533 -1.125 -1.375 -1.518 1.179 -1.690 -1.025 1.441 -1.728 -1.753 1.069 -2.314 -0.328 1.325 0.199 0.190 -0.897
+ ML 650 648 2 653 6 1 2 62 81 -6.372 -6.718 -1.147 -1.127 -6.568 -4.097 0.211 -0.364 -0.368 0.368
+ MR 651 648 2 653 6 1 2 62 81 -7.019 -5.748 -1.656 -5.726 -0.805 -3.939 0.319 -0.242 -0.290 0.123
+ D 652 648 2 653 6 0 0 59 79 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319
+ IL 653 653 5 653 6 1 3 63 82 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000
+ IR 654 654 6 654 5 1 3 63 82 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 167 ] 221 267 G C G C
+ MP 655 654 6 659 6 2 7 61 81 -9.152 -9.091 -0.020 -7.868 -8.147 -8.542 -4.524 -2.972 -4.587 0.400 -5.280 -4.681 -0.596 -4.948 -4.255 3.560 -4.606 -0.028 -0.893 -4.316 -2.618 -3.477
+ ML 656 654 6 659 6 1 2 60 79 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094
+ MR 657 654 6 659 6 1 2 60 79 -7.019 -5.748 -1.656 -5.726 -0.805 -3.939 0.319 -0.242 -0.290 0.123
+ D 658 654 6 659 6 0 0 57 77 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319
+ IL 659 659 5 659 6 1 3 61 80 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000
+ IR 660 660 6 660 5 1 3 61 80 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 168 ] 222 266 G C G C
+ MP 661 660 6 665 6 2 7 59 79 -9.152 -9.091 -0.020 -7.868 -8.147 -8.542 -3.552 -2.489 -3.497 1.079 -3.927 -4.126 0.610 -3.912 -3.689 3.073 -4.052 0.254 0.399 -3.441 -1.055 -2.457
+ ML 662 660 6 665 6 1 2 58 77 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094
+ MR 663 660 6 665 6 1 2 58 77 -7.019 -5.748 -1.656 -5.726 -0.805 -3.939 0.319 -0.242 -0.290 0.123
+ D 664 660 6 665 6 0 0 55 75 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319
+ IL 665 665 5 665 6 1 2 59 78 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000
+ IR 666 666 6 666 5 1 3 59 78 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 169 ] 223 265 c g a u
+ MP 667 666 6 671 6 2 6 57 77 -9.152 -7.182 -0.033 -7.007 -8.147 -8.542 -2.720 -2.399 -2.827 1.731 -2.659 -3.637 1.907 -3.004 -2.877 1.686 -3.379 0.358 1.105 -2.939 -0.460 -1.534
+ ML 668 666 6 671 6 1 2 56 75 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094
+ MR 669 666 6 671 6 1 2 56 75 -7.019 -5.748 -1.563 -5.726 -0.860 -3.939 0.317 -0.372 -0.249 0.189
+ D 670 666 6 671 6 0 0 53 73 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319
+ IL 671 671 5 671 6 1 2 57 76 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000
+ IR 672 672 6 672 5 1 2 57 76 -2.453 -0.479 -5.964 -4.131 -5.237 0.000 0.000 0.000 0.000
+ [ MATP 170 ] 224 263 g c g c
+ MP 673 672 6 677 6 2 6 55 75 -9.149 -9.089 -0.020 -7.865 -8.145 -8.540 -3.344 -2.409 -3.334 1.636 -3.729 -4.073 0.849 -3.716 -3.490 2.770 -3.900 0.593 0.371 -3.351 -1.276 -2.305
+ ML 674 672 6 677 6 1 2 54 73 -6.317 -6.664 -1.216 -1.072 -6.513 -4.043 0.368 -0.527 0.090 -0.072
+ MR 675 672 6 677 6 1 1 54 73 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094
+ D 676 672 6 677 6 0 0 52 71 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319
+ IL 677 677 5 677 6 1 2 55 74 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000
+ IR 678 678 6 678 5 1 2 55 74 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 171 ] 225 262 g c g c
+ MP 679 678 6 683 6 2 5 53 73 -9.154 -9.094 -0.020 -7.870 -8.150 -8.545 -3.397 -2.643 -3.349 0.964 -3.221 -4.017 1.463 -3.540 -3.518 2.780 -3.911 -0.414 0.843 -3.373 -0.285 -2.302
+ ML 680 678 6 683 6 1 1 52 72 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094
+ MR 681 678 6 683 6 1 1 52 72 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094
+ D 682 678 6 683 6 0 0 51 70 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319
+ IL 683 683 5 683 6 1 2 53 73 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000
+ IR 684 684 6 684 5 1 2 53 72 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 172 ] 226 261 g a g a
+ MP 685 684 6 689 4 2 3 51 71 -7.068 -7.275 -0.049 -5.689 -1.006 -2.362 -2.804 0.929 -2.736 -3.734 1.006 -2.973 2.433 1.023 -3.305 -0.325 0.649 -3.061 -0.719 -1.872
+ ML 686 684 6 689 4 1 1 52 71 -3.758 -3.940 -0.507 -2.670 0.368 -0.385 -0.191 0.094
+ MR 687 684 6 689 4 1 1 51 71 -4.809 -3.838 -1.706 -0.766 0.368 -0.385 -0.191 0.094
+ D 688 684 6 689 4 0 0 50 70 -4.568 -4.250 -2.265 -0.520
+ IL 689 689 5 689 4 1 2 53 73 -1.686 -2.369 -1.117 -4.855 0.000 0.000 0.000 0.000
+ IR 690 690 6 690 3 1 1 52 72 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000
+ [ MATL 173 ] 227 - c - a -
+ ML 691 690 6 693 3 1 2 49 68 -8.076 -0.019 -6.730 -0.039 0.279 -0.368 0.054
+ D 692 690 6 693 3 0 0 47 67 -6.174 -1.687 -0.566
+ IL 693 693 3 693 3 1 1 51 71 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000
+ [ MATL 174 ] 228 - A - A -
+ ML 694 693 3 696 3 1 2 48 67 -8.076 -0.019 -6.730 1.655 -2.113 -1.887 -1.521
+ D 695 693 3 696 3 0 0 46 66 -6.174 -1.687 -0.566
+ IL 696 696 3 696 3 1 1 50 69 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000
+ [ MATL 175 ] 229 - c - a -
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+ D 698 696 3 699 3 0 0 45 65 -5.620 -0.734 -1.403
+ IL 699 699 3 699 3 1 1 47 67 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000
+ [ MATR 176 ] - 260 - u - a
+ MR 700 699 3 702 5 1 1 46 65 -7.187 -0.043 -7.002 -6.471 -8.106 0.170 0.239 -1.117 0.303
+ D 701 699 3 702 5 0 0 44 64 -5.376 -0.692 -3.003 -4.434 -2.428
+ IR 702 702 3 702 5 1 1 46 65 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 177 ] 230 259 c g g c
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+ ML 704 702 3 707 6 1 1 43 62 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094
+ MR 705 702 3 707 6 1 1 43 62 -7.025 -5.754 -1.550 -5.732 -0.866 -3.946 0.495 -0.473 -0.195 -0.004
+ D 706 702 3 707 6 0 0 41 60 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319
+ IL 707 707 5 707 6 1 1 44 64 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000
+ IR 708 708 6 708 5 1 1 44 63 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 178 ] 231 258 g a g a
+ MP 709 708 6 713 6 2 2 43 62 -9.154 -9.094 -0.020 -7.870 -8.150 -8.545 -1.669 -2.087 -2.309 1.036 -2.029 -3.141 1.393 -2.559 1.618 1.214 -2.876 -0.058 1.128 -2.458 -0.273 -1.468
+ ML 710 708 6 713 6 1 1 41 60 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094
+ MR 711 708 6 713 6 1 1 41 60 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094
+ D 712 708 6 713 6 0 0 39 58 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319
+ IL 713 713 5 713 6 1 1 42 62 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000
+ IR 714 714 6 714 5 1 1 42 61 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 179 ] 232 257 C G C G
+ MP 715 714 6 719 6 2 2 41 60 -9.154 -9.094 -0.020 -7.870 -8.150 -8.545 -4.796 -4.724 -4.444 -0.935 -3.110 -4.823 3.621 -3.944 -4.502 -0.727 -4.736 -2.675 0.378 -4.849 -0.823 -3.334
+ ML 716 714 6 719 6 1 1 39 59 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094
+ MR 717 714 6 719 6 1 1 39 58 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094
+ D 718 714 6 719 6 0 0 37 56 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319
+ IL 719 719 5 719 6 1 1 40 60 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000
+ IR 720 720 6 720 5 1 1 40 59 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 180 ] 233 256 G C G C
+ MP 721 720 6 725 6 2 2 39 58 -9.154 -9.094 -0.020 -7.870 -8.150 -8.545 -4.405 -2.919 -4.452 0.796 -5.116 -4.660 -0.451 -4.806 -4.188 3.517 -4.550 -0.453 -0.752 -4.243 -2.469 -3.340
+ ML 722 720 6 725 6 1 1 38 57 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094
+ MR 723 720 6 725 6 1 1 38 57 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094
+ D 724 720 6 725 6 0 0 36 55 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319
+ IL 725 725 5 725 6 1 1 38 58 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000
+ IR 726 726 6 726 5 1 1 38 57 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 181 ] 234 255 u g u g
+ MP 727 726 6 731 4 2 2 37 56 -7.068 -7.275 -0.049 -5.689 -3.984 -3.987 -3.756 -0.332 -2.579 -4.217 1.707 -3.342 -3.800 -0.133 -4.124 -2.078 1.574 -4.081 2.797 -2.682
+ ML 728 726 6 731 4 1 1 37 57 -3.758 -3.940 -0.507 -2.670 0.368 -0.385 -0.191 0.094
+ MR 729 726 6 731 4 1 1 37 56 -4.809 -3.838 -1.706 -0.766 0.368 -0.385 -0.191 0.094
+ D 730 726 6 731 4 0 0 36 55 -4.568 -4.250 -2.265 -0.520
+ IL 731 731 5 731 4 1 1 39 58 -1.686 -2.369 -1.117 -4.855 0.000 0.000 0.000 0.000
+ IR 732 732 6 732 3 1 1 38 57 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000
+ [ MATL 182 ] 235 - G - G -
+ ML 733 732 6 735 3 1 1 34 53 -8.076 -0.019 -6.730 -0.881 -1.662 1.406 -1.026
+ D 734 732 6 735 3 0 0 33 52 -6.174 -1.687 -0.566
+ IL 735 735 3 735 3 1 1 37 56 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000
+ [ MATL 183 ] 236 - A - A -
+ ML 736 735 3 738 3 1 1 33 52 -8.076 -0.019 -6.730 1.763 -2.598 -2.208 -2.163
+ D 737 735 3 738 3 0 0 32 51 -6.174 -1.687 -0.566
+ IL 738 738 3 738 3 1 1 35 55 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000
+ [ MATL 184 ] 237 - G - G -
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+ D 740 738 3 741 3 0 0 31 50 -6.174 -1.687 -0.566
+ IL 741 741 3 741 3 1 1 34 54 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000
+ [ MATL 185 ] 238 - G - G -
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+ D 743 741 3 744 3 0 0 30 48 -5.620 -0.734 -1.403
+ IL 744 744 3 744 3 1 1 32 50 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000
+ [ MATR 186 ] - 254 - A - A
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+ D 746 744 3 747 3 0 0 28 47 -6.390 -1.568 -0.620
+ IR 747 747 3 747 3 1 1 31 49 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000
+ [ MATR 187 ] - 253 - C - C
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+ D 749 747 3 750 3 0 0 27 46 -6.390 -1.568 -0.620
+ IR 750 750 3 750 3 1 1 30 48 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000
+ [ MATR 188 ] - 252 - G - G
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+ D 752 750 3 753 3 0 0 26 45 -6.390 -1.568 -0.620
+ IR 753 753 3 753 3 1 1 29 47 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000
+ [ MATR 189 ] - 251 - A - A
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+ D 755 753 3 756 5 0 0 25 44 -5.352 -0.707 -2.978 -4.409 -2.404
+ IR 756 756 3 756 5 1 1 27 46 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 190 ] 239 250 C G C G
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+ ML 758 756 3 761 6 1 1 25 43 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094
+ MR 759 756 3 761 6 1 1 24 43 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094
+ D 760 756 3 761 6 0 0 22 41 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319
+ IL 761 761 5 761 6 1 1 26 44 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000
+ IR 762 762 6 762 5 1 1 25 44 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 191 ] 240 249 U A u a
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+ ML 764 762 6 767 6 1 1 23 42 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094
+ MR 765 762 6 767 6 1 1 23 42 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094
+ D 766 762 6 767 6 0 0 22 40 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319
+ IL 767 767 5 767 6 1 1 24 42 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000
+ IR 768 768 6 768 5 1 1 23 42 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 192 ] 241 248 G C G C
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+ ML 770 768 6 773 4 1 1 23 42 -3.758 -3.940 -0.507 -2.670 0.368 -0.385 -0.191 0.094
+ MR 771 768 6 773 4 1 1 22 41 -4.809 -3.838 -1.706 -0.766 0.368 -0.385 -0.191 0.094
+ D 772 768 6 773 4 0 0 21 40 -4.568 -4.250 -2.265 -0.520
+ IL 773 773 5 773 4 1 1 24 43 -1.686 -2.369 -1.117 -4.855 0.000 0.000 0.000 0.000
+ IR 774 774 6 774 3 1 1 23 42 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000
+ [ MATL 193 ] 242 - G - G -
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+ D 776 774 6 777 3 0 0 18 37 -6.174 -1.687 -0.566
+ IL 777 777 3 777 3 1 1 22 41 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000
+ [ MATL 194 ] 243 - u - u -
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+ D 779 777 3 780 3 0 0 17 36 -6.174 -1.687 -0.566
+ IL 780 780 3 780 3 1 1 21 39 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000
+ [ MATL 195 ] 244 - U - U -
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+ D 782 780 3 783 3 0 0 16 34 -6.174 -1.687 -0.566
+ IL 783 783 3 783 3 1 1 20 38 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000
+ [ MATL 196 ] 245 - U - U -
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+ D 785 783 3 786 3 0 0 14 33 -6.750 -2.263 -0.354
+ IL 786 786 3 786 3 1 1 19 37 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000
+ [ MATL 197 ] 246 - C - C -
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+ D 788 786 3 789 3 0 0 13 31 -6.750 -0.896 -1.141
+ IL 789 789 3 789 3 1 1 18 36 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000
+ [ MATL 198 ] 247 - A - A -
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+ D 791 789 3 792 2 0 0 0 0 * 0.000
+ IL 792 792 3 792 2 1 1 13 28 -1.823 -0.479 0.000 0.000 0.000 0.000
+ [ END 199 ] - - - - - -
+ E 793 792 3 -1 0 0 0 0 0
+ [ BEGL 133 ] - - - - - -
+ S 794 646 1 795 1 0 0 62 81 0.000
+ [ BIF 134 ] - - - - - -
+ B 795 794 1 796 918 0 0 62 81
+ [ BEGL 135 ] - - - - - -
+ S 796 795 1 797 4 0 0 54 73 -0.139 -4.325 -6.303 -5.096
+ [ MATP 136 ] 161 206 g c g c
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+ ML 798 796 1 801 6 1 1 53 71 -6.771 -7.117 -0.776 -1.526 -6.967 -4.497 0.143 -0.669 0.347 -0.007
+ MR 799 796 1 801 6 1 1 52 71 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094
+ D 800 796 1 801 6 0 0 51 70 -9.407 -8.105 -1.933 -4.585 -4.602 -0.621
+ IL 801 801 5 801 6 1 1 54 72 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000
+ IR 802 802 6 802 5 1 1 53 72 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 137 ] 162 205 g c g c
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+ ML 804 802 6 807 6 1 1 50 69 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094
+ MR 805 802 6 807 6 1 1 50 69 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094
+ D 806 802 6 807 6 0 0 48 67 -9.094 -7.792 -3.589 -4.272 -4.289 -0.308
+ IL 807 807 5 807 6 1 1 52 70 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000
+ IR 808 808 6 808 5 1 1 51 70 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 138 ] 163 204 g c g c
+ MP 809 808 6 813 6 2 2 50 69 -9.152 -9.091 -0.025 -7.031 -8.147 -8.542 -2.242 -1.797 -2.384 1.383 -2.414 -3.152 1.355 -2.711 -2.471 2.108 -2.310 0.379 1.123 -2.463 -0.101 -1.306
+ ML 810 808 6 813 6 1 1 48 67 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094
+ MR 811 808 6 813 6 1 1 48 67 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094
+ D 812 808 6 813 6 0 0 46 65 -9.094 -7.792 -3.589 -4.272 -4.289 -0.308
+ IL 813 813 5 813 6 1 1 50 68 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000
+ IR 814 814 6 814 5 1 1 49 68 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 139 ] 164 203 c g c g
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+ ML 816 814 6 819 6 1 1 46 65 -6.315 -6.661 -1.219 -1.070 -6.511 -4.041 0.282 -0.151 -0.352 0.137
+ MR 817 814 6 819 6 1 1 46 65 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094
+ D 818 814 6 819 6 0 0 44 63 -9.094 -7.792 -3.589 -4.272 -4.289 -0.308
+ IL 819 819 5 819 6 1 1 48 66 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000
+ IR 820 820 6 820 5 1 1 47 66 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 140 ] 165 202 c g c g
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+ ML 822 820 6 825 6 1 1 44 63 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094
+ MR 823 820 6 825 6 1 1 44 63 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094
+ D 824 820 6 825 6 0 0 42 61 -9.094 -7.792 -3.589 -4.272 -4.289 -0.308
+ IL 825 825 5 825 6 1 1 46 64 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000
+ IR 826 826 6 826 5 1 1 45 64 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 141 ] 166 201 g c a u
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+ ML 828 826 6 831 6 1 1 42 61 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094
+ MR 829 826 6 831 6 1 1 42 61 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094
