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Heng Li committed Jan 22, 2009
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2 changes: 1 addition & 1 deletion COPYING
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The MIT License

Copyright (c) 2008 Genome Research Ltd.
Copyright (c) 2008-2009 Genome Research Ltd.

Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
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363 changes: 363 additions & 0 deletions ChangeLog
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r104 | lh3lh3 | 2009-01-18 17:31:21 +0000 (Sun, 18 Jan 2009) | 3 lines
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M /branches/dev/samtools/bam.h
M /branches/dev/samtools/bam_lpileup.c
M /branches/dev/samtools/bamtk.c

* samtools-0.1.1-18
* fixed a bug in bam_lpileup.c: segment start and end are not correctly recognized

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r103 | lh3lh3 | 2009-01-18 16:34:03 +0000 (Sun, 18 Jan 2009) | 5 lines
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M /branches/dev/samtools/bam_import.c
M /branches/dev/samtools/bam_index.c
M /branches/dev/samtools/bamtk.c

* samtools-0.1.1-17
* fixed a bug when there are reads without coordinates
* also recognize type 'c' as 'A'
* found a bug in bam_lpileup.c; NOT fixed yet

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r102 | lh3lh3 | 2009-01-17 19:46:49 +0000 (Sat, 17 Jan 2009) | 2 lines
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A /branches/dev/samtools/INSTALL

Instruction for compilation

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r101 | lh3lh3 | 2009-01-17 19:31:36 +0000 (Sat, 17 Jan 2009) | 3 lines
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M /branches/dev/samtools/Makefile
A /branches/dev/samtools/Makefile.lite
M /branches/dev/samtools/bam.h
M /branches/dev/samtools/faidx.c
M /branches/dev/samtools/misc/Makefile
M /branches/dev/samtools/razf.c

* replaced HAVE_RAZF with _NO_RAZF
* added Makefile.lite for people who have trouble with razf.c

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r100 | lh3lh3 | 2009-01-16 10:03:37 +0000 (Fri, 16 Jan 2009) | 3 lines
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M /branches/dev/samtools/bam_mate.c
M /branches/dev/samtools/bamtk.c
M /branches/dev/samtools/misc/wgsim.c

* samtools-0.1.1-15
* fixed another bug in fixmate: unmapped pair has non-zero isize

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r99 | lh3lh3 | 2009-01-16 09:13:36 +0000 (Fri, 16 Jan 2009) | 4 lines
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M /branches/dev/samtools/ChangeLog
M /branches/dev/samtools/bam_mate.c
M /branches/dev/samtools/bamtk.c

* samtools-0.1.1-14
* fixed a bug in fixmate: isize not equal to zero if two ends mapped to
different chr

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r98 | lh3lh3 | 2009-01-15 16:47:41 +0000 (Thu, 15 Jan 2009) | 3 lines
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M /branches/dev/samtools/bam_maqcns.c
M /branches/dev/samtools/bamtk.c

* samtools-0.1.1-13
* fixed the prior for hom indels (Richard pointed this out)

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r97 | lh3lh3 | 2009-01-15 16:38:47 +0000 (Thu, 15 Jan 2009) | 4 lines
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M /branches/dev/samtools/COPYING
M /branches/dev/samtools/bam_sort.c
M /branches/dev/samtools/bamtk.c
M /branches/dev/samtools/source.dot

* samtools-0.1.1-12
* fixed a bug in sort
* update source file graph and copyright information

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r96 | lh3lh3 | 2009-01-14 21:46:14 +0000 (Wed, 14 Jan 2009) | 2 lines
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M /branches/dev/samtools/glf.c

fixed a typo

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r95 | lh3lh3 | 2009-01-14 21:44:53 +0000 (Wed, 14 Jan 2009) | 2 lines
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M /branches/dev/samtools/glf.c

added a main function for glf.c

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r94 | lh3lh3 | 2009-01-14 17:14:59 +0000 (Wed, 14 Jan 2009) | 4 lines
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M /branches/dev/samtools/Makefile
M /branches/dev/samtools/bam_plcmd.c
M /branches/dev/samtools/bamtk.c
M /branches/dev/samtools/bgzf.h
A /branches/dev/samtools/glf.c
M /branches/dev/samtools/glf.h

