Merge branch 'release-1.1.2'

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
+####

COPYRIGHT

@@ -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 <http://www.gnu.org/licenses/>.
-
-------------------------------------------------------------------
-The Infernal development team
-HHMI Janelia Farm Research Campus
-http://infernal.janelia.org/
-
-

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
 

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

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@
 ------------------------------------------------------------------
@@ -14,23 +15,19 @@ 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).
 
 
 -------------------------------------------------------------------
 The Infernal development team
-HHMI Janelia Farm Research Campus
-http://infernal.janelia.org/
-
-
-
+github.com/EddyRivasLab/infernal/
+http://eddylab.org/infernal

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      <package>     e.g. "Infernal"
 #     PACKAGE_VERSION   <version>     e.g. "1.0"
-#     PACKAGE_BUGREPORT <bug-report>  e.g. "eddys@janelia.hhmi.org"
+#     PACKAGE_BUGREPORT <bug-report>  e.g. "eric.nawrocki@nih.gov"
 #     PACKAGE_TARNAME   <tarname>     e.g. "infernal"
 # From them, it derives one more:
 #     PACKAGE_STRING    <package> <version>, 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([ \

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 " <f>"
 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 " <n>"
+specify the format of the tabular output file specified with
+.BI --tblout " <f>" 
+be in format 
+.I <n>.
+Possible values for 
+.I <n>
+are 1 or 2. By default
+.I <n>
+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 <n>
 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 " <f>"
+Read clan information on the models in 
+.I <cmfile> 
+from file
+.I <f>.
+Not all models in 
+.I <cmfile>
+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 <f>.
+
+.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 " <f>"
+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 " <n>"
 Set the number of parallel worker threads to 
 .I <n>.

documentation/manpages/cmsearch.man

@@ -167,7 +167,7 @@ to the file
 .BI --tblout " <f>"
 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