+ D 830 826 6 831 6 0 0 40 58 -9.094 -7.792 -3.589 -4.272 -4.289 -0.308
+ IL 831 831 5 831 6 1 1 43 62 -2.845 -2.923 -0.569 -5.401 -6.177 -5.837 0.000 0.000 0.000 0.000
+ IR 832 832 6 832 5 1 1 43 62 -2.548 -0.442 -6.060 -4.227 -5.333 0.000 0.000 0.000 0.000
+ [ MATP 142 ] 169 199 c g a u
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+ ML 834 832 6 837 6 1 1 40 59 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094
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+ D 836 832 6 837 6 0 0 38 56 -9.094 -7.792 -3.589 -4.272 -4.289 -0.308
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+ IR 838 838 6 838 5 1 1 41 60 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 143 ] 170 198 g c G C
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+ IR 844 844 6 844 5 1 1 39 58 -2.438 -0.484 -5.949 -4.117 -5.223 0.000 0.000 0.000 0.000
+ [ MATP 144 ] 171 196 u a g c
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+ IR 850 850 6 850 5 1 1 37 56 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 145 ] 172 195 g c g c
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+ IR 856 856 6 856 5 1 1 35 54 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 146 ] 173 194 g c g c
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+ IR 862 862 6 862 5 1 1 33 52 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 147 ] 174 193 c g c g
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+ IR 868 868 6 868 5 1 1 31 50 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 148 ] 175 192 c g c g
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+ IR 874 874 6 874 5 1 1 29 48 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 149 ] 176 191 c g c g
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+ IR 880 880 6 880 5 1 1 27 46 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 150 ] 177 190 g c a u
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+ [ END 158 ] - - - - - -
+ E 917 916 3 -1 0 0 0 0 0
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+ [ MATP 160 ] 211 218 c g C G
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+ IR 925 925 6 925 5 1 1 20 38 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 161 ] 212 217 u a u a
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+ [ MATL 162 ] 214 - A - A -
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+ [ MATL 163 ] 215 - a - A -
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+ D 936 934 3 937 2 0 0 0 0 * 0.000
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+ [ END 164 ] - - - - - -
+ E 938 937 3 -1 0 0 0 0 0
+//
+HMMER3/f [i1.1 | April 2012]
+NAME Plant_SRP
+ACC RF01855
+DESC Plant signal recognition particle RNA
+LENG 305
+MAXL 434
+ALPH RNA
+RF yes
+MM no
+CONS yes
+CS yes
+MAP yes
+DATE Mon Apr 30 08:55:06 2012
+COM [1] /groups/eddy/home/nawrockie/notebook/12_0423_inf_final_stress_tests/wd-infernal/src/cmbuild -F Plant_SRP.cm Plant_SRP.sto
+NSEQ 64
+EFFN 3.251465
+CKSUM 2513792503
+STATS LOCAL MSV -11.3181 0.70581
+STATS LOCAL VITERBI -12.7341 0.70581
+STATS LOCAL FORWARD -3.9419 0.70581
+HMM A C G U
+ m->m m->i m->d i->m i->i d->m d->d
+ COMPO 1.48744 1.41722 1.22017 1.44188
+ 1.38629 1.38629 1.38629 1.38629
+ 0.25534 3.97203 1.57740 1.46634 0.26236 0.00000 *
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+ 3 2.82994 0.42782 2.60306 1.53707 3 c C - (
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+ 7 2.22595 0.70823 2.07330 1.29554 8 c C - <
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+ 8 1.96944 1.35073 1.68289 0.87809 9 u u - <
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+ 0.04116 3.90390 3.90390 1.46634 0.26236 1.87129 0.16715
+ 15 2.74115 0.25831 3.32872 2.06113 16 c C - _
+ 1.38629 1.38629 1.38629 1.38629
+ 0.04116 3.90390 3.90390 1.46634 0.26236 1.87129 0.16715
+ 16 1.58958 1.76571 0.91225 1.49923 17 g c - >
+ 1.38629 1.38629 1.38629 1.38629
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+ 18 1.62196 1.61177 0.96738 1.50114 19 g g - >
+ 1.38629 1.38629 1.38629 1.38629
+ 0.04116 3.90390 3.90390 1.46634 0.26236 1.02816 0.44265
+ 19 1.16458 1.85238 1.02023 1.76861 20 a a - >
+ 1.38629 1.38629 1.38629 1.38629
+ 0.04007 3.93024 3.93024 1.46634 0.26236 1.64346 0.21481
+ 20 1.51379 2.24538 0.62481 1.97561 21 g G - >
+ 1.38629 1.38629 1.38629 1.38629
+ 0.04007 3.93024 3.93024 1.46634 0.26236 1.64346 0.21481
+ 21 2.33699 0.60631 1.97486 1.51759 22 c C - >
+ 1.38629 1.38629 1.38629 1.38629
+ 0.04007 3.93024 3.93024 1.46634 0.26236 1.64346 0.21481
+ 22 2.24042 1.18949 1.94292 0.80761 23 u u - >
+ 1.38629 1.38629 1.38629 1.38629
+ 0.04007 3.93024 3.93024 1.46634 0.26236 1.06477 0.42283
+ 23 2.93126 1.82255 2.80072 0.32256 24 u u - >
+ 1.38629 1.38629 1.38629 1.38629
+ 0.03945 3.94552 3.94552 1.46634 0.26236 1.47918 0.25854
+ 24 3.02947 3.94820 0.10229 3.51986 25 g G - ,
+ 1.38629 1.38629 1.38629 1.38629
+ 0.03945 3.94552 3.94552 1.46634 0.26236 1.47918 0.25854
+ 25 2.38970 2.42699 2.72593 0.28163 26 u U - ,
+ 1.38629 1.38629 1.38629 1.38629
+ 0.03945 3.94552 3.94552 1.46634 0.26236 1.47918 0.25854
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+ 0.07247 2.66065 * 0.58184 0.81842 0.00000 *
+//
+INFERNAL1/a [1.1.1 | July 2014]
+NAME tRNA-Sec
+ACC RF01852
+STATES 292
+NODES 75
+CLEN 91
+W 117
+ALPH RNA
+RF no
+CONS yes
+MAP yes
+DATE Tue Apr 8 16:22:29 2014
+COM [1] cmbuild -F CM SEED
+COM [2] cmcalibrate --mpi CM
+PBEGIN 0.05
+PEND 0.05
+WBETA 1e-07
+QDBBETA1 1e-07
+QDBBETA2 1e-15
+N2OMEGA 1.52588e-05
+N3OMEGA 1.52588e-05
+ELSELF -0.08926734
+NSEQ 109
+EFFN 2.318512
+CKSUM 3407454328
+NULL 0.000 0.000 0.000 0.000
+GA 47.00
+TC 47.00
+NC 46.90
+EFP7GF -12.3219 0.71862
+ECMLC 0.74414 -5.65122 2.12842 1600000 392081 0.003061
+ECMGC 0.38122 -15.57366 -3.55100 1600000 39136 0.010221
+ECMLI 0.59769 -5.29381 3.90232 1600000 292574 0.004102
+ECMGI 0.41821 -9.96424 0.79712 1600000 36025 0.011103
+CM
+ [ ROOT 0 ] - - - - - -
+ S 0 -1 0 1 6 0 1 117 148 -9.167 -9.106 -0.072 -5.457 -8.163 -5.750
+ IL 1 1 2 1 6 6 39 118 149 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000
+ IR 2 2 3 2 5 7 39 118 149 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 1 ] 1 115 G C - -
+ MP 3 2 3 7 6 9 42 117 148 -9.116 -9.056 -0.024 -7.832 -8.112 -7.729 -4.348 -2.912 -4.393 0.458 -4.887 -4.513 -0.299 -4.756 -4.149 3.538 -3.573 -0.513 -0.618 -4.122 -2.305 -3.323
+ ML 4 2 3 7 6 6 36 115 146 -6.580 -6.926 -1.327 -1.253 -3.149 -4.305 0.139 -0.737 0.521 -0.211
+ MR 5 2 3 7 6 5 36 115 146 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094
+ D 6 2 3 7 6 3 31 113 144 -9.406 -8.104 -2.271 -4.584 -3.055 -0.676
+ IL 7 7 5 7 6 6 38 116 147 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000
+ IR 8 8 6 8 5 6 38 116 147 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 2 ] 2 114 g c - -
+ MP 9 8 6 13 6 9 41 115 146 -9.139 -9.078 -0.021 -7.855 -8.135 -8.530 -3.276 -2.566 -3.279 1.111 -3.203 -4.000 1.685 -3.481 -3.399 2.629 -3.832 -0.206 0.910 -3.312 -0.792 -2.225
+ ML 10 8 6 13 6 5 36 113 144 -6.291 -6.637 -1.352 -0.965 -6.487 -4.017 0.312 -0.224 -0.303 0.126
+ MR 11 8 6 13 6 5 36 113 144 -7.229 -5.958 -1.223 -5.936 -1.070 -4.150 0.074 -0.101 -0.588 0.433
+ D 12 8 6 13 6 3 30 110 141 -9.096 -7.795 -3.116 -4.274 -4.291 -0.367
+ IL 13 13 5 13 6 6 37 114 145 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000
+ IR 14 14 6 14 5 6 38 114 145 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 3 ] 3 113 g c - -
+ MP 15 14 6 19 6 9 40 113 144 -9.164 -9.103 -0.020 -7.880 -8.160 -8.555 -3.059 -2.598 -3.107 1.726 -2.871 -3.889 1.887 -3.237 -3.185 2.067 -3.661 -0.462 1.105 -3.200 -0.554 -2.077
+ ML 16 14 6 19 6 5 35 111 142 -6.291 -6.637 -1.352 -0.965 -6.487 -4.017 0.312 -0.224 -0.303 0.126
+ MR 17 14 6 19 6 5 35 111 142 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094
+ D 18 14 6 19 6 3 30 108 139 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319
+ IL 19 19 5 19 6 6 37 112 143 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000
+ IR 20 20 6 20 5 6 37 112 143 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 4 ] 4 112 g c - -
+ MP 21 20 6 25 6 8 38 111 142 -9.164 -9.103 -0.023 -7.880 -8.160 -7.848 -2.838 -2.411 -2.916 1.911 -2.838 -3.719 1.635 -2.804 -3.006 2.034 -3.494 -0.012 0.978 -3.006 -0.601 -1.943
+ ML 22 20 6 25 6 5 34 109 140 -6.291 -6.637 -1.252 -1.046 -6.487 -4.017 0.312 -0.224 -0.303 0.126
+ MR 23 20 6 25 6 5 34 109 140 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094
+ D 24 20 6 25 6 2 29 106 137 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319
+ IL 25 25 5 25 6 5 36 110 141 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000
+ IR 26 26 6 26 5 6 36 110 141 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 5 ] 5 111 g c - -
+ MP 27 26 6 31 6 7 37 109 140 -9.165 -9.104 -0.029 -7.880 -8.160 -6.871 -3.198 -2.381 -3.189 1.285 -3.470 -3.883 1.067 -3.581 -3.389 2.835 -3.009 0.154 0.625 -3.173 -1.072 -2.201
+ ML 28 26 6 31 6 5 33 107 138 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094
+ MR 29 26 6 31 6 5 33 107 138 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094
+ D 30 26 6 31 6 2 29 104 135 -9.091 -7.789 -3.159 -4.268 -4.286 -0.361
+ IL 31 31 5 31 6 5 35 108 139 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000
+ IR 32 32 6 32 5 5 35 108 139 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 6 ] 6 110 g c - -
+ MP 33 32 6 37 6 7 35 107 138 -9.159 -9.098 -0.041 -7.874 -8.154 -5.900 -2.601 -2.356 -2.496 1.306 -2.555 -3.501 1.722 -2.922 -2.789 1.910 -3.295 0.417 1.434 -2.797 -0.320 -1.683
+ ML 34 32 6 37 6 5 32 105 136 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094
+ MR 35 32 6 37 6 4 32 105 136 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094
+ D 36 32 6 37 6 2 28 103 134 -9.191 -7.890 -2.845 -4.369 -4.386 -0.398
+ IL 37 37 5 37 6 5 34 106 137 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000
+ IR 38 38 6 38 5 5 34 106 137 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 7 ] 7 109 g c - -
+ MP 39 38 6 43 6 7 33 105 136 -9.144 -9.083 -0.098 -6.518 -4.513 -7.056 -2.619 -2.227 -2.701 1.606 -2.761 -3.469 1.297 -2.616 -2.839 2.388 -3.319 -0.236 1.043 -2.157 -0.610 -1.704
+ ML 40 38 6 43 6 4 31 103 134 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094
+ MR 41 38 6 43 6 4 31 103 134 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094
+ D 42 38 6 43 6 2 28 101 132 -9.408 -8.106 -3.903 -4.586 -4.603 -0.243
+ IL 43 43 5 43 6 5 32 104 135 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000
+ IR 44 44 6 44 5 5 32 104 135 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 8 ] 8 108 c g - -
+ MP 45 44 6 49 6 6 32 103 134 -9.067 -9.006 -0.042 -7.783 -6.674 -6.558 -1.733 -1.724 -1.921 1.261 -1.865 -2.742 1.729 -2.099 -1.975 1.321 -2.343 -0.309 1.470 -1.519 -0.016 -0.154
+ ML 46 44 6 49 6 4 30 102 133 -6.374 -6.721 -1.144 -1.129 -6.570 -4.100 0.208 -0.364 -0.371 0.373
+ MR 47 44 6 49 6 4 30 102 133 -7.550 -6.279 -0.937 -6.257 -1.317 -4.471 0.471 -0.317 -0.492 0.138
+ D 48 44 6 49 6 2 28 100 131 -9.499 -8.198 -1.993 -4.677 -4.694 -0.586
+ IL 49 49 5 49 6 5 31 102 133 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000
+ IR 50 50 6 50 5 5 30 102 133 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 9 ] 9 107 g c - -
+ MP 51 50 6 55 4 4 30 101 132 -7.021 -4.488 -0.428 -2.290 -2.324 -1.223 -2.449 1.483 -2.620 -3.188 1.020 -2.540 -2.566 2.391 -3.040 0.322 0.821 -1.577 -0.616 -1.387
+ ML 52 50 6 55 4 4 29 100 131 -3.758 -3.940 -0.507 -2.670 0.368 -0.385 -0.191 0.094
+ MR 53 50 6 55 4 3 28 100 131 -4.963 -3.992 -1.408 -0.920 0.184 0.053 -0.484 0.153
+ D 54 50 6 55 4 2 27 99 130 -4.857 -3.337 -2.554 -0.522
+ IL 55 55 5 55 4 4 29 102 132 -1.686 -2.369 -1.117 -4.855 0.000 0.000 0.000 0.000
+ IR 56 56 6 56 3 4 29 101 132 -1.455 -0.769 -4.366 0.000 0.000 0.000 0.000
+ [ MATL 10 ] 10 - a - - -
+ ML 57 56 6 59 3 3 28 99 130 -4.955 -0.105 -4.724 0.965 -0.869 -0.837 -0.087
+ D 58 56 6 59 3 2 27 98 129 -7.702 -0.655 -1.473
+ IL 59 59 3 59 3 3 28 100 131 -1.389 -0.818 -4.300 0.000 0.000 0.000 0.000
+ [ MATL 11 ] 13 - u - - -
+ ML 60 59 3 62 2 3 27 98 129 -8.424 -0.004 -0.279 -0.381 -0.896 0.903
+ D 61 59 3 62 2 2 26 97 128 -8.495 -0.004
+ IL 62 62 3 62 2 3 27 99 129 -1.823 -0.479 0.000 0.000 0.000 0.000
+ [ BIF 12 ] - - - - - -
+ B 63 62 3 64 176 2 26 97 128
+ [ BEGL 13 ] - - - - - -
+ S 64 63 1 65 1 0 1 50 70 0.000
+ [ BIF 14 ] - - - - - -
+ B 65 64 1 66 116 0 1 50 70
+ [ BEGL 15 ] - - - - - -
+ S 66 65 1 67 4 0 0 30 49 -0.042 -6.912 -6.319 -6.959
+ [ MATP 16 ] 14 35 c g - -
+ MP 67 66 1 71 6 2 2 30 49 -6.798 -9.106 -0.031 -7.883 -8.163 -8.558 -3.032 -2.754 -3.106 0.976 -2.632 -3.903 2.376 -3.105 -3.126 1.723 -3.627 -0.252 1.332 -3.225 -0.143 -2.033
+ ML 68 66 1 71 6 1 1 29 47 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094
+ MR 69 66 1 71 6 1 1 29 47 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094
+ D 70 66 1 71 6 0 0 26 45 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319
+ IL 71 71 5 71 6 1 1 30 49 -2.250 -3.042 -0.789 -4.697 -5.473 -5.134 0.000 0.000 0.000 0.000
+ IR 72 72 6 72 5 1 1 30 48 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 17 ] 17 34 g c - -
+ MP 73 72 6 77 6 2 2 28 47 -9.167 -9.106 -0.020 -7.883 -8.163 -8.558 -2.304 -2.200 -2.445 1.157 -2.323 -2.663 1.868 -2.693 -2.513 1.925 -2.649 -0.192 1.293 -2.552 0.053 -1.574
+ ML 74 72 6 77 6 1 1 27 45 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094
+ MR 75 72 6 77 6 1 1 27 45 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094
+ D 76 72 6 77 6 0 0 24 43 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319
+ IL 77 77 5 77 6 1 1 28 46 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000
+ IR 78 78 6 78 5 1 1 28 46 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 18 ] 18 33 g c - -
+ MP 79 78 6 83 6 2 2 26 45 -6.199 -9.106 -0.038 -7.883 -8.163 -8.558 -2.051 -1.780 -1.979 1.148 -2.133 -2.855 1.662 -2.500 -2.284 1.751 -2.830 -0.286 1.325 -2.145 0.719 -1.392
+ ML 80 78 6 83 6 1 1 25 43 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094
+ MR 81 78 6 83 6 1 1 25 43 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094
+ D 82 78 6 83 6 0 0 22 41 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319
+ IL 83 83 5 83 6 1 1 26 44 -2.745 -3.008 -0.656 -4.663 -5.439 -5.099 0.000 0.000 0.000 0.000
+ IR 84 84 6 84 5 1 1 26 44 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 19 ] 20 32 c g - -
+ MP 85 84 6 89 6 2 2 24 43 -9.167 -9.106 -0.029 -7.883 -6.759 -8.558 -2.496 -2.177 -2.622 1.184 -2.415 -3.428 1.985 -2.812 -2.164 1.875 -3.202 -0.302 1.303 -2.730 0.069 -1.701
+ ML 86 84 6 89 6 1 1 23 41 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094
+ MR 87 84 6 89 6 1 1 23 41 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094
+ D 88 84 6 89 6 0 0 21 39 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319
+ IL 89 89 5 89 6 1 1 24 42 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000
+ IR 90 90 6 90 5 1 1 24 42 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 20 ] 21 31 c g - -
+ MP 91 90 6 95 6 2 2 22 41 -5.985 -9.098 -0.041 -7.875 -8.154 -8.549 -1.740 -2.113 -2.031 1.361 -2.098 -3.062 1.786 -2.486 -2.289 1.503 -2.711 -0.274 1.532 -2.356 0.234 -1.340
+ ML 92 90 6 95 6 1 1 21 40 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094
+ MR 93 90 6 95 6 1 1 21 39 -7.084 -5.813 -1.443 -5.791 -0.925 -4.005 0.327 -0.563 0.180 -0.096
+ D 94 90 6 95 6 0 0 19 38 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319
+ IL 95 95 5 95 6 1 1 22 40 -2.772 -3.035 -0.640 -4.690 -5.466 -5.127 0.000 0.000 0.000 0.000
+ IR 96 96 6 96 5 1 1 22 40 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 21 ] 23 30 c g - -
+ MP 97 96 6 101 4 2 2 20 38 -5.143 -7.306 -0.079 -5.720 -3.314 -2.955 -3.350 0.745 -2.761 -4.135 2.600 -3.259 -3.344 1.765 -3.829 -0.539 1.205 -3.505 -0.393 -2.223
+ ML 98 96 6 101 4 1 1 20 38 -3.758 -3.940 -0.507 -2.670 0.368 -0.385 -0.191 0.094
+ MR 99 96 6 101 4 1 1 20 38 -4.809 -3.838 -1.706 -0.766 0.368 -0.385 -0.191 0.094
+ D 100 96 6 101 4 0 0 19 37 -4.568 -4.250 -2.265 -0.520
+ IL 101 101 5 101 4 1 1 21 40 -1.826 -2.071 -1.156 -4.995 0.000 0.000 0.000 0.000
+ IR 102 102 6 102 3 1 1 20 39 -1.490 -0.763 -4.190 0.000 0.000 0.000 0.000
+ [ MATL 22 ] 25 - U - - -
+ ML 103 102 6 105 3 1 1 16 35 -8.105 -0.019 -6.759 -0.740 -0.096 -1.426 1.066
+ D 104 102 6 105 3 0 0 16 34 -6.174 -1.687 -0.566
+ IL 105 105 3 105 3 1 1 20 38 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000
+ [ MATL 23 ] 26 - G - - -
+ ML 106 105 3 108 3 1 1 15 33 -8.105 -0.019 -6.759 -1.880 -3.144 1.783 -2.531
+ D 107 105 3 108 3 0 0 15 33 -6.174 -1.687 -0.566
+ IL 108 108 3 108 3 1 1 19 37 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000
+ [ MATL 24 ] 27 - G - - -
+ ML 109 108 3 111 3 1 1 13 31 -8.105 -0.019 -6.759 -1.880 -3.144 1.783 -2.531
+ D 110 108 3 111 3 0 0 13 32 -6.174 -1.687 -0.566
+ IL 111 111 3 111 3 1 1 18 36 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000
+ [ MATL 25 ] 28 - U - - -
+ ML 112 111 3 114 2 1 1 1 1 * 0.000 -1.751 -1.701 -2.496 1.686
+ D 113 111 3 114 2 0 0 0 0 * 0.000
+ IL 114 114 3 114 2 1 1 13 28 -1.823 -0.479 0.000 0.000 0.000 0.000
+ [ END 26 ] - - - - - -
+ E 115 114 3 -1 0 0 0 0 0
+ [ BEGR 27 ] - - - - - -
+ S 116 65 1 117 5 0 0 33 52 -7.217 -0.036 -7.033 -7.245 -8.136
+ IL 117 117 2 117 5 1 1 34 53 -2.408 -0.496 -4.087 -5.920 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 28 ] 36 57 u a - -
+ MP 118 117 2 122 6 2 2 33 52 -9.167 -4.681 -0.076 -7.883 -8.163 -8.558 -1.639 -1.771 -1.838 1.129 -1.711 -2.242 1.584 -0.530 -1.783 1.151 -2.443 0.219 1.594 -1.825 0.069 -0.990
+ ML 119 117 2 122 6 1 1 31 50 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094
+ MR 120 117 2 122 6 1 1 31 50 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094
+ D 121 117 2 122 6 0 0 29 48 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319
+ IL 122 122 5 122 6 1 1 33 52 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000
+ IR 123 123 6 123 5 1 1 32 51 -2.145 -0.519 -6.349 -4.517 -5.623 0.000 0.000 0.000 0.000
+ [ MATP 29 ] 37 54 c g - -
+ MP 124 123 6 128 6 2 2 31 50 -9.167 -7.048 -0.029 -7.883 -8.163 -8.558 -1.388 -1.676 -1.908 1.183 -1.481 -2.550 1.865 -2.101 -1.699 1.114 -2.485 0.567 1.339 -2.032 0.003 -1.131
+ ML 125 123 6 128 6 1 1 29 48 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094
+ MR 126 123 6 128 6 1 1 29 48 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094
+ D 127 123 6 128 6 0 0 27 46 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319
+ IL 128 128 5 128 6 1 1 31 49 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000
+ IR 129 129 6 129 5 1 1 30 49 -2.459 -0.476 -5.970 -4.138 -5.244 0.000 0.000 0.000 0.000
+ [ MATP 30 ] 38 52 c g - -
+ MP 130 129 6 134 6 2 2 29 48 -9.167 -9.106 -0.020 -7.883 -8.163 -8.558 -3.673 -3.556 -3.597 0.380 -2.601 -4.232 2.940 -3.279 -3.589 0.573 -4.011 -1.471 1.754 -3.834 -0.252 -2.451
+ ML 131 129 6 134 6 1 1 27 46 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094
+ MR 132 129 6 134 6 1 1 27 46 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094
+ D 133 129 6 134 6 0 0 25 44 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319
+ IL 134 134 5 134 6 1 1 29 47 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000
+ IR 135 135 6 135 5 1 1 28 47 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 31 ] 39 51 G C - -
+ MP 136 135 6 140 6 2 2 27 46 -9.167 -9.106 -0.020 -7.883 -8.163 -8.558 -3.681 -2.565 -3.653 1.528 -4.147 -4.307 0.389 -4.037 -3.755 3.089 -4.143 -0.172 0.272 -3.632 -1.595 -2.586
+ ML 137 135 6 140 6 1 1 26 45 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094
+ MR 138 135 6 140 6 1 1 26 44 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094
+ D 139 135 6 140 6 0 0 23 42 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319
+ IL 140 140 5 140 6 1 1 27 45 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000
+ IR 141 141 6 141 5 1 1 26 45 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 32 ] 40 50 G C - -
+ MP 142 141 6 146 6 2 2 25 44 -9.167 -9.106 -0.020 -7.883 -8.163 -8.558 -4.900 -3.170 -5.012 0.196 -5.551 -4.782 -0.845 -5.298 -4.450 3.670 -4.777 -0.869 -1.201 -4.577 -2.892 -3.886
+ ML 143 141 6 146 6 1 1 24 43 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094
+ MR 144 141 6 146 6 1 1 24 43 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094
+ D 145 141 6 146 6 0 0 23 42 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319
+ IL 146 146 5 146 6 1 1 25 44 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000
+ IR 147 147 6 147 5 1 1 24 43 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 33 ] 41 49 g c - -
+ MP 148 147 6 152 4 2 2 23 42 -7.099 -7.306 -0.048 -5.720 -3.060 -2.532 -3.112 1.787 -3.004 -3.921 1.260 -3.295 -3.193 2.197 -3.672 -0.363 1.556 -3.211 -0.697 -2.092
+ ML 149 147 6 152 4 1 1 24 43 -3.758 -3.940 -0.507 -2.670 0.368 -0.385 -0.191 0.094
+ MR 150 147 6 152 4 1 1 23 42 -4.809 -3.838 -1.706 -0.766 0.368 -0.385 -0.191 0.094
+ D 151 147 6 152 4 0 0 22 41 -4.568 -4.250 -2.265 -0.520
+ IL 152 152 5 152 4 1 1 25 44 -1.686 -2.369 -1.117 -4.855 0.000 0.000 0.000 0.000
+ IR 153 153 6 153 3 1 1 24 43 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000
+ [ MATL 34 ] 42 - C - - -
+ ML 154 153 6 156 3 1 1 20 39 -8.105 -0.019 -6.759 -1.740 1.591 -2.575 -0.941
+ D 155 153 6 156 3 0 0 19 38 -6.174 -1.687 -0.566
+ IL 156 156 3 156 3 1 1 23 42 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000
+ [ MATL 35 ] 43 - U - - -
+ ML 157 156 3 159 3 1 1 19 37 -8.105 -0.019 -6.759 -1.751 -1.701 -2.496 1.686
+ D 158 156 3 159 3 0 0 18 37 -6.174 -1.687 -0.566
+ IL 159 159 3 159 3 1 1 22 41 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000
+ [ MATL 36 ] 44 - U - - -
+ ML 160 159 3 162 3 1 1 17 36 -8.105 -0.019 -6.759 -1.751 -1.701 -2.496 1.686
+ D 161 159 3 162 3 0 0 17 36 -6.174 -1.687 -0.566
+ IL 162 162 3 162 3 1 1 21 40 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000
+ [ MATL 37 ] 45 - C - - -
+ ML 163 162 3 165 3 1 1 16 35 -8.105 -0.019 -6.759 -2.087 1.706 -2.918 -1.431
+ D 164 162 3 165 3 0 0 16 34 -6.174 -1.687 -0.566
+ IL 165 165 3 165 3 1 1 20 38 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000
+ [ MATL 38 ] 46 - A - - -
+ ML 166 165 3 168 3 1 1 15 33 -8.105 -0.019 -6.759 1.774 -2.658 -2.261 -2.229
+ D 167 165 3 168 3 0 0 15 33 -6.174 -1.687 -0.566
+ IL 168 168 3 168 3 1 1 19 37 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000
+ [ MATL 39 ] 47 - A - - -
+ ML 169 168 3 171 3 1 1 13 31 -8.105 -0.019 -6.759 1.615 -2.105 -1.370 -1.653
+ D 170 168 3 171 3 0 0 13 32 -6.174 -1.687 -0.566
+ IL 171 171 3 171 3 1 1 18 36 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000
+ [ MATL 40 ] 48 - A - - -
+ ML 172 171 3 174 2 1 1 1 1 * 0.000 1.673 -2.026 -1.909 -1.735
+ D 173 171 3 174 2 0 0 0 0 * 0.000
+ IL 174 174 3 174 2 1 1 13 28 -1.823 -0.479 0.000 0.000 0.000 0.000
+ [ END 41 ] - - - - - -
+ E 175 174 3 -1 0 0 0 0 0
+ [ BEGR 42 ] - - - - - -
+ S 176 63 1 177 3 0 2 62 92 -5.308 -0.051 -6.759
+ IL 177 177 2 177 3 1 3 64 94 -1.391 -0.817 -4.293 0.000 0.000 0.000 0.000
+ [ MATL 43 ] 60 - G - - -
+ ML 178 177 2 180 2 1 2 61 92 -8.524 -0.004 -0.345 -1.363 1.036 -0.372
+ D 179 177 2 180 2 0 1 60 91 -8.445 -0.004
+ IL 180 180 3 180 2 1 2 62 93 -1.823 -0.479 0.000 0.000 0.000 0.000
+ [ BIF 44 ] - - - - - -
+ B 181 180 3 182 238 0 1 60 91
+ [ BEGL 45 ] - - - - - -
+ S 182 181 1 183 4 0 0 43 74 -0.077 -6.912 -5.572 -5.472
+ [ MATP 46 ] 61 84 g c - -
+ MP 183 182 1 187 6 2 2 43 74 -9.141 -9.081 -0.021 -7.857 -8.137 -8.532 -2.828 -2.518 -2.910 1.330 -2.640 -3.701 1.923 -3.043 -2.978 1.956 -3.475 -0.185 1.424 -3.002 -0.292 -1.816
+ ML 184 182 1 187 6 1 1 41 72 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094
+ MR 185 182 1 187 6 1 1 41 72 -7.096 -5.825 -1.734 -5.804 -0.750 -4.017 0.214 -0.006 -0.446 0.151
+ D 186 182 1 187 6 0 0 39 70 -9.307 -8.005 -2.087 -4.484 -4.502 -0.577
+ IL 187 187 5 187 6 1 1 43 74 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000
+ IR 188 188 6 188 5 1 1 42 73 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 47 ] 62 83 g c - -
+ MP 189 188 6 193 6 2 2 41 72 -9.158 -9.097 -0.033 -7.873 -8.153 -6.483 -2.851 -2.030 -2.914 1.298 -2.856 -3.683 1.516 -3.163 -3.034 2.316 -3.508 -0.046 1.396 -2.973 -0.600 -1.947
+ ML 190 188 6 193 6 1 1 39 70 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094
+ MR 191 188 6 193 6 1 1 39 70 -7.096 -5.825 -1.422 -5.804 -0.937 -4.017 0.314 -0.574 0.206 -0.102
+ D 192 188 6 193 6 0 0 36 67 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319
+ IL 193 193 5 193 6 1 1 41 72 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000
+ IR 194 194 6 194 5 1 1 40 71 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 48 ] 63 82 g c - -
+ MP 195 194 6 199 6 2 2 39 70 -9.155 -9.094 -0.020 -7.871 -8.150 -8.545 -3.292 -2.415 -3.262 1.373 -3.524 -3.960 1.123 -3.632 -3.471 2.795 -3.864 0.186 0.611 -3.244 -0.920 -2.242
+ ML 196 194 6 199 6 1 1 38 68 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094
+ MR 197 194 6 199 6 1 1 37 68 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094
+ D 198 194 6 199 6 0 0 35 65 -9.249 -7.948 -3.745 -4.427 -4.444 -0.274
+ IL 199 199 5 199 6 1 1 39 70 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000
+ IR 200 200 6 200 5 1 1 38 69 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 49 ] 64 81 g c - -
+ MP 201 200 6 205 6 2 2 37 68 -7.257 -9.094 -0.031 -7.871 -8.150 -7.617 -2.686 -2.330 -2.543 1.156 -2.710 -3.547 1.558 -3.032 -2.883 2.243 -3.099 0.365 1.334 -2.839 -0.459 -1.837
+ ML 202 200 6 205 6 1 1 36 67 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094
+ MR 203 200 6 205 6 1 1 36 66 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094
+ D 204 200 6 205 6 0 0 33 64 -9.249 -7.948 -3.745 -4.427 -4.444 -0.274
+ IL 205 205 5 205 6 1 1 37 68 -2.648 -2.911 -0.715 -4.566 -5.342 -5.002 0.000 0.000 0.000 0.000
+ IR 206 206 6 206 5 1 1 36 67 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 50 ] 66 80 c g - -
+ MP 207 206 6 211 4 2 2 35 66 -7.060 -7.267 -0.049 -5.681 -2.458 -2.323 -2.596 1.137 -2.363 -3.390 2.101 -2.767 -2.635 1.669 -2.380 0.065 1.311 -2.707 -0.002 -1.672
+ ML 208 206 6 211 4 1 1 35 66 -3.758 -3.940 -0.507 -2.670 0.368 -0.385 -0.191 0.094
+ MR 209 206 6 211 4 1 1 34 65 -4.809 -3.838 -1.706 -0.766 0.368 -0.385 -0.191 0.094
+ D 210 206 6 211 4 0 0 33 64 -4.806 -4.487 -1.607 -0.758
+ IL 211 211 5 211 4 1 1 36 67 -1.686 -2.369 -1.117 -4.855 0.000 0.000 0.000 0.000
+ IR 212 212 6 212 3 1 1 35 66 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000
+ [ MATL 51 ] 67 - u - - -
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+ D 214 212 6 215 3 0 0 31 62 -6.174 -1.687 -0.566
+ IL 215 215 3 215 3 1 1 34 65 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000
+ [ MATL 52 ] 68 - a - - -
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+ D 217 215 3 218 3 0 0 30 61 -6.174 -1.687 -0.566
+ IL 218 218 3 218 3 1 1 33 64 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000
+ [ MATL 53 ] 69 - g - - -
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+ D 220 218 3 221 3 0 0 29 60 -6.174 -1.687 -0.566
+ IL 221 221 3 221 3 1 1 32 63 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000
+ [ MATL 54 ] 70 - c - - -
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+ D 223 221 3 224 3 0 0 28 59 -6.174 -1.687 -0.566
+ IL 224 224 3 224 3 1 1 31 62 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000
+ [ MATL 55 ] 71 - a - - -
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+ D 226 224 3 227 3 0 0 25 56 -7.646 -3.159 -0.179
+ IL 227 227 3 227 3 1 1 30 61 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000
+ [ MATL 56 ] 72 - a - - -
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+ D 229 227 3 230 3 0 0 20 51 -7.963 -2.073 -0.399
+ IL 230 230 3 230 3 1 1 30 60 -0.859 -1.224 -5.595 0.000 0.000 0.000 0.000
+ [ MATL 57 ] 78 - c - - -
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+ D 232 230 3 233 3 0 0 12 31 -7.732 -2.169 -0.372
+ IL 233 233 3 233 3 1 1 18 36 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000
+ [ MATL 58 ] 79 - g - - -
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+ D 235 233 3 236 2 0 0 0 0 * 0.000
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+ [ END 59 ] - - - - - -
+ E 237 236 3 -1 0 0 0 0 0
+ [ BEGR 60 ] - - - - - -
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+ [ MATL 61 ] 85 - g - - -
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+ D 241 239 2 242 3 0 0 29 48 -6.174 -1.687 -0.566
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+ [ MATL 62 ] 88 - G - - -
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+ [ MATP 63 ] 89 103 g c - -
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+ ML 247 245 3 250 6 1 1 27 46 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094
+ MR 248 245 3 250 6 1 1 27 46 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094
+ D 249 245 3 250 6 0 0 25 44 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319
+ IL 250 250 5 250 6 1 1 29 47 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000
+ IR 251 251 6 251 5 1 1 28 47 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 64 ] 90 102 g c - -
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+ ML 253 251 6 256 6 1 1 26 45 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094
+ MR 254 251 6 256 6 1 1 26 44 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094
+ D 255 251 6 256 6 0 0 23 42 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319
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+ IR 257 257 6 257 5 1 1 26 45 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 65 ] 91 101 G C - -
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+ ML 259 257 6 262 6 1 1 24 43 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094
+ MR 260 257 6 262 6 1 1 24 43 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094
+ D 261 257 6 262 6 0 0 23 42 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319
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+ IR 263 263 6 263 5 1 1 24 43 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 66 ] 92 100 G C - -
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+ ML 265 263 6 268 4 1 1 24 43 -3.758 -3.940 -0.507 -2.670 0.368 -0.385 -0.191 0.094
+ MR 266 263 6 268 4 1 1 23 42 -4.809 -3.838 -1.706 -0.766 0.368 -0.385 -0.191 0.094
+ D 267 263 6 268 4 0 0 22 41 -4.568 -4.250 -2.265 -0.520
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+ IR 269 269 6 269 3 1 1 24 43 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000
+ [ MATL 67 ] 93 - U - - -
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+ D 271 269 6 272 3 0 0 19 38 -6.174 -1.687 -0.566
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+ [ MATL 68 ] 94 - U - - -
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+ D 274 272 3 275 3 0 0 18 37 -6.174 -1.687 -0.566
+ IL 275 275 3 275 3 1 1 22 41 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000
+ [ MATL 69 ] 95 - C - - -
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+ D 277 275 3 278 3 0 0 17 36 -6.174 -1.687 -0.566
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+ [ MATL 70 ] 96 - G - - -
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+ [ MATL 71 ] 97 - A - - -
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+ D 283 281 3 284 3 0 0 15 33 -6.174 -1.687 -0.566
+ IL 284 284 3 284 3 1 1 19 37 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000
+ [ MATL 72 ] 98 - U - - -
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+ D 286 284 3 287 3 0 0 13 32 -6.174 -1.687 -0.566
+ IL 287 287 3 287 3 1 1 18 36 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000
+ [ MATL 73 ] 99 - U - - -
+ ML 288 287 3 290 2 1 1 1 1 * 0.000 -1.751 -1.701 -2.496 1.686
+ D 289 287 3 290 2 0 0 0 0 * 0.000
+ IL 290 290 3 290 2 1 1 13 28 -1.823 -0.479 0.000 0.000 0.000 0.000
+ [ END 74 ] - - - - - -
+ E 291 290 3 -1 0 0 0 0 0
+//
+HMMER3/f [i1.1.1 | July 2014]
+NAME tRNA-Sec
+ACC RF01852
+LENG 91
+MAXL 164
+ALPH RNA
+RF no
+MM no
+CONS yes
+CS yes
+MAP yes
+DATE Tue Apr 8 16:22:29 2014
+COM [1] cmbuild -F CM SEED
+NSEQ 109
+EFFN 12.031647
+CKSUM 3407454328
+STATS LOCAL MSV -8.8824 0.71862
+STATS LOCAL VITERBI -9.9312 0.71862
+STATS LOCAL FORWARD -3.8558 0.71862
+HMM A C G U
+ m->m m->i m->d i->m i->i d->m d->d
+ COMPO 1.70134 1.32390 1.18487 1.40373
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+ 0.01415 4.95852 4.95852 1.46634 0.26236 1.09861 0.40547
+ 55 1.86138 1.70656 0.70926 1.76582 69 g - - _
+ 1.38629 1.38629 1.38629 1.38629
+ 0.01415 4.95852 4.95852 1.46634 0.26236 1.09861 0.40547
+ 56 1.47976 0.91726 1.83821 1.54367 70 c - - _
+ 1.38629 1.38629 1.38629 1.38629
+ 0.32769 4.95852 1.30051 1.46634 0.26236 1.09861 0.40547
+ 57 0.97318 2.06516 1.55730 1.25661 71 a - - _
+ 1.38629 1.38629 1.38629 1.38629
+ 0.17155 4.65013 1.90998 1.46634 0.26236 3.70829 0.02482
+ 58 1.06331 2.38788 0.93712 1.76545 72 g - - _
+ 1.38629 1.38629 1.38629 1.38629
+ 0.87578 0.55798 4.50103 1.07474 0.41762 1.53834 0.24174
+ 59 1.38578 0.97732 1.80136 1.56793 78 c - - _
+ 1.38629 1.38629 1.38629 1.38629
+ 0.02000 4.61491 4.61491 1.46634 0.26236 1.67341 0.20777
+ 60 1.57377 1.68541 0.97877 1.46276 79 g - - _
+ 1.38629 1.38629 1.38629 1.38629
+ 0.07096 4.68499 2.82574 1.46634 0.26236 0.05546 2.91976
+ 61 2.06062 1.64562 0.77989 1.50833 80 g - - >
+ 1.38629 1.38629 1.38629 1.38629
+ 0.01471 4.91972 4.91972 1.46634 0.26236 1.34349 0.30237
+ 62 1.70713 1.02312 1.54036 1.40716 81 c - - >
+ 1.38629 1.38629 1.38629 1.38629
+ 0.01458 4.92842 4.92842 1.46634 0.26236 1.97715 0.14904
+ 63 2.89857 0.56210 2.04339 1.40528 82 C - - >
+ 1.38629 1.38629 1.38629 1.38629
+ 0.01458 4.92842 4.92842 1.46634 0.26236 0.32424 1.28400
+ 64 1.63664 0.90314 1.74469 1.48999 83 c - - >
+ 1.38629 1.38629 1.38629 1.38629
+ 0.05438 4.95852 3.08113 1.46634 0.26236 1.09861 0.40547
+ 65 1.72370 1.36000 1.14821 1.39542 84 g - - >
+ 1.38629 1.38629 1.38629 1.38629
+ 0.01472 4.91886 4.91886 1.46634 0.26236 0.26695 1.45119
+ 66 1.35133 2.33276 0.83027 1.56953 85 g - - ,
+ 1.38629 1.38629 1.38629 1.38629
+ 0.91781 1.29094 1.12211 0.26730 1.45005 1.09861 0.40547
+ 67 3.42263 4.76246 0.05610 4.31361 88 G - - ,
+ 1.38629 1.38629 1.38629 1.38629
+ 0.02083 4.57496 4.57496 1.46634 0.26236 0.04224 3.18550
+ 68 2.40165 1.46418 1.09113 1.07198 89 u - - <
+ 1.38629 1.38629 1.38629 1.38629
+ 0.01415 4.95852 4.95852 1.46634 0.26236 1.09861 0.40547
+ 69 1.46579 2.34101 0.72522 1.66783 90 g - - <
+ 1.38629 1.38629 1.38629 1.38629
+ 0.01415 4.95852 4.95852 1.46634 0.26236 1.09861 0.40547
+ 70 2.53454 3.29649 0.16181 3.40871 91 G - - <
+ 1.38629 1.38629 1.38629 1.38629
+ 0.01415 4.95852 4.95852 1.46634 0.26236 1.09861 0.40547
+ 71 3.94603 5.00978 0.03331 4.99753 92 G - - <
+ 1.38629 1.38629 1.38629 1.38629
+ 0.01415 4.95852 4.95852 1.46634 0.26236 1.09861 0.40547
+ 72 4.62647 4.34036 5.19036 0.02880 93 U - - _
+ 1.38629 1.38629 1.38629 1.38629
+ 0.01415 4.95852 4.95852 1.46634 0.26236 1.09861 0.40547
+ 73 4.62647 4.34036 5.19036 0.02880 94 U - - _
+ 1.38629 1.38629 1.38629 1.38629
+ 0.01415 4.95852 4.95852 1.46634 0.26236 1.09861 0.40547
+ 74 4.57048 0.05600 4.95731 3.29483 95 C - - _
+ 1.38629 1.38629 1.38629 1.38629
+ 0.01415 4.95852 4.95852 1.46634 0.26236 1.09861 0.40547
+ 75 1.39428 4.02231 0.34268 3.72093 96 G - - _
+ 1.38629 1.38629 1.38629 1.38629
+ 0.01415 4.95852 4.95852 1.46634 0.26236 1.09861 0.40547
+ 76 0.03754 4.71976 4.55271 4.05206 97 A - - _
+ 1.38629 1.38629 1.38629 1.38629
+ 0.01415 4.95852 4.95852 1.46634 0.26236 1.09861 0.40547
+ 77 2.76170 1.38220 3.65009 0.41582 98 U - - _
+ 1.38629 1.38629 1.38629 1.38629
+ 0.01415 4.95852 4.95852 1.46634 0.26236 1.09861 0.40547
+ 78 4.62647 4.34036 5.19036 0.02880 99 U - - _
+ 1.38629 1.38629 1.38629 1.38629
+ 0.01415 4.95852 4.95852 1.46634 0.26236 1.09861 0.40547
+ 79 4.99796 0.04217 4.88940 3.61140 100 C - - >
+ 1.38629 1.38629 1.38629 1.38629
+ 0.01415 4.95852 4.95852 1.46634 0.26236 1.09861 0.40547
+ 80 3.56964 0.18145 3.17643 2.34297 101 C - - >
+ 1.38629 1.38629 1.38629 1.38629
+ 0.01415 4.95852 4.95852 1.46634 0.26236 1.09861 0.40547
+ 81 1.78072 0.76538 2.20592 1.36189 102 c - - >
+ 1.38629 1.38629 1.38629 1.38629
+ 0.01415 4.95852 4.95852 1.46634 0.26236 1.09861 0.40547
+ 82 1.19739 1.28841 1.31644 1.86936 103 a - - >
+ 1.38629 1.38629 1.38629 1.38629
+ 0.10289 2.84385 3.22957 0.62979 0.76079 1.09861 0.40547
+ 83 2.74933 0.64577 2.53047 1.10217 107 C - - )
+ 1.38629 1.38629 1.38629 1.38629
+ 0.11206 4.92543 2.31516 1.46634 0.26236 0.50228 0.92925
+ 84 1.45207 1.72283 1.27059 1.18192 108 u - - )
+ 1.38629 1.38629 1.38629 1.38629
+ 0.01565 4.85800 4.85800 1.46634 0.26236 0.92103 0.50768
+ 85 2.27145 0.78905 2.07976 1.14697 109 c - - )
+ 1.38629 1.38629 1.38629 1.38629
+ 0.02960 4.90068 3.82920 1.46634 0.26236 0.32022 1.29460
+ 86 1.58507 1.54867 1.32564 1.14917 110 u - - )
+ 1.38629 1.38629 1.38629 1.38629
+ 0.02055 4.93770 4.32961 1.46634 0.26236 0.41102 1.08760
+ 87 2.77949 0.51912 2.06907 1.52978 111 C - - )
+ 1.38629 1.38629 1.38629 1.38629
+ 0.02174 4.95263 4.23795 1.46634 0.26236 0.73658 0.65152
+ 88 2.70354 1.36407 1.56126 0.76027 112 u - - )
+ 1.38629 1.38629 1.38629 1.38629
+ 0.01425 4.95116 4.95116 1.46634 0.26236 1.39712 0.28410
+ 89 2.36677 1.28174 1.23556 1.08473 113 u - - )
+ 1.38629 1.38629 1.38629 1.38629
+ 0.02107 4.95116 4.28509 1.46634 0.26236 1.39712 0.28410
+ 90 2.57152 0.65054 1.45004 1.78822 114 C - - )
+ 1.38629 1.38629 1.38629 1.38629
+ 0.13853 4.94445 2.10175 1.46634 0.26236 0.51215 0.91431
+ 91 4.88296 0.06879 4.12716 3.15179 115 C - - )
+ 1.38629 1.38629 1.38629 1.38629
+ 0.27766 1.41698 * 1.16143 0.37548 0.00000 *
+//
diff --git a/testsuite/5.claninfo b/testsuite/5.claninfo
new file mode 100644
index 00000000..50816e4a
--- /dev/null
+++ b/testsuite/5.claninfo
@@ -0,0 +1 @@
+CL00001 tRNA tRNA-Sec
diff --git a/testsuite/Rfam.12.1.clanin b/testsuite/Rfam.12.1.clanin
new file mode 100644
index 00000000..fbdf3770
--- /dev/null
+++ b/testsuite/Rfam.12.1.clanin
@@ -0,0 +1,104 @@
+CL00001 tRNA cyano_tmRNA tRNA-Sec mt-tmRNA
+CL00003 Metazoa_SRP Bacteria_small_SRP Fungi_SRP Dictyostelium_SRP Bacteria_large_SRP Plant_SRP Protozoa_SRP Archaea_SRP
+CL00004 Telomerase-cil
+CL00008 U54 snoU54
+CL00010 Hammerhead_3 Hammerhead_1 Hammerhead_HH9 Hammerhead_II Hammerhead_HH10
+CL00011 GlmZ_SraJ GlmY_tke1
+CL00012 SAM SAM-IV
+CL00013 7SK Arthropod_7SK
+CL00014 CRISPR-DR2 CRISPR-DR4 CRISPR-DR14 CRISPR-DR17 CRISPR-DR25 CRISPR-DR43 CRISPR-DR66
+CL00015 CRISPR-DR5 CRISPR-DR7 CRISPR-DR63 CRISPR-DR64
+CL00016 FinP traJ_5
+CL00017 IRES_HCV IRES_Pesti
+CL00018 SCARNA24 SCARNA3
+CL00019 SCARNA4 SCARNA15
+CL00021 SNORA16 SNORA2 snopsi28S-3327 snR189 snR46 S_pombe_snR46
+CL00022 SNORA3 snR11
+CL00023 SNORA4 snR83
+CL00024 SNORA5 snR85
+CL00025 SNORA7 snR81
+CL00026 SNORA8 snR31
+CL00027 SNORA9 snR33 snR43 S_pombe_snR33
+CL00028 SNORA13 snR35 S_pombe_snR35
+CL00029 SNORA43 SNORA17
+CL00030 SNORA20 SNORA29
+CL00031 SNORA21 snR10 S_pombe_snR10
+CL00032 SNORA27 SNORA26 snR42 S_pombe_snR42
+CL00033 SNORA28 snopsi18S-841 snR80
+CL00034 SNORA50 SNORA54 SNORA35 SNORA76
+CL00035 SNORA36 snR36 snR44 S_pombe_snR36
+CL00036 SNORA44 SNORA58 snR161 snR9
+CL00037 SNORA48 snR86
+CL00038 SNORA66 snoR98 SNORA52 SNORA18 snoR80 snR49 snR5 S_pombe_snR5
+CL00039 SNORA56 snR8
+CL00040 SNORA62 snR3 snR82 S_pombe_snR3
+CL00041 SNORA64 snR37
+CL00042 SNORA65 snR34 snoR2
+CL00043 SNORA74 snR191
+CL00044 SNORD12 snR190
+CL00045 SNORD15 snR75 snR13 snoZ5
+CL00046 SNORD16 snR87
+CL00047 SNORD18 snoU18
+CL00048 SNORD19 SNORD19B
+CL00049 SNORD25 snR56
+CL00050 SNORD26 SNORD81
+CL00051 SNORD36 SNORD29 snoZ223 SNORD38 snosnR69 snosnR61 snosnR71 SNORD78 snoR69Y snR47 snoU36a
+CL00052 SNORD30 snoU30
+CL00053 SNORD31 snoZ17 snR67 snoR35
+CL00054 SNORD33 snoZ196 SNORD51 snosnR55 snoMe18S-Um1356 snoMe28S-Am982 snR39 snR40
+CL00055 SNORD34 snR62
+CL00056 SNORD35 snoZ161_228 snR73
+CL00057 SNORD39 snoZ7 snoZ101 SNORD65 snoR77Y snR77
+CL00058 SNORD57 SNORD41 snR51
+CL00059 SNORD43 snR70
+CL00060 SNORD44 snoZ102_R77
+CL00061 SNORD46 snR63
+CL00062 SNORD49 snoZ112 snoU49
+CL00063 SNORD52 SNORD53_SNORD92 snoZ157 snR78
+CL00064 SNORD58 SNORD99
+CL00065 snoZ159 SNORD59 snosnR54
+CL00066 SNORD60 snoR1 snosnR48 snoMe28S-G3255 sn2903
+CL00067 SNORD61 snoU61 SNORD125
+CL00068 SNORD62 snoR41 snR41
+CL00069 SNORD79 SNORD113 SNORD74 snoR44_J54 snosnR64 snoMe28S-Cm2645 SNORD64 SNORD112 SNORD109A
+CL00070 snosnR60_Z15 SNORD77 Afu_263
+CL00071 SNORD88 snR76 snoR118
+CL00072 SNORD96 SNORD2
+CL00073 snoR30 SNORD100
+CL00074 SNORD101 snoR60
+CL00075 SNORD105 snoU105B
+CL00076 SNORD110 snoR14
+CL00077 SNORND104 snR58
+CL00078 SNORA73 snR30
+CL00079 snR68 snoR27
+CL00080 snoR53 snoR53Y
+CL00081 snoZ279_R105_R108 snoU13
+CL00082 snoU89 snoU85
+CL00083 mir-6 mir-11
+CL00084 mir-3 mir-318
+CL00085 mir-16 mir-15
+CL00086 mir-28 mir-708
+CL00087 mir-34 mir-449
+CL00088 mir-36 mir-42 mir-35
+CL00089 mir-190 mir-50
+CL00090 mir-74 mir-73
+CL00091 bantam mir-81
+CL00092 mir-137 mir-234
+CL00093 mir-183 mir-182 mir-263 mir-228
+CL00094 mir-216 mir-283
+CL00095 mir-279 mir-996
+CL00096 mir-515 mir-290 mir-302 miR-430
+CL00097 mir-BART1 mir-BART3
+CL00098 MIR169_2 MIR169_5
+CL00099 MIR171_1 MIR171_2
+CL00100 U3 Fungi_U3 Plant_U3 ACEA_U3
+CL00101 Cobalamin
+CL00102 group-II-D1D4-1 group-II-D1D4-2 group-II-D1D4-3 group-II-D1D4-4 group-II-D1D4-5 group-II-D1D4-6 group-II-D1D4-7
+CL00103 SNORD11 SNORD11B
+CL00104 HBV_epsilon AHBV_epsilon
+CL00105 SraC_RyeA RyeB
+CL00106 CsrB CsrC PrrB_RsmZ RsmY TwoAYGGAY rsmX
+CL00108 suhB
+CL00110 mir-19 mir-363
+CL00111 SSU_rRNA_bacteria SSU_rRNA_archaea SSU_rRNA_eukarya SSU_rRNA_microsporidia
+CL00112 LSU_rRNA_archaea LSU_rRNA_bacteria LSU_rRNA_eukarya
diff --git a/testsuite/bug-i38.pl b/testsuite/bug-i38.pl
index 13f67d71..8520a278 100755
--- a/testsuite/bug-i38.pl
+++ b/testsuite/bug-i38.pl
@@ -52,7 +52,7 @@ END
}
foreach $tmpfile ("i38.1", "i38.2", "i38.3", "i38.cm") {
-# unlink $tmpfile if -e $tmpfile;
+ unlink $tmpfile if -e $tmpfile;
}
if ($ok) { print "ok\n"; exit 0; }
else { print "FAILED\n"; exit 1; }
diff --git a/testsuite/bug-i44.pl b/testsuite/bug-i44.pl
index f8a1be3a..eb75c471 100755
--- a/testsuite/bug-i44.pl
+++ b/testsuite/bug-i44.pl
@@ -74,7 +74,7 @@ END
}
foreach $tmpfile ("i44.1", "i44.2", "i44.3", "i44.cm") {
-# unlink $tmpfile if -e $tmpfile;
+ unlink $tmpfile if -e $tmpfile;
}
if ($ok) { print "ok\n"; exit 0; }
else { print "FAILED\n"; exit 1; }
diff --git a/testsuite/dev_testsuite.sqc b/testsuite/dev_testsuite.sqc
index abc20514..af46b75d 100644
--- a/testsuite/dev_testsuite.sqc
+++ b/testsuite/dev_testsuite.sqc
@@ -1,4 +1,4 @@
-# Infernal's cmalign crash exercises, in sqc command format.
+# Infernal's 'developer testsuite' crash exercises, in sqc command format.
# EPN, Thu Jan 3 05:20:12 2008
# EPN, Mon Mar 5 15:24:44 2012 [Updated for 1.1 release]
#
@@ -59,6 +59,7 @@
1 exercise itest/sensitivity !testsuite/itest6-sensitivity.pl! @@ !! %OUTFILES%
1 exercise itest/trunc !testsuite/itest7-trunc.pl! @@ !! %OUTFILES%
1 exercise itest/scan-glist !testsuite/itest8-glist.pl! @@ !! %OUTFILES%
+1 exercise itest/scan-overlaps !testsuite/itest9-overlaps.pl! @@ !! %OUTFILES%
1 exercise itest/brute @src/itest_brute@
################################################################
@@ -85,6 +86,7 @@
1 exercise bug/i38-mapali-noss !testsuite/bug-i38.pl! @src/cmbuild@ @src/cmalign@
1 exercise bug/i39-build-O-0bp !testsuite/bug-i39.pl! @src/cmbuild@
1 exercise bug/i43-oa-loc-beg !testsuite/bug-i43.pl! @src/cmsearch@ !testsuite/bug-i43.cm! !testsuite/bug-i43.fa!
+1 exercise bug/i44-mapstr !testsuite/bug-i44.pl! @src/cmbuild@ @src/cmalign@
################################################################
# Option tests
@@ -106,6 +108,7 @@
1 prep copy/sC cp !testsuite/Plant_SRP.c.cm! %SRP.C.CM%
1 prep copy/zbpC cp !testsuite/snR75.c.cm! %ZBP.C.CM%
1 prep copy/4C cp !testsuite/4.c.cm! %4.C.CM%
+1 prep copy/5C cp !testsuite/5.c.cm! %5.C.CM%
1 exercise search/help/1 @src/cmsearch@ -h
1 exercise search/help/2 @src/cmsearch@ --devhelp
@@ -135,6 +138,7 @@
1 exercise press/sC @src/cmpress@ %SRP.C.CM%
1 exercise press/zC @src/cmpress@ %ZBP.C.CM%
1 exercise press/4C @src/cmpress@ %4.C.CM%
+1 exercise press/5C @src/cmpress@ %5.C.CM%
# cmscan exercises (cmscan requires a press'd CM file with E-values)
1 exercise scan/help/1 @src/cmscan@ -h
@@ -149,6 +153,8 @@
1 prep cleanup/zC rm -f %ZBP.C.CM%.*
1 exercise scan/4C @src/cmscan@ -Z 1000 %4.C.CM% !testsuite/emitted-tRNA.fa!
1 prep cleanup/4C rm -f %4.C.CM%.*
+1 exercise scan/5C @src/cmscan@ --fmt 2 --tblout %5.C.TBLOUT% --oskip --oclan --clanin !testsuite/5.claninfo! -Z 1000 %5.C.CM% !testsuite/emitted-tRNA.fa!
+1 prep cleanup/5C rm -f %5.C.CM%.*
# cmemit exercises
1 exercise emit/help/1 @src/cmemit@ -h
@@ -1055,9 +1061,11 @@
1 prep scan:copy/tC cp !testsuite/tRNA.c.cm! %T.CM%
1 prep scan:copy/vC cp !testsuite/Vault.c.cm! %V.CM%
1 prep scan:copy/4C cp !testsuite/4.c.cm! %4.CM%
+1 prep scan:copy/5C cp !testsuite/5.c.cm! %5.CM%
1 exercise scan:press/tC @src/cmpress@ %T.CM%
1 exercise scan:press/vC @src/cmpress@ %V.CM%
1 exercise scan:press/4C @src/cmpress@ %4.CM%
+1 exercise scan:press/5C @src/cmpress@ %5.CM%
# copy fasta files, only so the names are more convenient in rest of this file
1 prep scan:copy/t/fa1k cp !testsuite/1k-tRNA.fa! %T1K%
@@ -1071,6 +1079,7 @@
1 prep scan:copy/4/fa10k cp !testsuite/10k-4.fa! %410K%
1 prep scan:copy/4/fa100k cp !testsuite/100k-4.fa! %4100K%
1 prep scan:copy/4/faemit cp !testsuite/emitted-4.fa! %4EMIT%
+1 prep scan:copy/5/faemit cp !testsuite/emitted-5.fa! %5EMIT%
1 prep scan:copy/rand/fa1k cp !testsuite/1k.fa! %R1K%
1 exercise scan:t/10k @src/cmscan@ %T.CM% %T10K%
@@ -1079,9 +1088,21 @@
1 exercise scan:t/emit @src/cmscan@ %T.CM% %TEMIT%
1 exercise scan:v/emit @src/cmscan@ %V.CM% %VEMIT%
1 exercise scan:4/emit @src/cmscan@ %4.CM% %4EMIT%
+1 exercise scan:5/emit @src/cmscan@ %5.CM% %5EMIT%
1 exercise scan:4/emit/glist @src/cmscan@ --glist !testsuite/2name.list! %4.CM% %4EMIT%
+# new-as-of-1.2 exercises with new cmscan options --fmt, --clanin, --oclan, --oskip
+1 exercise scan:5/emit/fmt1 @src/cmscan@ --fmt 1 --tblout %TMPOUT% %5.CM% %5EMIT%
+1 exercise scan:5/emit/fmt2 @src/cmscan@ --fmt 2 --tblout %TMPOUT% %5.CM% %5EMIT%
+1 exercise scan:5/emit/clan @src/cmscan@ --clanin !testsuite/5.claninfo! --fmt 2 --tblout %TMPOUT% %5.CM% %5EMIT%
+1 exercise scan:5/emit/oclan @src/cmscan@ --oclan --clanin !testsuite/5.claninfo! --fmt 2 --tblout %TMPOUT% %5.CM% %5EMIT%
+1 exercise scan:5/emit/oskip1 @src/cmscan@ --oskip --fmt 2 --tblout %TMPOUT% %5.CM% %5EMIT%
+1 exercise scan:5/emit/oskip2 @src/cmscan@ --oskip --oclan --clanin !testsuite/5.claninfo! --fmt 2 --tblout %TMPOUT% %5.CM% %5EMIT%
+1 fail scan:5/emit/nofmt1 @src/cmscan@ --clanin !testsuite/5.claninfo! --tblout %TMPOUT% %5.CM% %5EMIT%
+1 fail scan:5/emit/nofmt2 @src/cmscan@ --oskip --tblout %TMPOUT% %5.CM% %5EMIT%
+1 fail scan:5/emit/noclan @src/cmscan@ --oclan --fmt 2 --tblout %TMPOUT% %5.CM% %5EMIT%
+
1 fail scan:t/cm/stdin cat %T.CM% | @src/cmscan@ - %TEMIT%
1 fail scan:4/cm/stdin cat %4.CM% | @src/cmscan@ - %4EMIT%
1 exercise scan:t/sq/stdin cat %TEMIT% | @src/cmscan@ %T.CM% -
diff --git a/testsuite/emitted-5.fa b/testsuite/emitted-5.fa
new file mode 100644
index 00000000..b828559a
--- /dev/null
+++ b/testsuite/emitted-5.fa
@@ -0,0 +1,19 @@
+>tRNA-cmconsensus
+GgggaugUAGCucAgUGGUAgaGCaucgGaCUuuuAAuCcgaaggcgcgGGUUCgAaUCC
+cgccaucccCA
+>Vault-cmconsensus
+GgGccGGCUUUAGCucAGcGGUUACuUCgacuauuauaauuuuauuuuuuuauauuuuuc
+uuuuggGGUucGAaaCCCgCggGCGCUgUCCggCccUUUU
+>snR75-hmmconsensus
+uuauGAUGAguuuuuuUAGAUGACGAGUCugAuucGaGuUuuCcauGauGAcAaaacuuU
+UUUuaUUACCAUUCAUGCaUUUCUGAaa
+>Plant_SRP-cmconsensus
+GcCgagcucacUAACgugagcuuGUaACCCaAGuGGGGgCAucaagguGguggaccguug
+ggccgcuccacccggccGGgcccgcugucugccauuuuccgGcccGcCCguUCCAcGccg
+ggAGcUgggccgcguggcccgggCGAAGGcccgggccacgcggccccuAaagcGGcgggc
+AccgCGuGAGGCUGGuUUCACAGAGCAgCGaguaccgCCggCUcccggCgGUGGAaGGAU
+aaCgggCcggugcagcgcgggcCCAcuaaggccgggugggcggccccaaucggAccacCa
+ccuug
+>tRNA-Sec-cmconsensus
+GggggggcgaucggcccUGGUgggccguccGGgCUUCAAAcCCggaGggggcuagcaacg
+gccccgGggGGUUCGAUUCCcccgccccccC
diff --git a/testsuite/i1.pm b/testsuite/i1.pm
index 9bdba621..c12121c5 100644
--- a/testsuite/i1.pm
+++ b/testsuite/i1.pm
@@ -2,7 +2,7 @@
package i1;
-sub ParseTbl {
+sub ParseTblFormat1 {
my ($tblfile) = @_;
my (@fields);
@@ -23,6 +23,7 @@ sub ParseTbl {
@hitbias = ();
@hitsc = ();
@hitE = ();
+ @inc = ();
@tdesc = ();
if (! open(TBLFILE, $tblfile)) { print "FAIL: couldn't open table file"; exit 1 ; }
@@ -30,7 +31,7 @@ sub ParseTbl {
{
if (/^\#/) { next; }
chop;
- @fields = split(' ', $_, 17);
+ @fields = split(' ', $_, 18);
$tname[$ntbl] = $fields[0];
$tacc[$ntbl] = $fields[1];
@@ -48,7 +49,81 @@ sub ParseTbl {
$hitbias[$ntbl] = $fields[13];
$hitsc[$ntbl] = $fields[14];
$hitE[$ntbl] = $fields[15];
- $tdesc[$ntbl] = $fields[16];
+ $inc[$ntbl] = $fields[16];
+ $tdesc[$ntbl] = $fields[17];
+ $ntbl++;
+ }
+ close TBLFILE;
+ 1;
+}
+
+sub ParseTblFormat2 {
+ my ($tblfile) = @_;
+ my (@fields);
+
+ $ntbl = 0;
+ @tidx = ();
+ @tname = ();
+ @tacc = ();
+ @qname = ();
+ @qacc = ();
+ @clan = ();
+ @model = ();
+ @mfrom = ();
+ @mto = ();
+ @sfrom = ();
+ @sto = ();
+ @strand = ();
+ @trunc = ();
+ @pass = ();
+ @hitgc = ();
+ @hitbias = ();
+ @hitsc = ();
+ @hitE = ();
+ @inc = ();
+ @olp = ();
+ @anyidx = ();
+ @anyfrct1 = ();
+ @anyfrct2 = ();
+ @winidx = ();
+ @winfrct1 = ();
+ @winfrct2 = ();
+ @tdesc = ();
+
+ if (! open(TBLFILE, $tblfile)) { print "FAIL: couldn't open table file"; exit 1 ; }
+ while ()
+ {
+ if (/^\#/) { next; }
+ chop;
+ @fields = split(' ', $_, 27);
+
+ $tidx[$ntbl] = $fields[0];
+ $tname[$ntbl] = $fields[1];
+ $tacc[$ntbl] = $fields[2];
+ $qname[$ntbl] = $fields[3];
+ $qacc[$ntbl] = $fields[4];
+ $clan[$ntbl] = $fields[5];
+ $model[$ntbl] = $fields[6];
+ $mfrom[$ntbl] = $fields[7];
+ $mto[$ntbl] = $fields[8];
+ $sfrom[$ntbl] = $fields[9];
+ $sto[$ntbl] = $fields[10];
+ $strand[$ntbl] = $fields[11];
+ $trunc[$ntbl] = $fields[12];
+ $pass[$ntbl] = $fields[13];
+ $hitgc[$ntbl] = $fields[14];
+ $hitbias[$ntbl] = $fields[15];
+ $hitsc[$ntbl] = $fields[16];
+ $hitE[$ntbl] = $fields[17];
+ $inc[$ntbl] = $fields[18];
+ $olp[$ntbl] = $fields[19];
+ $anyidx[$ntbl] = $fields[20];
+ $anyfrct1[$ntbl] = $fields[21];
+ $anyfrct2[$ntbl] = $fields[22];
+ $winidx[$ntbl] = $fields[23];
+ $winfrct1[$ntbl] = $fields[24];
+ $winfrct2[$ntbl] = $fields[25];
+ $tdesc[$ntbl] = $fields[26];
$ntbl++;
}
close TBLFILE;
diff --git a/testsuite/itest2-duplicate-names.pl b/testsuite/itest2-duplicate-names.pl
index 147e6cb2..7bf453ff 100755
--- a/testsuite/itest2-duplicate-names.pl
+++ b/testsuite/itest2-duplicate-names.pl
@@ -77,14 +77,14 @@ BEGIN
$output = `$builddir/src/cmsearch --tblout $tmppfx.tbl $tmppfx.cm $tmppfx.fa 2>&1`;
if ($? != 0) { die "FAIL: cmsearch failed\n"; }
-&i1::ParseTbl("$tmppfx.tbl");
+&i1::ParseTblFormat1("$tmppfx.tbl");
if ($i1::ntbl != 4) { die "FAIL: on expected number of hits, cmsearch\n"; }
# cmscan should show four results
$output = `$builddir/src/cmscan --tblout $tmppfx.tbl $tmppfx.cm $tmppfx.fa 2>&1`;
if ($? != 0) { die "FAIL: cmscan failed\n"; }
-&i1::ParseTbl("$tmppfx.tbl");
+&i1::ParseTblFormat1("$tmppfx.tbl");
if ($i1::ntbl != 4) { die "FAIL: on expected number of hits, cmscan\n"; }
print "ok\n";
diff --git a/testsuite/itest5-pipeline.pl b/testsuite/itest5-pipeline.pl
index 6f02581e..d506a5cd 100755
--- a/testsuite/itest5-pipeline.pl
+++ b/testsuite/itest5-pipeline.pl
@@ -63,7 +63,7 @@ BEGIN
$output = `$builddir/src/cmsearch -E 0.1 --tblout $tmppfx.tbl $tmppfx.cm $tmppfx.fa 2>&1`;
if ($? != 0) { die "FAIL: cmsearch failed\n"; }
-&i1::ParseTbl("$tmppfx.tbl");
+&i1::ParseTblFormat1("$tmppfx.tbl");
if ($i1::ntbl != 2) { die "FAIL: on expected number of hits, cmsearch (single model)\n"; }
if ($i1::sfrom[0] ne "199872") { die "FAIL: on seq from, hit 1, cmsearch (single model)\n"; }
if ($i1::sto[0] ne "199963") { die "FAIL: on seq to, hit 1, cmsearch (single model)\n"; }
@@ -76,7 +76,7 @@ BEGIN
$output = `$builddir/src/cmsearch -E 0.1 --tblout $tmppfx.tbl $tmppfx.cm2 $tmppfx.fa 2>&1`;
if ($? != 0) { die "FAIL: cmsearch failed\n"; }
-&i1::ParseTbl("$tmppfx.tbl");
+&i1::ParseTblFormat1("$tmppfx.tbl");
if ($i1::ntbl != 2) { die "FAIL: on expected number of hits, cmsearch (multi model)\n"; }
if ($i1::sfrom[0] ne "199872") { die "FAIL: on seq from, hit 1, cmsearch (multi model)\n"; }
if ($i1::sto[0] ne "199963") { die "FAIL: on seq to, hit 1, cmsearch (multi model)\n"; }
@@ -103,7 +103,7 @@ BEGIN
$output = `$builddir/src/cmscan -E 0.1 --tblout $tmppfx.tbl $tmppfx.cm $tmppfx.fa 2>&1`;
if ($? != 0) { die "FAIL: cmscan failed\n"; }
-&i1::ParseTbl("$tmppfx.tbl");
+&i1::ParseTblFormat1("$tmppfx.tbl");
if ($i1::ntbl != 2) { die "FAIL: on expected number of hits, cmscan (single model)\n"; }
if ($i1::sfrom[0] ne "199872") { die "FAIL: on seq from, hit 1, cmscan (single model)\n"; }
if ($i1::sto[0] ne "199963") { die "FAIL: on seq to, hit 1, cmscan (single model)\n"; }
@@ -116,7 +116,7 @@ BEGIN
$output = `$builddir/src/cmscan -E 0.1 --tblout $tmppfx.tbl $tmppfx.cm2 $tmppfx.fa 2>&1`;
if ($? != 0) { die "FAIL: cmscan failed\n"; }
-&i1::ParseTbl("$tmppfx.tbl");
+&i1::ParseTblFormat1("$tmppfx.tbl");
if ($i1::ntbl != 2) { die "FAIL: on expected number of hits, cmscan (multi model)\n"; }
if ($i1::sfrom[0] ne "199872") { die "FAIL: on seq from, hit 1, cmscan (multi model)\n"; }
if ($i1::sto[0] ne "199963") { die "FAIL: on seq to, hit 1, cmscan (multi model)\n"; }
diff --git a/testsuite/itest6-sensitivity.pl b/testsuite/itest6-sensitivity.pl
index d4081ac5..61eff339 100755
--- a/testsuite/itest6-sensitivity.pl
+++ b/testsuite/itest6-sensitivity.pl
@@ -108,7 +108,7 @@ BEGIN
$output = `$builddir/src/cmsearch -E 1E-3 --tblout $tmppfx.tbl $tmppfx.cm1 $tmppfx.fa 2>&1`;
if ($? != 0) { die "FAIL: cmsearch failed\n"; }
# first hit should be the best (and only real) tRNAscan-SE hit, 4169..4230
-&i1::ParseTbl("$tmppfx.tbl");
+&i1::ParseTblFormat1("$tmppfx.tbl");
if ($i1::ntbl < 1) { die "FAIL: cmsearch tRNA, no hits found\n"; }
if ($i1::sfrom[0] ne "4169") { die "FAIL: cmsearch tRNA hit 1, start position\n"; }
if ($i1::sto[0] ne "4230") { die "FAIL: cmsearch tRNA hit 1, stop position\n"; }
@@ -124,7 +124,7 @@ BEGIN
$output = `$builddir/src/cmscan -E 1E-3 --tblout $tmppfx.tbl $tmppfx.cm1 $tmppfx.fa 2>&1`;
if ($? != 0) { die "FAIL: cmscan failed\n"; }
# first hit should be the best (and only real) tRNAscan-SE hit, 4169..4230
-&i1::ParseTbl("$tmppfx.tbl");
+&i1::ParseTblFormat1("$tmppfx.tbl");
if ($i1::ntbl < 1) { die "FAIL: cmscan tRNA, no hits found\n"; }
if ($i1::sfrom[0] ne "4169") { die "FAIL: cmscan tRNA hit 1, start position\n"; }
if ($i1::sto[0] ne "4230") { die "FAIL: cmscan tRNA hit 1, stop position\n"; }
@@ -146,7 +146,7 @@ BEGIN
# larger subseq
$output = `$builddir/src/cmsearch -E 0.01 --nohmm --fbeta 1E-2 --beta 1E-4 --tblout $tmppfx.tbl $tmppfx.cm2 $tmppfx.fa 2>&1`;
if ($? != 0) { die "FAIL: cmsearch failed\n"; }
-&i1::ParseTbl("$tmppfx.tbl");
+&i1::ParseTblFormat1("$tmppfx.tbl");
if ($i1::ntbl < 1) { die "FAIL: cmsearch long SRP, no hits found\n"; }
if ($i1::sfrom[0] ne "15714") { die "FAIL: cmsearch long SRP hit 1, start position\n"; }
if ($i1::sto[0] ne "15739") { die "FAIL: cmsearch long SRP hit 1, stop position\n"; }
@@ -154,7 +154,7 @@ BEGIN
# shorter subseq
$output = `$builddir/src/cmsearch -E 0.01 --nohmm --fbeta 1E-2 --beta 1E-4 --tblout $tmppfx.tbl $tmppfx.cm2 $tmppfx.fa2 2>&1`;
if ($? != 0) { die "FAIL: cmsearch failed\n"; }
-&i1::ParseTbl("$tmppfx.tbl");
+&i1::ParseTblFormat1("$tmppfx.tbl");
if ($i1::ntbl < 1) { die "FAIL: cmsearch short SRP, no hits found\n"; }
if ($i1::sfrom[0] ne "43") { die "FAIL: cmsearch short SRP hit 1, start position\n"; }
if ($i1::sto[0] ne "68") { die "FAIL: cmsearch short SRP hit 1, stop position\n"; }
@@ -172,7 +172,7 @@ BEGIN
$output = `$builddir/src/cmscan -E 0.01 --nohmm --fbeta 1E-2 --beta 1E-4 --tblout $tmppfx.tbl $tmppfx.cm2 $tmppfx.fa2 2>&1`;
if ($? != 0) { die "FAIL: cmscan failed\n"; }
-&i1::ParseTbl("$tmppfx.tbl");
+&i1::ParseTblFormat1("$tmppfx.tbl");
if ($i1::ntbl < 1) { die "FAIL: cmscan short SRP, no hits found\n"; }
if ($i1::sfrom[0] ne "43") { die "FAIL: cmscan short SRP hit 1, start position\n"; }
if ($i1::sto[0] ne "68") { die "FAIL: cmscan short SRP hit 1, stop position\n"; }
@@ -192,7 +192,7 @@ BEGIN
$output = `$builddir/src/cmsearch -E 0.1 --tblout $tmppfx.tbl $tmppfx.cm3 $tmppfx.fa 2>&1`;
if ($? != 0) { die "FAIL: cmsearch failed\n"; }
-&i1::ParseTbl("$tmppfx.tbl");
+&i1::ParseTblFormat1("$tmppfx.tbl");
if ($i1::ntbl < 1) { die "FAIL: cmsearch long Rnase P, no hits found\n"; }
if ($i1::sfrom[0] ne "10920") { die "FAIL: cmsearch long Rnase P hit 1, start position\n"; }
if ($i1::sto[0] ne "10580") { die "FAIL: cmsearch long Rnase P hit 1, stop position\n"; }
@@ -201,7 +201,7 @@ BEGIN
$output = `$builddir/src/cmsearch -E 0.1 --tblout $tmppfx.tbl $tmppfx.cm3 $tmppfx.fa2 2>&1`;
if ($? != 0) { die "FAIL: cmsearch failed\n"; }
-&i1::ParseTbl("$tmppfx.tbl");
+&i1::ParseTblFormat1("$tmppfx.tbl");
if ($i1::ntbl < 1) { die "FAIL: cmsearch short Rnase P, no hits found\n"; }
if ($i1::sfrom[0] ne "43") { die "FAIL: cmsearch short Rnase P hit 1, start position\n"; }
if ($i1::sto[0] ne "383") { die "FAIL: cmsearch short Rnase P hit 1, stop position\n"; }
@@ -219,7 +219,7 @@ BEGIN
$output = `$builddir/src/cmscan -E 0.1 --tblout $tmppfx.tbl $tmppfx.cm3 $tmppfx.fa2 2>&1`;
if ($? != 0) { die "FAIL: cmscan failed\n"; }
-&i1::ParseTbl("$tmppfx.tbl");
+&i1::ParseTblFormat1("$tmppfx.tbl");
if ($i1::ntbl < 1) { die "FAIL: cmscan short Rnase P, no hits found\n"; }
if ($i1::sfrom[0] ne "43") { die "FAIL: cmscan short Rnase P hit 1, start position\n"; }
if ($i1::sto[0] ne "383") { die "FAIL: cmscan short Rnase P hit 1, stop position\n"; }
diff --git a/testsuite/itest7-trunc.pl b/testsuite/itest7-trunc.pl
index 5fcdfb86..7eb8e6ef 100755
--- a/testsuite/itest7-trunc.pl
+++ b/testsuite/itest7-trunc.pl
@@ -58,7 +58,7 @@ BEGIN
$output = `$builddir/src/cmsearch -E 0.01 --tblout $tmppfx.tbl $tmppfx.cm1 $tmppfx.fa1 2>&1`;
if ($? != 0) { die "FAIL: cmsearch failed\n"; }
-&i1::ParseTbl("$tmppfx.tbl");
+&i1::ParseTblFormat1("$tmppfx.tbl");
if ($i1::ntbl != 2) { die "FAIL: cmsearch Vault, not 2 hits found\n"; }
if ($i1::sfrom[0] ne "1") { die "FAIL: cmsearch Vault, on seq from, hit 1\n"; }
if ($i1::sto[0] ne "63") { die "FAIL: cmsearch Vault, on seq to, hit 1\n"; }
@@ -71,14 +71,14 @@ BEGIN
$output = `$builddir/src/cmsearch --notrunc --tblout $tmppfx.tbl $tmppfx.cm1 $tmppfx.fa1 2>&1`;
if ($? != 0) { die "FAIL: cmsearch failed\n"; }
-&i1::ParseTbl("$tmppfx.tbl");
+&i1::ParseTblFormat1("$tmppfx.tbl");
if ($i1::ntbl != 0) { die "FAIL: cmsearch Vault, --notrunc, > 0 hits found\n"; }
# cmsearch --anytrunc, finds 3 hits E < 0.01
$output = `$builddir/src/cmsearch --anytrunc -E 0.01 --tblout $tmppfx.tbl $tmppfx.cm1 $tmppfx.fa1 2>&1`;
if ($? != 0) { die "FAIL: cmsearch failed\n"; }
-&i1::ParseTbl("$tmppfx.tbl");
+&i1::ParseTblFormat1("$tmppfx.tbl");
if ($i1::ntbl != 3) { die "FAIL: cmsearch Vault, --anytrunc, not 3 hits found\n"; }
# cmscan
@@ -94,7 +94,7 @@ BEGIN
$output = `$builddir/src/cmscan -E 0.01 --tblout $tmppfx.tbl $tmppfx.cm1 $tmppfx.fa1 2>&1`;
if ($? != 0) { die "FAIL: cmscan failed\n"; }
-&i1::ParseTbl("$tmppfx.tbl");
+&i1::ParseTblFormat1("$tmppfx.tbl");
if ($i1::ntbl != 3) { die "FAIL: cmscan Vault, not 3 hits found\n"; }
if ($i1::sfrom[0] ne "1") { die "FAIL: cmscan Vault, on seq from, hit 1\n"; }
if ($i1::sto[0] ne "63") { die "FAIL: cmscan Vault, on seq to, hit 1\n"; }
@@ -107,14 +107,14 @@ BEGIN
$output = `$builddir/src/cmscan --notrunc --tblout $tmppfx.tbl $tmppfx.cm1 $tmppfx.fa1 2>&1`;
if ($? != 0) { die "FAIL: cmscan failed\n"; }
-&i1::ParseTbl("$tmppfx.tbl");
+&i1::ParseTblFormat1("$tmppfx.tbl");
if ($i1::ntbl != 0) { die "FAIL: cmscan Vault, --notrunc, > 0 hits found\n"; }
# cmscan --anytrunc, finds 3 hits E < 0.01
$output = `$builddir/src/cmscan --anytrunc -E 0.01 --tblout $tmppfx.tbl $tmppfx.cm1 $tmppfx.fa1 2>&1`;
if ($? != 0) { die "FAIL: cmscan failed\n"; }
-&i1::ParseTbl("$tmppfx.tbl");
+&i1::ParseTblFormat1("$tmppfx.tbl");
if ($i1::ntbl != 3) { die "FAIL: cmscan Vault, --anytrunc, not 3 hits found\n"; }
######################
@@ -124,7 +124,7 @@ BEGIN
$output = `$builddir/src/cmsearch -E 0.01 --tblout $tmppfx.tbl $tmppfx.cm2 $tmppfx.fa2 2>&1`;
if ($? != 0) { die "FAIL: cmsearch failed\n"; }
-&i1::ParseTbl("$tmppfx.tbl");
+&i1::ParseTblFormat1("$tmppfx.tbl");
if ($i1::ntbl != 3) { die "FAIL: cmsearch Plant_SRP, not 3 hits found\n"; }
if ($i1::sfrom[0] ne "1") { die "FAIL: cmsearch Plant_SRP, on seq from, hit 1\n"; }
if ($i1::sto[0] ne "110") { die "FAIL: cmsearch Plant_SRP, on seq to, hit 1\n"; }
@@ -140,14 +140,14 @@ BEGIN
$output = `$builddir/src/cmsearch --notrunc --tblout $tmppfx.tbl $tmppfx.cm2 $tmppfx.fa2 2>&1`;
if ($? != 0) { die "FAIL: cmsearch failed\n"; }
-&i1::ParseTbl("$tmppfx.tbl");
+&i1::ParseTblFormat1("$tmppfx.tbl");
if ($i1::ntbl != 0) { die "FAIL: cmsearch Plant_SRP, --notrunc, > 0 hits found\n"; }
# cmsearch --anytrunc, finds 3 hits E < 0.01
$output = `$builddir/src/cmsearch --anytrunc -E 0.01 --tblout $tmppfx.tbl $tmppfx.cm2 $tmppfx.fa2 2>&1`;
if ($? != 0) { die "FAIL: cmsearch failed\n"; }
-&i1::ParseTbl("$tmppfx.tbl");
+&i1::ParseTblFormat1("$tmppfx.tbl");
if ($i1::ntbl != 3) { die "FAIL: cmsearch Plant_SRP, --anytrunc, not 3 hits found\n"; }
# cmscan
@@ -164,7 +164,7 @@ BEGIN
if ($? != 0) { die "FAIL: cmscan failed\n"; }
# Careful: order is different from cmsearch, since pipeline outputs all hits per sequence at once
-&i1::ParseTbl("$tmppfx.tbl");
+&i1::ParseTblFormat1("$tmppfx.tbl");
if ($i1::ntbl != 3) { die "FAIL: cmscan Plant_SRP, not 3 hits found\n"; }
if ($i1::sfrom[0] ne "1") { die "FAIL: cmscan Plant_SRP, on seq from, hit 1\n"; }
if ($i1::sto[0] ne "110") { die "FAIL: cmscan Plant_SRP, on seq to, hit 1\n"; }
@@ -180,14 +180,14 @@ BEGIN
$output = `$builddir/src/cmscan --notrunc --tblout $tmppfx.tbl $tmppfx.cm2 $tmppfx.fa2 2>&1`;
if ($? != 0) { die "FAIL: cmscan failed\n"; }
-&i1::ParseTbl("$tmppfx.tbl");
+&i1::ParseTblFormat1("$tmppfx.tbl");
if ($i1::ntbl != 0) { die "FAIL: cmscan Plant_SRP, --notrunc, > 0 hits found\n"; }
# cmscan --anytrunc, finds 3 hits E < 0.01
$output = `$builddir/src/cmscan --anytrunc -E 0.01 --tblout $tmppfx.tbl $tmppfx.cm2 $tmppfx.fa2 2>&1`;
if ($? != 0) { die "FAIL: cmscan failed\n"; }
-&i1::ParseTbl("$tmppfx.tbl");
+&i1::ParseTblFormat1("$tmppfx.tbl");
if ($i1::ntbl != 3) { die "FAIL: cmscan Plant_SRP, --anytrunc, not 3 hits found\n"; }
print "ok.\n";
diff --git a/testsuite/itest8-glist.pl b/testsuite/itest8-glist.pl
index 7e47c265..dced494f 100755
--- a/testsuite/itest8-glist.pl
+++ b/testsuite/itest8-glist.pl
@@ -76,7 +76,7 @@ BEGIN
# trial one, no --glist, all hits should be local
$output = `$builddir/src/cmscan -E 0.1 --tblout $tmppfx.tbl $tmppfx.cm $tmppfx.fa 2>&1`;
if ($? != 0) { die "FAIL: cmscan failed\n"; }
-&i1::ParseTbl("$tmppfx.tbl");
+&i1::ParseTblFormat1("$tmppfx.tbl");
if ($i1::ntbl != 2) { die "FAIL: on expected number of hits, trial 1\n"; }
if ($i1::hitE[0] !~ m/1.\de-38/) { die "FAIL: on cfg, hit 1, trial 1\n"; }
if ($i1::hitE[1] !~ m/3.\de-08/) { die "FAIL: on cfg, hit 2, trial 1\n"; }
@@ -84,7 +84,7 @@ BEGIN
# trial two, tRNA in --glist, tRNA hit should be glocal, Plant_SRP hit should be local
$output = `$builddir/src/cmscan --glist $tmppfx.list1 -E 0.1 --tblout $tmppfx.tbl $tmppfx.cm $tmppfx.fa 2>&1`;
if ($? != 0) { die "FAIL: cmscan failed\n"; }
-&i1::ParseTbl("$tmppfx.tbl");
+&i1::ParseTblFormat1("$tmppfx.tbl");
if ($i1::ntbl != 2) { die "FAIL: on expected number of hits, trial 2\n"; }
if ($i1::hitE[0] !~ m/1.\de-38/) { die "FAIL: on cfg, hit 1, trial 2\n"; }
if ($i1::hitE[1] !~ m/2.\de-06/) { die "FAIL: on cfg, hit 2, trail 2\n"; }
@@ -92,7 +92,7 @@ BEGIN
# trial three, tRNA and Plant_SRP in --glist, both hits should be glocal
$output = `$builddir/src/cmscan --glist $tmppfx.list2 -E 0.1 --tblout $tmppfx.tbl $tmppfx.cm $tmppfx.fa 2>&1`;
if ($? != 0) { die "FAIL: cmscan failed\n"; }
-&i1::ParseTbl("$tmppfx.tbl");
+&i1::ParseTblFormat1("$tmppfx.tbl");
if ($i1::ntbl != 2) { die "FAIL: on expected number of hits, tRNA and Plant_SRP in glist\n"; }
if ($i1::hitE[0] !~ m/1.\de-20/) { die "FAIL: on cfg, hit 1, trial 3\n"; }
if ($i1::hitE[1] !~ m/2.\de-06/) { die "FAIL: on cfg, hit 2, trail 3\n"; }
diff --git a/testsuite/itest9-overlaps.pl b/testsuite/itest9-overlaps.pl
new file mode 100755
index 00000000..9b9e1e8c
--- /dev/null
+++ b/testsuite/itest9-overlaps.pl
@@ -0,0 +1,174 @@
+#! /usr/bin/perl
+
+# Test of the cmscan overlap annotation and
+# options related to clans. Tests that
+# overlapping hits are properly annotated
+# and clan options work as they're supposed
+# to.
+#
+# Usage: ./itest9-overlaps.pl
+# Example: ./itest9-overlaps.pl .. .. tmpfoo
+#
+# EPN, Tue Jun 21 10:17:32 2016
+# Similar to itest5-pipeline.pl and itest8-glist.pl
+
+BEGIN {
+ $builddir = shift;
+ $srcdir = shift;
+ $tmppfx = shift;
+}
+use lib "$srcdir/testsuite"; # The BEGIN is necessary to make this work: sets $srcdir at compile-time
+use i1;
+
+$verbose = 1;
+
+# The test makes use of the following files:
+#
+# tRNA.c.cm calibrated tRNA model
+# tRNA-Sec.c.cm calibrated tRNA-Sec model
+# Plant_SRP.c.cm calibrated Plant_SRP model
+
+# It creates the following files:
+# $tmppfx.cm 3 models Plant_SRP, tRNA, tRNA-Sec
+# $tmppfx.fa Roughly 300Kb, with a single tRNA, Plant_SRP, tRNA-Sec consensus sequences (from cmemit -c) in the middle)
+# $tmppfx.clanin1 clan input file with "tRNA" and "tRNA-Sec" together in a clan
+# $tmppfx.clanin2 clan input file with "tRNA" in its own clan
+# $tmppfx.clanin3 clan input file with "tRNA" and "bogus" together in a clan (should cause failures)
+
+# All models assumed to be in testsuite subdirectory.
+$model1 = "tRNA";
+$model2 = "Plant_SRP";
+$model3 = "tRNA-Sec";
+
+@i1progs = ( "cmemit", "cmpress", "cmscan");
+@eslprogs = ("esl-shuffle");
+
+# Verify that we have all the executables and datafiles we need for the test.
+foreach $i1prog (@i1progs) { if (! -x "$builddir/src/$i1prog") { die "FAIL: didn't find $i1prog executable in $builddir/src\n"; } }
+foreach $eslprog (@eslprogs) { if (! -x "$builddir/easel/miniapps/$eslprog") { die "FAIL: didn't find $eslprog executable in $builddir/easel/miniapps\n"; } }
+
+if (! -r "$srcdir/testsuite/$model1.c.cm") { die "FAIL: can't read profile $model1.c.cm in $srcdir/testsuite\n"; }
+if (! -r "$srcdir/testsuite/$model2.c.cm") { die "FAIL: can't read profile $model2.c.cm in $srcdir/testsuite\n"; }
+if (! -r "$srcdir/testsuite/$model3.c.cm") { die "FAIL: can't read profile $model3.c.cm in $srcdir/testsuite\n"; }
+
+# Create the test CM file
+`cat $srcdir/testsuite/$model1.c.cm $srcdir/testsuite/$model2.c.cm $srcdir/testsuite/$model3.c.cm > $tmppfx.cm`; if ($?) { die "FAIL: cat\n"; }
+
+# Create a roughly 30Kb database against which to search
+$database = "$tmppfx.fa";
+do_cmd ( "$builddir/easel/miniapps/esl-shuffle --seed 1 --rna -G -N 1 -L 20000 > $tmppfx.fa" );
+do_cmd ( "$builddir/src/cmemit -c $tmppfx.cm | grep -v \"^\>\" >> $tmppfx.fa " );
+do_cmd ( "$builddir/easel/miniapps/esl-shuffle --seed 3 --rna -G -N 1 -L 10000 | grep -v \"^\>\" >> $tmppfx.fa" );
+
+# Create list files
+do_cmd ( "echo \"tRNA-clan tRNA tRNA-Sec\" > $tmppfx.clanin1" );
+do_cmd ( "echo \"tRNA-clan tRNA\" > $tmppfx.clanin2" );
+do_cmd ( "echo \"tRNA-clan tRNA bogus\" > $tmppfx.clanin3" );
+
+# press model, for cmscan
+if(-e "$tmppfx.cm.i1m") { unlink "$tmppfx.cm.i1m"; }
+if(-e "$tmppfx.cm.i1p") { unlink "$tmppfx.cm.i1p"; }
+if(-e "$tmppfx.cm.i1f") { unlink "$tmppfx.cm.i1f"; }
+if(-e "$tmppfx.cm.i1i") { unlink "$tmppfx.cm.i1i"; }
+if(-e "$tmppfx.cm.ssi") { unlink "$tmppfx.cm.ssi"; }
+
+`$builddir/src/cmpress $tmppfx.cm`; if ($?) { die "FAIL: cmpress\n"; }
+
+# cmscan
+# trial 1, --fmt 2 only option, should mark up all overlaps
+$output = `$builddir/src/cmscan --fmt 2 -E 0.1 --tblout $tmppfx.tbl $tmppfx.cm $tmppfx.fa 2>&1`;
+if ($? != 0) { die "FAIL: cmscan failed\n"; }
+&i1::ParseTblFormat2("$tmppfx.tbl");
+if ($i1::ntbl != 5) { die "FAIL: on expected number of hits, trial 1\n"; }
+if ($i1::hitE[0] !~ m/4.\de-98/) { die "FAIL: on cfg, hit 1, trial 1\n"; }
+if ($i1::hitE[3] !~ m/1.\de-07/) { die "FAIL: on cfg, hit 4, trial 1\n"; }
+if ($i1::olp[0] !~ m/^\*$/) { die "FAIL: on cfg, hit 1 olp, trial 1\n"; }
+if ($i1::olp[1] !~ m/^\^$/) { die "FAIL: on cfg, hit 2 olp, trial 1\n"; }
+if ($i1::olp[2] !~ m/^\^$/) { die "FAIL: on cfg, hit 3 olp, trial 1\n"; }
+if ($i1::olp[3] !~ m/^\=$/) { die "FAIL: on cfg, hit 4 olp, trial 1\n"; }
+if ($i1::olp[4] !~ m/^\=$/) { die "FAIL: on cfg, hit 5 olp, trial 1\n"; }
+if ($i1::clan[0] !~ m/^\-$/) { die "FAIL: on cfg, hit 1 clan name, trial 1\n"; }
+if ($i1::clan[1] !~ m/^\-$/) { die "FAIL: on cfg, hit 2 clan name, trial 1\n"; }
+if ($i1::clan[2] !~ m/^\-$/) { die "FAIL: on cfg, hit 3 clan name, trial 1\n"; }
+
+# trial 2, --fmt 2 with --clanin, but no --oskip or --oclan, so should be same result as trial 1
+$output = `$builddir/src/cmscan --fmt 2 --clanin $tmppfx.clanin1 -E 0.1 --tblout $tmppfx.tbl $tmppfx.cm $tmppfx.fa 2>&1`;
+if ($? != 0) { die "FAIL: cmscan failed\n"; }
+&i1::ParseTblFormat2("$tmppfx.tbl");
+if ($i1::ntbl != 5) { die "FAIL: on expected number of hits, trial 2\n"; }
+if ($i1::hitE[0] !~ m/4.\de-98/) { die "FAIL: on cfg, hit 1, trial 2\n"; }
+if ($i1::hitE[3] !~ m/1.\de-07/) { die "FAIL: on cfg, hit 4, trial 2\n"; }
+if ($i1::olp[0] !~ m/^\*$/) { die "FAIL: on cfg, hit 1 olp, trial 2\n"; }
+if ($i1::olp[1] !~ m/^\^$/) { die "FAIL: on cfg, hit 2 olp, trial 2\n"; }
+if ($i1::olp[2] !~ m/^\^$/) { die "FAIL: on cfg, hit 3 olp, trial 2\n"; }
+if ($i1::olp[3] !~ m/^\=$/) { die "FAIL: on cfg, hit 4 olp, trial 2\n"; }
+if ($i1::olp[4] !~ m/^\=$/) { die "FAIL: on cfg, hit 5 olp, trial 2\n"; }
+if ($i1::clan[0] !~ m/^\-$/) { die "FAIL: on cfg, hit 1 clan name, trial 2\n"; }
+if ($i1::clan[1] !~ m/^tRNA\-clan$/) { die "FAIL: on cfg, hit 2 clan name, trial 2\n"; }
+if ($i1::clan[2] !~ m/^tRNA\-clan$/) { die "FAIL: on cfg, hit 3 clan name, trial 2\n"; }
+
+# trial 3, --fmt 2 with --oskip, so only top scoring hits should print
+$output = `$builddir/src/cmscan --fmt 2 --oskip -E 0.1 --tblout $tmppfx.tbl $tmppfx.cm $tmppfx.fa 2>&1`;
+if ($? != 0) { die "FAIL: cmscan failed\n"; }
+&i1::ParseTblFormat2("$tmppfx.tbl");
+if ($i1::ntbl != 3) { die "FAIL: on expected number of hits, trial 2\n"; }
+if ($i1::hitE[0] !~ m/4.\de-98/) { die "FAIL: on cfg, hit 1, trial 2\n"; }
+if ($i1::olp[0] !~ m/^\*$/) { die "FAIL: on cfg, hit 1 olp, trial 3\n"; }
+if ($i1::olp[1] !~ m/^\^$/) { die "FAIL: on cfg, hit 2 olp, trial 3\n"; }
+if ($i1::olp[2] !~ m/^\^$/) { die "FAIL: on cfg, hit 3 olp, trial 3\n"; }
+if ($i1::clan[0] !~ m/^\-$/) { die "FAIL: on cfg, hit 1 clan name, trial 3\n"; }
+if ($i1::clan[1] !~ m/^\-$/) { die "FAIL: on cfg, hit 2 clan name, trial 3\n"; }
+if ($i1::clan[2] !~ m/^\-$/) { die "FAIL: on cfg, hit 3 clan name, trial 3\n"; }
+
+# trial 4, --fmt 2 with --clanin and --oclan using clan file with only tRNA, so no within clan overlaps
+$output = `$builddir/src/cmscan --fmt 2 --clanin $tmppfx.clanin2 --oclan -E 0.1 --tblout $tmppfx.tbl $tmppfx.cm $tmppfx.fa 2>&1`;
+if ($? != 0) { die "FAIL: cmscan failed\n"; }
+&i1::ParseTblFormat2("$tmppfx.tbl");
+if ($i1::ntbl != 5) { die "FAIL: on expected number of hits, trial 4\n"; }
+if ($i1::hitE[0] !~ m/4.\de-98/) { die "FAIL: on cfg, hit 1, trial 4\n"; }
+if ($i1::hitE[3] !~ m/1.\de-07/) { die "FAIL: on cfg, hit 4, trial 4\n"; }
+if ($i1::olp[0] !~ m/^\*$/) { die "FAIL: on cfg, hit 1 olp, trial 4\n"; }
+if ($i1::olp[1] !~ m/^\*$/) { die "FAIL: on cfg, hit 2 olp, trial 4\n"; }
+if ($i1::olp[2] !~ m/^\*$/) { die "FAIL: on cfg, hit 3 olp, trial 4\n"; }
+if ($i1::olp[3] !~ m/^\*$/) { die "FAIL: on cfg, hit 4 olp, trial 4\n"; }
+if ($i1::olp[4] !~ m/^\*$/) { die "FAIL: on cfg, hit 5 olp, trial 4\n"; }
+if ($i1::clan[0] !~ m/^\-$/) { die "FAIL: on cfg, hit 1 clan name, trial 4\n"; }
+if ($i1::clan[1] !~ m/^\-$/) { die "FAIL: on cfg, hit 2 clan name, trial 4\n"; }
+if ($i1::clan[2] !~ m/^tRNA\-clan$/) { die "FAIL: on cfg, hit 3 clan name, trial 4\n"; }
+
+# trial 5, --fmt 2 with --clanin, --oclan and --oskip using clan file with only tRNA, so no within clan overlaps, should
+# be same results as trial 4
+$output = `$builddir/src/cmscan --fmt 2 --clanin $tmppfx.clanin2 --oclan --oskip -E 0.1 --tblout $tmppfx.tbl $tmppfx.cm $tmppfx.fa 2>&1`;
+if ($? != 0) { die "FAIL: cmscan failed\n"; }
+&i1::ParseTblFormat2("$tmppfx.tbl");
+if ($i1::ntbl != 5) { die "FAIL: on expected number of hits, trial 4\n"; }
+if ($i1::hitE[0] !~ m/4.\de-98/) { die "FAIL: on cfg, hit 1, trial 5\n"; }
+if ($i1::hitE[3] !~ m/1.\de-07/) { die "FAIL: on cfg, hit 4, trial 5\n"; }
+if ($i1::olp[0] !~ m/^\*$/) { die "FAIL: on cfg, hit 1 olp, trial 5\n"; }
+if ($i1::olp[1] !~ m/^\*$/) { die "FAIL: on cfg, hit 2 olp, trial 5\n"; }
+if ($i1::olp[2] !~ m/^\*$/) { die "FAIL: on cfg, hit 3 olp, trial 5\n"; }
+if ($i1::olp[3] !~ m/^\*$/) { die "FAIL: on cfg, hit 4 olp, trial 5\n"; }
+if ($i1::olp[4] !~ m/^\*$/) { die "FAIL: on cfg, hit 5 olp, trial 5\n"; }
+if ($i1::clan[0] !~ m/^\-$/) { die "FAIL: on cfg, hit 1 clan name, trial 5\n"; }
+if ($i1::clan[1] !~ m/^\-$/) { die "FAIL: on cfg, hit 2 clan name, trial 5\n"; }
+if ($i1::clan[2] !~ m/^tRNA\-clan$/) { die "FAIL: on cfg, hit 3 clan name, trial 5\n"; }
+
+# trial 6, bogus name in clan input file, cmscan should fail
+$output = `$builddir/src/cmscan --fmt 2 --clanin $tmppfx.clanin3 -E 0.1 --tblout $tmppfx.tbl $tmppfx.cm $tmppfx.fa 2>&1`;
+if ($? == 0) { die "FAIL: cmscan did not fail when it should have\n"; }
+
+print "ok.\n";
+unlink <$tmppfx.cm*>;
+unlink "$tmppfx.tbl";
+unlink "$tmppfx.fa";
+unlink "$tmppfx.clanin1";
+unlink "$tmppfx.clanin2";
+unlink "$tmppfx.clanin3";
+
+exit 0;
+
+sub do_cmd {
+ $cmd = shift;
+ print "$cmd\n" if $verbose;
+ return `$cmd`;
+}
diff --git a/testsuite/tRNA-Sec.c.cm b/testsuite/tRNA-Sec.c.cm
new file mode 100644
index 00000000..9c5c8c09
--- /dev/null
+++ b/testsuite/tRNA-Sec.c.cm
@@ -0,0 +1,701 @@
+INFERNAL1/a [1.1.1 | July 2014]
+NAME tRNA-Sec
+ACC RF01852
+STATES 292
+NODES 75
+CLEN 91
+W 117
+ALPH RNA
+RF no
+CONS yes
+MAP yes
+DATE Tue Apr 8 16:22:29 2014
+COM [1] cmbuild -F CM SEED
+COM [2] cmcalibrate --mpi CM
+PBEGIN 0.05
+PEND 0.05
+WBETA 1e-07
+QDBBETA1 1e-07
+QDBBETA2 1e-15
+N2OMEGA 1.52588e-05
+N3OMEGA 1.52588e-05
+ELSELF -0.08926734
+NSEQ 109
+EFFN 2.318512
+CKSUM 3407454328
+NULL 0.000 0.000 0.000 0.000
+GA 47.00
+TC 47.00
+NC 46.90
+EFP7GF -12.3219 0.71862
+ECMLC 0.74414 -5.65122 2.12842 1600000 392081 0.003061
+ECMGC 0.38122 -15.57366 -3.55100 1600000 39136 0.010221
+ECMLI 0.59769 -5.29381 3.90232 1600000 292574 0.004102
+ECMGI 0.41821 -9.96424 0.79712 1600000 36025 0.011103
+CM
+ [ ROOT 0 ] - - - - - -
+ S 0 -1 0 1 6 0 1 117 148 -9.167 -9.106 -0.072 -5.457 -8.163 -5.750
+ IL 1 1 2 1 6 6 39 118 149 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000
+ IR 2 2 3 2 5 7 39 118 149 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 1 ] 1 115 G C - -
+ MP 3 2 3 7 6 9 42 117 148 -9.116 -9.056 -0.024 -7.832 -8.112 -7.729 -4.348 -2.912 -4.393 0.458 -4.887 -4.513 -0.299 -4.756 -4.149 3.538 -3.573 -0.513 -0.618 -4.122 -2.305 -3.323
+ ML 4 2 3 7 6 6 36 115 146 -6.580 -6.926 -1.327 -1.253 -3.149 -4.305 0.139 -0.737 0.521 -0.211
+ MR 5 2 3 7 6 5 36 115 146 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094
+ D 6 2 3 7 6 3 31 113 144 -9.406 -8.104 -2.271 -4.584 -3.055 -0.676
+ IL 7 7 5 7 6 6 38 116 147 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000
+ IR 8 8 6 8 5 6 38 116 147 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 2 ] 2 114 g c - -
+ MP 9 8 6 13 6 9 41 115 146 -9.139 -9.078 -0.021 -7.855 -8.135 -8.530 -3.276 -2.566 -3.279 1.111 -3.203 -4.000 1.685 -3.481 -3.399 2.629 -3.832 -0.206 0.910 -3.312 -0.792 -2.225
+ ML 10 8 6 13 6 5 36 113 144 -6.291 -6.637 -1.352 -0.965 -6.487 -4.017 0.312 -0.224 -0.303 0.126
+ MR 11 8 6 13 6 5 36 113 144 -7.229 -5.958 -1.223 -5.936 -1.070 -4.150 0.074 -0.101 -0.588 0.433
+ D 12 8 6 13 6 3 30 110 141 -9.096 -7.795 -3.116 -4.274 -4.291 -0.367
+ IL 13 13 5 13 6 6 37 114 145 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000
+ IR 14 14 6 14 5 6 38 114 145 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 3 ] 3 113 g c - -
+ MP 15 14 6 19 6 9 40 113 144 -9.164 -9.103 -0.020 -7.880 -8.160 -8.555 -3.059 -2.598 -3.107 1.726 -2.871 -3.889 1.887 -3.237 -3.185 2.067 -3.661 -0.462 1.105 -3.200 -0.554 -2.077
+ ML 16 14 6 19 6 5 35 111 142 -6.291 -6.637 -1.352 -0.965 -6.487 -4.017 0.312 -0.224 -0.303 0.126
+ MR 17 14 6 19 6 5 35 111 142 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094
+ D 18 14 6 19 6 3 30 108 139 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319
+ IL 19 19 5 19 6 6 37 112 143 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000
+ IR 20 20 6 20 5 6 37 112 143 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 4 ] 4 112 g c - -
+ MP 21 20 6 25 6 8 38 111 142 -9.164 -9.103 -0.023 -7.880 -8.160 -7.848 -2.838 -2.411 -2.916 1.911 -2.838 -3.719 1.635 -2.804 -3.006 2.034 -3.494 -0.012 0.978 -3.006 -0.601 -1.943
+ ML 22 20 6 25 6 5 34 109 140 -6.291 -6.637 -1.252 -1.046 -6.487 -4.017 0.312 -0.224 -0.303 0.126
+ MR 23 20 6 25 6 5 34 109 140 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094
+ D 24 20 6 25 6 2 29 106 137 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319
+ IL 25 25 5 25 6 5 36 110 141 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000
+ IR 26 26 6 26 5 6 36 110 141 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 5 ] 5 111 g c - -
+ MP 27 26 6 31 6 7 37 109 140 -9.165 -9.104 -0.029 -7.880 -8.160 -6.871 -3.198 -2.381 -3.189 1.285 -3.470 -3.883 1.067 -3.581 -3.389 2.835 -3.009 0.154 0.625 -3.173 -1.072 -2.201
+ ML 28 26 6 31 6 5 33 107 138 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094
+ MR 29 26 6 31 6 5 33 107 138 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094
+ D 30 26 6 31 6 2 29 104 135 -9.091 -7.789 -3.159 -4.268 -4.286 -0.361
+ IL 31 31 5 31 6 5 35 108 139 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000
+ IR 32 32 6 32 5 5 35 108 139 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 6 ] 6 110 g c - -
+ MP 33 32 6 37 6 7 35 107 138 -9.159 -9.098 -0.041 -7.874 -8.154 -5.900 -2.601 -2.356 -2.496 1.306 -2.555 -3.501 1.722 -2.922 -2.789 1.910 -3.295 0.417 1.434 -2.797 -0.320 -1.683
+ ML 34 32 6 37 6 5 32 105 136 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094
+ MR 35 32 6 37 6 4 32 105 136 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094
+ D 36 32 6 37 6 2 28 103 134 -9.191 -7.890 -2.845 -4.369 -4.386 -0.398
+ IL 37 37 5 37 6 5 34 106 137 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000
+ IR 38 38 6 38 5 5 34 106 137 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 7 ] 7 109 g c - -
+ MP 39 38 6 43 6 7 33 105 136 -9.144 -9.083 -0.098 -6.518 -4.513 -7.056 -2.619 -2.227 -2.701 1.606 -2.761 -3.469 1.297 -2.616 -2.839 2.388 -3.319 -0.236 1.043 -2.157 -0.610 -1.704
+ ML 40 38 6 43 6 4 31 103 134 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094
+ MR 41 38 6 43 6 4 31 103 134 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094
+ D 42 38 6 43 6 2 28 101 132 -9.408 -8.106 -3.903 -4.586 -4.603 -0.243
+ IL 43 43 5 43 6 5 32 104 135 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000
+ IR 44 44 6 44 5 5 32 104 135 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 8 ] 8 108 c g - -
+ MP 45 44 6 49 6 6 32 103 134 -9.067 -9.006 -0.042 -7.783 -6.674 -6.558 -1.733 -1.724 -1.921 1.261 -1.865 -2.742 1.729 -2.099 -1.975 1.321 -2.343 -0.309 1.470 -1.519 -0.016 -0.154
+ ML 46 44 6 49 6 4 30 102 133 -6.374 -6.721 -1.144 -1.129 -6.570 -4.100 0.208 -0.364 -0.371 0.373
+ MR 47 44 6 49 6 4 30 102 133 -7.550 -6.279 -0.937 -6.257 -1.317 -4.471 0.471 -0.317 -0.492 0.138
+ D 48 44 6 49 6 2 28 100 131 -9.499 -8.198 -1.993 -4.677 -4.694 -0.586
+ IL 49 49 5 49 6 5 31 102 133 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000
+ IR 50 50 6 50 5 5 30 102 133 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 9 ] 9 107 g c - -
+ MP 51 50 6 55 4 4 30 101 132 -7.021 -4.488 -0.428 -2.290 -2.324 -1.223 -2.449 1.483 -2.620 -3.188 1.020 -2.540 -2.566 2.391 -3.040 0.322 0.821 -1.577 -0.616 -1.387
+ ML 52 50 6 55 4 4 29 100 131 -3.758 -3.940 -0.507 -2.670 0.368 -0.385 -0.191 0.094
+ MR 53 50 6 55 4 3 28 100 131 -4.963 -3.992 -1.408 -0.920 0.184 0.053 -0.484 0.153
+ D 54 50 6 55 4 2 27 99 130 -4.857 -3.337 -2.554 -0.522
+ IL 55 55 5 55 4 4 29 102 132 -1.686 -2.369 -1.117 -4.855 0.000 0.000 0.000 0.000
+ IR 56 56 6 56 3 4 29 101 132 -1.455 -0.769 -4.366 0.000 0.000 0.000 0.000
+ [ MATL 10 ] 10 - a - - -
+ ML 57 56 6 59 3 3 28 99 130 -4.955 -0.105 -4.724 0.965 -0.869 -0.837 -0.087
+ D 58 56 6 59 3 2 27 98 129 -7.702 -0.655 -1.473
+ IL 59 59 3 59 3 3 28 100 131 -1.389 -0.818 -4.300 0.000 0.000 0.000 0.000
+ [ MATL 11 ] 13 - u - - -
+ ML 60 59 3 62 2 3 27 98 129 -8.424 -0.004 -0.279 -0.381 -0.896 0.903
+ D 61 59 3 62 2 2 26 97 128 -8.495 -0.004
+ IL 62 62 3 62 2 3 27 99 129 -1.823 -0.479 0.000 0.000 0.000 0.000
+ [ BIF 12 ] - - - - - -
+ B 63 62 3 64 176 2 26 97 128
+ [ BEGL 13 ] - - - - - -
+ S 64 63 1 65 1 0 1 50 70 0.000
+ [ BIF 14 ] - - - - - -
+ B 65 64 1 66 116 0 1 50 70
+ [ BEGL 15 ] - - - - - -
+ S 66 65 1 67 4 0 0 30 49 -0.042 -6.912 -6.319 -6.959
+ [ MATP 16 ] 14 35 c g - -
+ MP 67 66 1 71 6 2 2 30 49 -6.798 -9.106 -0.031 -7.883 -8.163 -8.558 -3.032 -2.754 -3.106 0.976 -2.632 -3.903 2.376 -3.105 -3.126 1.723 -3.627 -0.252 1.332 -3.225 -0.143 -2.033
+ ML 68 66 1 71 6 1 1 29 47 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094
+ MR 69 66 1 71 6 1 1 29 47 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094
+ D 70 66 1 71 6 0 0 26 45 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319
+ IL 71 71 5 71 6 1 1 30 49 -2.250 -3.042 -0.789 -4.697 -5.473 -5.134 0.000 0.000 0.000 0.000
+ IR 72 72 6 72 5 1 1 30 48 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 17 ] 17 34 g c - -
+ MP 73 72 6 77 6 2 2 28 47 -9.167 -9.106 -0.020 -7.883 -8.163 -8.558 -2.304 -2.200 -2.445 1.157 -2.323 -2.663 1.868 -2.693 -2.513 1.925 -2.649 -0.192 1.293 -2.552 0.053 -1.574
+ ML 74 72 6 77 6 1 1 27 45 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094
+ MR 75 72 6 77 6 1 1 27 45 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094
+ D 76 72 6 77 6 0 0 24 43 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319
+ IL 77 77 5 77 6 1 1 28 46 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000
+ IR 78 78 6 78 5 1 1 28 46 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 18 ] 18 33 g c - -
+ MP 79 78 6 83 6 2 2 26 45 -6.199 -9.106 -0.038 -7.883 -8.163 -8.558 -2.051 -1.780 -1.979 1.148 -2.133 -2.855 1.662 -2.500 -2.284 1.751 -2.830 -0.286 1.325 -2.145 0.719 -1.392
+ ML 80 78 6 83 6 1 1 25 43 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094
+ MR 81 78 6 83 6 1 1 25 43 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094
+ D 82 78 6 83 6 0 0 22 41 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319
+ IL 83 83 5 83 6 1 1 26 44 -2.745 -3.008 -0.656 -4.663 -5.439 -5.099 0.000 0.000 0.000 0.000
+ IR 84 84 6 84 5 1 1 26 44 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 19 ] 20 32 c g - -
+ MP 85 84 6 89 6 2 2 24 43 -9.167 -9.106 -0.029 -7.883 -6.759 -8.558 -2.496 -2.177 -2.622 1.184 -2.415 -3.428 1.985 -2.812 -2.164 1.875 -3.202 -0.302 1.303 -2.730 0.069 -1.701
+ ML 86 84 6 89 6 1 1 23 41 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094
+ MR 87 84 6 89 6 1 1 23 41 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094
+ D 88 84 6 89 6 0 0 21 39 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319
+ IL 89 89 5 89 6 1 1 24 42 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000
+ IR 90 90 6 90 5 1 1 24 42 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 20 ] 21 31 c g - -
+ MP 91 90 6 95 6 2 2 22 41 -5.985 -9.098 -0.041 -7.875 -8.154 -8.549 -1.740 -2.113 -2.031 1.361 -2.098 -3.062 1.786 -2.486 -2.289 1.503 -2.711 -0.274 1.532 -2.356 0.234 -1.340
+ ML 92 90 6 95 6 1 1 21 40 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094
+ MR 93 90 6 95 6 1 1 21 39 -7.084 -5.813 -1.443 -5.791 -0.925 -4.005 0.327 -0.563 0.180 -0.096
+ D 94 90 6 95 6 0 0 19 38 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319
+ IL 95 95 5 95 6 1 1 22 40 -2.772 -3.035 -0.640 -4.690 -5.466 -5.127 0.000 0.000 0.000 0.000
+ IR 96 96 6 96 5 1 1 22 40 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 21 ] 23 30 c g - -
+ MP 97 96 6 101 4 2 2 20 38 -5.143 -7.306 -0.079 -5.720 -3.314 -2.955 -3.350 0.745 -2.761 -4.135 2.600 -3.259 -3.344 1.765 -3.829 -0.539 1.205 -3.505 -0.393 -2.223
+ ML 98 96 6 101 4 1 1 20 38 -3.758 -3.940 -0.507 -2.670 0.368 -0.385 -0.191 0.094
+ MR 99 96 6 101 4 1 1 20 38 -4.809 -3.838 -1.706 -0.766 0.368 -0.385 -0.191 0.094
+ D 100 96 6 101 4 0 0 19 37 -4.568 -4.250 -2.265 -0.520
+ IL 101 101 5 101 4 1 1 21 40 -1.826 -2.071 -1.156 -4.995 0.000 0.000 0.000 0.000
+ IR 102 102 6 102 3 1 1 20 39 -1.490 -0.763 -4.190 0.000 0.000 0.000 0.000
+ [ MATL 22 ] 25 - U - - -
+ ML 103 102 6 105 3 1 1 16 35 -8.105 -0.019 -6.759 -0.740 -0.096 -1.426 1.066
+ D 104 102 6 105 3 0 0 16 34 -6.174 -1.687 -0.566
+ IL 105 105 3 105 3 1 1 20 38 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000
+ [ MATL 23 ] 26 - G - - -
+ ML 106 105 3 108 3 1 1 15 33 -8.105 -0.019 -6.759 -1.880 -3.144 1.783 -2.531
+ D 107 105 3 108 3 0 0 15 33 -6.174 -1.687 -0.566
+ IL 108 108 3 108 3 1 1 19 37 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000
+ [ MATL 24 ] 27 - G - - -
+ ML 109 108 3 111 3 1 1 13 31 -8.105 -0.019 -6.759 -1.880 -3.144 1.783 -2.531
+ D 110 108 3 111 3 0 0 13 32 -6.174 -1.687 -0.566
+ IL 111 111 3 111 3 1 1 18 36 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000
+ [ MATL 25 ] 28 - U - - -
+ ML 112 111 3 114 2 1 1 1 1 * 0.000 -1.751 -1.701 -2.496 1.686
+ D 113 111 3 114 2 0 0 0 0 * 0.000
+ IL 114 114 3 114 2 1 1 13 28 -1.823 -0.479 0.000 0.000 0.000 0.000
+ [ END 26 ] - - - - - -
+ E 115 114 3 -1 0 0 0 0 0
+ [ BEGR 27 ] - - - - - -
+ S 116 65 1 117 5 0 0 33 52 -7.217 -0.036 -7.033 -7.245 -8.136
+ IL 117 117 2 117 5 1 1 34 53 -2.408 -0.496 -4.087 -5.920 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 28 ] 36 57 u a - -
+ MP 118 117 2 122 6 2 2 33 52 -9.167 -4.681 -0.076 -7.883 -8.163 -8.558 -1.639 -1.771 -1.838 1.129 -1.711 -2.242 1.584 -0.530 -1.783 1.151 -2.443 0.219 1.594 -1.825 0.069 -0.990
+ ML 119 117 2 122 6 1 1 31 50 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094
+ MR 120 117 2 122 6 1 1 31 50 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094
+ D 121 117 2 122 6 0 0 29 48 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319
+ IL 122 122 5 122 6 1 1 33 52 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000
+ IR 123 123 6 123 5 1 1 32 51 -2.145 -0.519 -6.349 -4.517 -5.623 0.000 0.000 0.000 0.000
+ [ MATP 29 ] 37 54 c g - -
+ MP 124 123 6 128 6 2 2 31 50 -9.167 -7.048 -0.029 -7.883 -8.163 -8.558 -1.388 -1.676 -1.908 1.183 -1.481 -2.550 1.865 -2.101 -1.699 1.114 -2.485 0.567 1.339 -2.032 0.003 -1.131
+ ML 125 123 6 128 6 1 1 29 48 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094
+ MR 126 123 6 128 6 1 1 29 48 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094
+ D 127 123 6 128 6 0 0 27 46 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319
+ IL 128 128 5 128 6 1 1 31 49 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000
+ IR 129 129 6 129 5 1 1 30 49 -2.459 -0.476 -5.970 -4.138 -5.244 0.000 0.000 0.000 0.000
+ [ MATP 30 ] 38 52 c g - -
+ MP 130 129 6 134 6 2 2 29 48 -9.167 -9.106 -0.020 -7.883 -8.163 -8.558 -3.673 -3.556 -3.597 0.380 -2.601 -4.232 2.940 -3.279 -3.589 0.573 -4.011 -1.471 1.754 -3.834 -0.252 -2.451
+ ML 131 129 6 134 6 1 1 27 46 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094
+ MR 132 129 6 134 6 1 1 27 46 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094
+ D 133 129 6 134 6 0 0 25 44 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319
+ IL 134 134 5 134 6 1 1 29 47 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000
+ IR 135 135 6 135 5 1 1 28 47 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 31 ] 39 51 G C - -
+ MP 136 135 6 140 6 2 2 27 46 -9.167 -9.106 -0.020 -7.883 -8.163 -8.558 -3.681 -2.565 -3.653 1.528 -4.147 -4.307 0.389 -4.037 -3.755 3.089 -4.143 -0.172 0.272 -3.632 -1.595 -2.586
+ ML 137 135 6 140 6 1 1 26 45 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094
+ MR 138 135 6 140 6 1 1 26 44 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094
+ D 139 135 6 140 6 0 0 23 42 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319
+ IL 140 140 5 140 6 1 1 27 45 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000
+ IR 141 141 6 141 5 1 1 26 45 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 32 ] 40 50 G C - -
+ MP 142 141 6 146 6 2 2 25 44 -9.167 -9.106 -0.020 -7.883 -8.163 -8.558 -4.900 -3.170 -5.012 0.196 -5.551 -4.782 -0.845 -5.298 -4.450 3.670 -4.777 -0.869 -1.201 -4.577 -2.892 -3.886
+ ML 143 141 6 146 6 1 1 24 43 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094
+ MR 144 141 6 146 6 1 1 24 43 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094
+ D 145 141 6 146 6 0 0 23 42 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319
+ IL 146 146 5 146 6 1 1 25 44 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000
+ IR 147 147 6 147 5 1 1 24 43 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 33 ] 41 49 g c - -
+ MP 148 147 6 152 4 2 2 23 42 -7.099 -7.306 -0.048 -5.720 -3.060 -2.532 -3.112 1.787 -3.004 -3.921 1.260 -3.295 -3.193 2.197 -3.672 -0.363 1.556 -3.211 -0.697 -2.092
+ ML 149 147 6 152 4 1 1 24 43 -3.758 -3.940 -0.507 -2.670 0.368 -0.385 -0.191 0.094
+ MR 150 147 6 152 4 1 1 23 42 -4.809 -3.838 -1.706 -0.766 0.368 -0.385 -0.191 0.094
+ D 151 147 6 152 4 0 0 22 41 -4.568 -4.250 -2.265 -0.520
+ IL 152 152 5 152 4 1 1 25 44 -1.686 -2.369 -1.117 -4.855 0.000 0.000 0.000 0.000
+ IR 153 153 6 153 3 1 1 24 43 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000
+ [ MATL 34 ] 42 - C - - -
+ ML 154 153 6 156 3 1 1 20 39 -8.105 -0.019 -6.759 -1.740 1.591 -2.575 -0.941
+ D 155 153 6 156 3 0 0 19 38 -6.174 -1.687 -0.566
+ IL 156 156 3 156 3 1 1 23 42 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000
+ [ MATL 35 ] 43 - U - - -
+ ML 157 156 3 159 3 1 1 19 37 -8.105 -0.019 -6.759 -1.751 -1.701 -2.496 1.686
+ D 158 156 3 159 3 0 0 18 37 -6.174 -1.687 -0.566
+ IL 159 159 3 159 3 1 1 22 41 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000
+ [ MATL 36 ] 44 - U - - -
+ ML 160 159 3 162 3 1 1 17 36 -8.105 -0.019 -6.759 -1.751 -1.701 -2.496 1.686
+ D 161 159 3 162 3 0 0 17 36 -6.174 -1.687 -0.566
+ IL 162 162 3 162 3 1 1 21 40 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000
+ [ MATL 37 ] 45 - C - - -
+ ML 163 162 3 165 3 1 1 16 35 -8.105 -0.019 -6.759 -2.087 1.706 -2.918 -1.431
+ D 164 162 3 165 3 0 0 16 34 -6.174 -1.687 -0.566
+ IL 165 165 3 165 3 1 1 20 38 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000
+ [ MATL 38 ] 46 - A - - -
+ ML 166 165 3 168 3 1 1 15 33 -8.105 -0.019 -6.759 1.774 -2.658 -2.261 -2.229
+ D 167 165 3 168 3 0 0 15 33 -6.174 -1.687 -0.566
+ IL 168 168 3 168 3 1 1 19 37 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000
+ [ MATL 39 ] 47 - A - - -
+ ML 169 168 3 171 3 1 1 13 31 -8.105 -0.019 -6.759 1.615 -2.105 -1.370 -1.653
+ D 170 168 3 171 3 0 0 13 32 -6.174 -1.687 -0.566
+ IL 171 171 3 171 3 1 1 18 36 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000
+ [ MATL 40 ] 48 - A - - -
+ ML 172 171 3 174 2 1 1 1 1 * 0.000 1.673 -2.026 -1.909 -1.735
+ D 173 171 3 174 2 0 0 0 0 * 0.000
+ IL 174 174 3 174 2 1 1 13 28 -1.823 -0.479 0.000 0.000 0.000 0.000
+ [ END 41 ] - - - - - -
+ E 175 174 3 -1 0 0 0 0 0
+ [ BEGR 42 ] - - - - - -
+ S 176 63 1 177 3 0 2 62 92 -5.308 -0.051 -6.759
+ IL 177 177 2 177 3 1 3 64 94 -1.391 -0.817 -4.293 0.000 0.000 0.000 0.000
+ [ MATL 43 ] 60 - G - - -
+ ML 178 177 2 180 2 1 2 61 92 -8.524 -0.004 -0.345 -1.363 1.036 -0.372
+ D 179 177 2 180 2 0 1 60 91 -8.445 -0.004
+ IL 180 180 3 180 2 1 2 62 93 -1.823 -0.479 0.000 0.000 0.000 0.000
+ [ BIF 44 ] - - - - - -
+ B 181 180 3 182 238 0 1 60 91
+ [ BEGL 45 ] - - - - - -
+ S 182 181 1 183 4 0 0 43 74 -0.077 -6.912 -5.572 -5.472
+ [ MATP 46 ] 61 84 g c - -
+ MP 183 182 1 187 6 2 2 43 74 -9.141 -9.081 -0.021 -7.857 -8.137 -8.532 -2.828 -2.518 -2.910 1.330 -2.640 -3.701 1.923 -3.043 -2.978 1.956 -3.475 -0.185 1.424 -3.002 -0.292 -1.816
+ ML 184 182 1 187 6 1 1 41 72 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094
+ MR 185 182 1 187 6 1 1 41 72 -7.096 -5.825 -1.734 -5.804 -0.750 -4.017 0.214 -0.006 -0.446 0.151
+ D 186 182 1 187 6 0 0 39 70 -9.307 -8.005 -2.087 -4.484 -4.502 -0.577
+ IL 187 187 5 187 6 1 1 43 74 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000
+ IR 188 188 6 188 5 1 1 42 73 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 47 ] 62 83 g c - -
+ MP 189 188 6 193 6 2 2 41 72 -9.158 -9.097 -0.033 -7.873 -8.153 -6.483 -2.851 -2.030 -2.914 1.298 -2.856 -3.683 1.516 -3.163 -3.034 2.316 -3.508 -0.046 1.396 -2.973 -0.600 -1.947
+ ML 190 188 6 193 6 1 1 39 70 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094
+ MR 191 188 6 193 6 1 1 39 70 -7.096 -5.825 -1.422 -5.804 -0.937 -4.017 0.314 -0.574 0.206 -0.102
+ D 192 188 6 193 6 0 0 36 67 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319
+ IL 193 193 5 193 6 1 1 41 72 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000
+ IR 194 194 6 194 5 1 1 40 71 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 48 ] 63 82 g c - -
+ MP 195 194 6 199 6 2 2 39 70 -9.155 -9.094 -0.020 -7.871 -8.150 -8.545 -3.292 -2.415 -3.262 1.373 -3.524 -3.960 1.123 -3.632 -3.471 2.795 -3.864 0.186 0.611 -3.244 -0.920 -2.242
+ ML 196 194 6 199 6 1 1 38 68 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094
+ MR 197 194 6 199 6 1 1 37 68 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094
+ D 198 194 6 199 6 0 0 35 65 -9.249 -7.948 -3.745 -4.427 -4.444 -0.274
+ IL 199 199 5 199 6 1 1 39 70 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000
+ IR 200 200 6 200 5 1 1 38 69 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 49 ] 64 81 g c - -
+ MP 201 200 6 205 6 2 2 37 68 -7.257 -9.094 -0.031 -7.871 -8.150 -7.617 -2.686 -2.330 -2.543 1.156 -2.710 -3.547 1.558 -3.032 -2.883 2.243 -3.099 0.365 1.334 -2.839 -0.459 -1.837
+ ML 202 200 6 205 6 1 1 36 67 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094
+ MR 203 200 6 205 6 1 1 36 66 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094
+ D 204 200 6 205 6 0 0 33 64 -9.249 -7.948 -3.745 -4.427 -4.444 -0.274
+ IL 205 205 5 205 6 1 1 37 68 -2.648 -2.911 -0.715 -4.566 -5.342 -5.002 0.000 0.000 0.000 0.000
+ IR 206 206 6 206 5 1 1 36 67 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 50 ] 66 80 c g - -
+ MP 207 206 6 211 4 2 2 35 66 -7.060 -7.267 -0.049 -5.681 -2.458 -2.323 -2.596 1.137 -2.363 -3.390 2.101 -2.767 -2.635 1.669 -2.380 0.065 1.311 -2.707 -0.002 -1.672
+ ML 208 206 6 211 4 1 1 35 66 -3.758 -3.940 -0.507 -2.670 0.368 -0.385 -0.191 0.094
+ MR 209 206 6 211 4 1 1 34 65 -4.809 -3.838 -1.706 -0.766 0.368 -0.385 -0.191 0.094
+ D 210 206 6 211 4 0 0 33 64 -4.806 -4.487 -1.607 -0.758
+ IL 211 211 5 211 4 1 1 36 67 -1.686 -2.369 -1.117 -4.855 0.000 0.000 0.000 0.000
+ IR 212 212 6 212 3 1 1 35 66 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000
+ [ MATL 51 ] 67 - u - - -
+ ML 213 212 6 215 3 1 1 33 64 -8.105 -0.019 -6.759 -0.210 -0.199 -0.420 0.601
+ D 214 212 6 215 3 0 0 31 62 -6.174 -1.687 -0.566
+ IL 215 215 3 215 3 1 1 34 65 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000
+ [ MATL 52 ] 68 - a - - -
+ ML 216 215 3 218 3 1 1 32 63 -8.105 -0.019 -6.759 0.285 -0.558 0.188 -0.053
+ D 217 215 3 218 3 0 0 30 61 -6.174 -1.687 -0.566
+ IL 218 218 3 218 3 1 1 33 64 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000
+ [ MATL 53 ] 69 - g - - -
+ ML 219 218 3 221 3 1 1 31 62 -8.105 -0.019 -6.759 -0.112 -0.454 0.486 -0.083
+ D 220 218 3 221 3 0 0 29 60 -6.174 -1.687 -0.566
+ IL 221 221 3 221 3 1 1 32 63 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000
+ [ MATL 54 ] 70 - c - - -
+ ML 222 221 3 224 3 1 1 30 61 -8.105 -0.298 -2.448 0.059 0.279 -0.562 0.094
+ D 223 221 3 224 3 0 0 28 59 -6.174 -1.687 -0.566
+ IL 224 224 3 224 3 1 1 31 62 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000
+ [ MATL 55 ] 71 - a - - -
+ ML 225 224 3 227 3 1 1 29 60 -7.829 -0.146 -3.443 0.459 -0.620 -0.287 0.208
+ D 226 224 3 227 3 0 0 25 56 -7.646 -3.159 -0.179
+ IL 227 227 3 227 3 1 1 30 61 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000
+ [ MATL 56 ] 72 - a - - -
+ ML 228 227 3 230 3 1 1 29 59 -1.682 -0.564 -6.362 0.433 -0.836 0.242 -0.140
+ D 229 227 3 230 3 0 0 20 51 -7.963 -2.073 -0.399
+ IL 230 230 3 230 3 1 1 30 60 -0.859 -1.224 -5.595 0.000 0.000 0.000 0.000
+ [ MATL 57 ] 78 - c - - -
+ ML 231 230 3 233 3 1 1 13 32 -7.800 -0.023 -6.454 0.137 0.192 -0.515 0.082
+ D 232 230 3 233 3 0 0 12 31 -7.732 -2.169 -0.372
+ IL 233 233 3 233 3 1 1 18 36 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000
+ [ MATL 58 ] 79 - g - - -
+ ML 234 233 3 236 2 1 1 1 1 * 0.000 0.041 -0.409 0.191 0.107
+ D 235 233 3 236 2 0 0 0 0 * 0.000
+ IL 236 236 3 236 2 1 1 13 28 -1.823 -0.479 0.000 0.000 0.000 0.000
+ [ END 59 ] - - - - - -
+ E 237 236 3 -1 0 0 0 0 0
+ [ BEGR 60 ] - - - - - -
+ S 238 181 1 239 3 0 0 32 51 -8.105 -0.019 -6.759
+ IL 239 239 2 239 3 1 1 35 55 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000
+ [ MATL 61 ] 85 - g - - -
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+ D 241 239 2 242 3 0 0 29 48 -6.174 -1.687 -0.566
+ IL 242 242 3 242 3 1 1 32 51 -1.693 -0.612 -4.789 0.000 0.000 0.000 0.000
+ [ MATL 62 ] 88 - G - - -
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+ D 244 242 3 245 5 0 0 29 48 -6.096 -0.312 -5.357 -3.732 -3.645
+ IL 245 245 3 245 5 1 1 30 49 -2.408 -0.496 -4.087 -5.920 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 63 ] 89 103 g c - -
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+ ML 247 245 3 250 6 1 1 27 46 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094
+ MR 248 245 3 250 6 1 1 27 46 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094
+ D 249 245 3 250 6 0 0 25 44 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319
+ IL 250 250 5 250 6 1 1 29 47 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000
+ IR 251 251 6 251 5 1 1 28 47 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 64 ] 90 102 g c - -
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+ ML 253 251 6 256 6 1 1 26 45 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094
+ MR 254 251 6 256 6 1 1 26 44 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094
+ D 255 251 6 256 6 0 0 23 42 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319
+ IL 256 256 5 256 6 1 1 27 45 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000
+ IR 257 257 6 257 5 1 1 26 45 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 65 ] 91 101 G C - -
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+ ML 259 257 6 262 6 1 1 24 43 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094
+ MR 260 257 6 262 6 1 1 24 43 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094
+ D 261 257 6 262 6 0 0 23 42 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319
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+ IR 263 263 6 263 5 1 1 24 43 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 66 ] 92 100 G C - -
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+ ML 265 263 6 268 4 1 1 24 43 -3.758 -3.940 -0.507 -2.670 0.368 -0.385 -0.191 0.094
+ MR 266 263 6 268 4 1 1 23 42 -4.809 -3.838 -1.706 -0.766 0.368 -0.385 -0.191 0.094
+ D 267 263 6 268 4 0 0 22 41 -4.568 -4.250 -2.265 -0.520
+ IL 268 268 5 268 4 1 1 25 44 -1.686 -2.369 -1.117 -4.855 0.000 0.000 0.000 0.000
+ IR 269 269 6 269 3 1 1 24 43 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000
+ [ MATL 67 ] 93 - U - - -
+ ML 270 269 6 272 3 1 1 20 39 -8.105 -0.019 -6.759 -1.751 -1.701 -2.496 1.686
+ D 271 269 6 272 3 0 0 19 38 -6.174 -1.687 -0.566
+ IL 272 272 3 272 3 1 1 23 42 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000
+ [ MATL 68 ] 94 - U - - -
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+ D 274 272 3 275 3 0 0 18 37 -6.174 -1.687 -0.566
+ IL 275 275 3 275 3 1 1 22 41 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000
+ [ MATL 69 ] 95 - C - - -
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+ D 277 275 3 278 3 0 0 17 36 -6.174 -1.687 -0.566
+ IL 278 278 3 278 3 1 1 21 40 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000
+ [ MATL 70 ] 96 - G - - -
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+ D 280 278 3 281 3 0 0 16 34 -6.174 -1.687 -0.566
+ IL 281 281 3 281 3 1 1 20 38 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000
+ [ MATL 71 ] 97 - A - - -
+ ML 282 281 3 284 3 1 1 15 33 -8.105 -0.019 -6.759 1.723 -2.390 -2.085 -1.875
+ D 283 281 3 284 3 0 0 15 33 -6.174 -1.687 -0.566
+ IL 284 284 3 284 3 1 1 19 37 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000
+ [ MATL 72 ] 98 - U - - -
+ ML 285 284 3 287 3 1 1 13 31 -8.105 -0.019 -6.759 -0.664 -0.084 -1.491 1.049
+ D 286 284 3 287 3 0 0 13 32 -6.174 -1.687 -0.566
+ IL 287 287 3 287 3 1 1 18 36 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000
+ [ MATL 73 ] 99 - U - - -
+ ML 288 287 3 290 2 1 1 1 1 * 0.000 -1.751 -1.701 -2.496 1.686
+ D 289 287 3 290 2 0 0 0 0 * 0.000
+ IL 290 290 3 290 2 1 1 13 28 -1.823 -0.479 0.000 0.000 0.000 0.000
+ [ END 74 ] - - - - - -
+ E 291 290 3 -1 0 0 0 0 0
+//
+HMMER3/f [i1.1.1 | July 2014]
+NAME tRNA-Sec
+ACC RF01852
+LENG 91
+MAXL 164
+ALPH RNA
+RF no
+MM no
+CONS yes
+CS yes
+MAP yes
+DATE Tue Apr 8 16:22:29 2014
+COM [1] cmbuild -F CM SEED
+NSEQ 109
+EFFN 12.031647
+CKSUM 3407454328
+STATS LOCAL MSV -8.8824 0.71862
+STATS LOCAL VITERBI -9.9312 0.71862
+STATS LOCAL FORWARD -3.8558 0.71862
+HMM A C G U
+ m->m m->i m->d i->m i->i d->m d->d
+ COMPO 1.70134 1.32390 1.18487 1.40373
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+ 0.01415 4.95852 4.95852 1.46634 0.26236 1.09861 0.40547
+ 71 3.94603 5.00978 0.03331 4.99753 92 G - - <
+ 1.38629 1.38629 1.38629 1.38629
+ 0.01415 4.95852 4.95852 1.46634 0.26236 1.09861 0.40547
+ 72 4.62647 4.34036 5.19036 0.02880 93 U - - _
+ 1.38629 1.38629 1.38629 1.38629
+ 0.01415 4.95852 4.95852 1.46634 0.26236 1.09861 0.40547
+ 73 4.62647 4.34036 5.19036 0.02880 94 U - - _
+ 1.38629 1.38629 1.38629 1.38629
+ 0.01415 4.95852 4.95852 1.46634 0.26236 1.09861 0.40547
+ 74 4.57048 0.05600 4.95731 3.29483 95 C - - _
+ 1.38629 1.38629 1.38629 1.38629
+ 0.01415 4.95852 4.95852 1.46634 0.26236 1.09861 0.40547
+ 75 1.39428 4.02231 0.34268 3.72093 96 G - - _
+ 1.38629 1.38629 1.38629 1.38629
+ 0.01415 4.95852 4.95852 1.46634 0.26236 1.09861 0.40547
+ 76 0.03754 4.71976 4.55271 4.05206 97 A - - _
+ 1.38629 1.38629 1.38629 1.38629
+ 0.01415 4.95852 4.95852 1.46634 0.26236 1.09861 0.40547
+ 77 2.76170 1.38220 3.65009 0.41582 98 U - - _
+ 1.38629 1.38629 1.38629 1.38629
+ 0.01415 4.95852 4.95852 1.46634 0.26236 1.09861 0.40547
+ 78 4.62647 4.34036 5.19036 0.02880 99 U - - _
+ 1.38629 1.38629 1.38629 1.38629
+ 0.01415 4.95852 4.95852 1.46634 0.26236 1.09861 0.40547
+ 79 4.99796 0.04217 4.88940 3.61140 100 C - - >
+ 1.38629 1.38629 1.38629 1.38629
+ 0.01415 4.95852 4.95852 1.46634 0.26236 1.09861 0.40547
+ 80 3.56964 0.18145 3.17643 2.34297 101 C - - >
+ 1.38629 1.38629 1.38629 1.38629
+ 0.01415 4.95852 4.95852 1.46634 0.26236 1.09861 0.40547
+ 81 1.78072 0.76538 2.20592 1.36189 102 c - - >
+ 1.38629 1.38629 1.38629 1.38629
+ 0.01415 4.95852 4.95852 1.46634 0.26236 1.09861 0.40547
+ 82 1.19739 1.28841 1.31644 1.86936 103 a - - >
+ 1.38629 1.38629 1.38629 1.38629
+ 0.10289 2.84385 3.22957 0.62979 0.76079 1.09861 0.40547
+ 83 2.74933 0.64577 2.53047 1.10217 107 C - - )
+ 1.38629 1.38629 1.38629 1.38629
+ 0.11206 4.92543 2.31516 1.46634 0.26236 0.50228 0.92925
+ 84 1.45207 1.72283 1.27059 1.18192 108 u - - )
+ 1.38629 1.38629 1.38629 1.38629
+ 0.01565 4.85800 4.85800 1.46634 0.26236 0.92103 0.50768
+ 85 2.27145 0.78905 2.07976 1.14697 109 c - - )
+ 1.38629 1.38629 1.38629 1.38629
+ 0.02960 4.90068 3.82920 1.46634 0.26236 0.32022 1.29460
+ 86 1.58507 1.54867 1.32564 1.14917 110 u - - )
+ 1.38629 1.38629 1.38629 1.38629
+ 0.02055 4.93770 4.32961 1.46634 0.26236 0.41102 1.08760
+ 87 2.77949 0.51912 2.06907 1.52978 111 C - - )
+ 1.38629 1.38629 1.38629 1.38629
+ 0.02174 4.95263 4.23795 1.46634 0.26236 0.73658 0.65152
+ 88 2.70354 1.36407 1.56126 0.76027 112 u - - )
+ 1.38629 1.38629 1.38629 1.38629
+ 0.01425 4.95116 4.95116 1.46634 0.26236 1.39712 0.28410
+ 89 2.36677 1.28174 1.23556 1.08473 113 u - - )
+ 1.38629 1.38629 1.38629 1.38629
+ 0.02107 4.95116 4.28509 1.46634 0.26236 1.39712 0.28410
+ 90 2.57152 0.65054 1.45004 1.78822 114 C - - )
+ 1.38629 1.38629 1.38629 1.38629
+ 0.13853 4.94445 2.10175 1.46634 0.26236 0.51215 0.91431
+ 91 4.88296 0.06879 4.12716 3.15179 115 C - - )
+ 1.38629 1.38629 1.38629 1.38629
+ 0.27766 1.41698 * 1.16143 0.37548 0.00000 *
+//
diff --git a/testsuite/testsuite.sqc b/testsuite/testsuite.sqc
index c75d75fa..759879b5 100644
--- a/testsuite/testsuite.sqc
+++ b/testsuite/testsuite.sqc
@@ -43,6 +43,7 @@
1 exercise itest/sensitivity !testsuite/itest6-sensitivity.pl! @@ !! %OUTFILES%
1 exercise itest/trunc !testsuite/itest7-trunc.pl! @@ !! %OUTFILES%
1 exercise itest/scan-glist !testsuite/itest8-glist.pl! @@ !! %OUTFILES%
+1 exercise itest/scan-overlaps !testsuite/itest9-overlaps.pl! @@ !! %OUTFILES%
1 exercise itest/brute @src/itest_brute@
################################################################
@@ -91,6 +92,7 @@
1 prep copy/sC cp !testsuite/Plant_SRP.c.cm! %SRP.C.CM%
1 prep copy/zbpC cp !testsuite/snR75.c.cm! %ZBP.C.CM%
1 prep copy/4C cp !testsuite/4.c.cm! %4.C.CM%
+1 prep copy/5C cp !testsuite/5.c.cm! %5.C.CM%
1 exercise search/help/1 @src/cmsearch@ -h
1 exercise search/help/2 @src/cmsearch@ --devhelp
@@ -120,6 +122,7 @@
1 exercise press/sC @src/cmpress@ %SRP.C.CM%
1 exercise press/zC @src/cmpress@ %ZBP.C.CM%
1 exercise press/4C @src/cmpress@ %4.C.CM%
+1 exercise press/5C @src/cmpress@ %5.C.CM%
# cmscan exercises (cmscan requires a press'd CM file with E-values)
1 exercise scan/help/1 @src/cmscan@ -h
@@ -134,6 +137,8 @@
1 prep cleanup/zC rm -f %ZBP.C.CM%.*
1 exercise scan/4C @src/cmscan@ -Z 1000 %4.C.CM% !testsuite/emitted-tRNA.fa!
1 prep cleanup/4C rm -f %4.C.CM%.*
+1 exercise scan/5C @src/cmscan@ --fmt 2 --tblout %5.C.TBLOUT% --oskip --oclan --clanin !testsuite/5.claninfo! -Z 1000 %5.C.CM% !testsuite/emitted-tRNA.fa!
+1 prep cleanup/5C rm -f %5.C.CM%.*
# cmemit exercises
1 exercise emit/help/1 @src/cmemit@ -h
diff --git a/tutorial/tRNA5.c.cm b/tutorial/tRNA5.c.cm
index 7e50cdd7..22c28b91 100644
--- a/tutorial/tRNA5.c.cm
+++ b/tutorial/tRNA5.c.cm
@@ -1,4 +1,4 @@
-INFERNAL1/a [1.1rc1 | June 2012]
+INFERNAL1/a [1.1.1 | July 2014]
NAME tRNA5
STATES 230
NODES 61
@@ -8,9 +8,9 @@ ALPH RNA
RF no
CONS yes
MAP yes
-DATE Tue Jun 12 17:22:37 2012
-COM [1] ./cmbuild tRNA5.cm ../tutorial/tRNA5.sto
-COM [2] ./cmcalibrate ./tRNA5.cm
+DATE Mon Jun 27 12:35:45 2016
+COM [1] ./src/cmbuild tRNA5.cm tutorial/tRNA5.sto
+COM [2] cmcalibrate tRNA5.cm
PBEGIN 0.05
PEND 0.05
WBETA 1e-07
@@ -321,7 +321,7 @@ CM
[ END 41 ] - - - - - -
E 229 228 3 -1 0 0 0 0 0
//
-HMMER3/f [i1.1rc1 | June 2012]
+HMMER3/f [i1.1.1 | July 2014]
NAME tRNA5
LENG 72
MAXL 152
@@ -331,8 +331,8 @@ MM no
CONS yes
CS yes
MAP yes
-DATE Tue Jun 12 17:22:38 2012
-COM [1] ./cmbuild tRNA5.cm ../tutorial/tRNA5.sto
+DATE Mon Jun 27 12:35:45 2016
+COM [1] ./src/cmbuild tRNA5.cm tutorial/tRNA5.sto
NSEQ 5
EFFN 4.575195
CKSUM 3535941971