* samtools-0.1.1-11
* generate binary GLFv2
* added glfview command to dump GLFv2 binary file

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r93 | lh3lh3 | 2009-01-14 15:07:44 +0000 (Wed, 14 Jan 2009) | 4 lines
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M /branches/dev/samtools/bam_rmdup.c
M /branches/dev/samtools/bamtk.c
M /branches/dev/samtools/glf.h

* samtools-0.1.1-10
* fixed several bugs in rmdup
* prepare to generate GLF2

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r92 | lh3lh3 | 2009-01-14 13:27:44 +0000 (Wed, 14 Jan 2009) | 3 lines
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M /branches/dev/samtools/Makefile
M /branches/dev/samtools/bam.h
M /branches/dev/samtools/bam_import.c
A /branches/dev/samtools/bam_rmdup.c
M /branches/dev/samtools/bamtk.c

* samtools-0.1.1-9
* implemented rmdup; NOT tested yet

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r91 | lh3lh3 | 2009-01-13 20:15:43 +0000 (Tue, 13 Jan 2009) | 2 lines
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M /branches/dev/samtools/examples/00README.txt

update README for typos

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r90 | lh3lh3 | 2009-01-13 19:57:50 +0000 (Tue, 13 Jan 2009) | 2 lines
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M /branches/dev/samtools/examples/ex1.sam.gz

update example

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r89 | lh3lh3 | 2009-01-13 17:21:38 +0000 (Tue, 13 Jan 2009) | 3 lines
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M /branches/dev/samtools/Makefile
M /branches/dev/samtools/bam.c
A /branches/dev/samtools/bam_mate.c
M /branches/dev/samtools/bamtk.c

* samtools-0.1.1-8
* added fixmate command

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r88 | lh3lh3 | 2009-01-13 10:48:23 +0000 (Tue, 13 Jan 2009) | 3 lines
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M /branches/dev/samtools/bam_plcmd.c
M /branches/dev/samtools/bamtk.c

* samtools-0.1.1-7
* change the reported indel position to the previous way

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r87 | lh3lh3 | 2009-01-12 22:12:12 +0000 (Mon, 12 Jan 2009) | 4 lines
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M /branches/dev/samtools/bam_plcmd.c
M /branches/dev/samtools/bamtk.c

* samtools-0.1.1-6
* addd glt output
* allow to change indel calling parameters at the command line

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r86 | lh3lh3 | 2009-01-12 21:16:48 +0000 (Mon, 12 Jan 2009) | 4 lines
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M /branches/dev/samtools/bam.h
M /branches/dev/samtools/bam_pileup.c
M /branches/dev/samtools/bam_plcmd.c
M /branches/dev/samtools/bamtk.c

* samtools-0.1.1-5
* added two more flags
* allowed to select reads shown in pileup with a mask

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r85 | lh3lh3 | 2009-01-12 20:47:51 +0000 (Mon, 12 Jan 2009) | 4 lines
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M /branches/dev/samtools/bam_index.c
M /branches/dev/samtools/bam_plcmd.c
M /branches/dev/samtools/bamtk.c

* samtools-0.1.1-4
* fixed a bug in indexing (linear index)
* prepare to add glt output from pileup

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r84 | lh3lh3 | 2009-01-12 09:22:35 +0000 (Mon, 12 Jan 2009) | 3 lines
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M /branches/dev/samtools/bam_plcmd.c
M /branches/dev/samtools/bamtk.c

* samtools-0.1.1-3
* fixed a bug in outputing the coordinate of an indel

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r83 | lh3lh3 | 2009-01-11 15:18:01 +0000 (Sun, 11 Jan 2009) | 3 lines
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M /branches/dev/samtools/bam_plcmd.c
M /branches/dev/samtools/bamtk.c

* samtools-0.1.1-2
* pileup: allows to output indel sites only

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r82 | lh3lh3 | 2009-01-10 23:34:31 +0000 (Sat, 10 Jan 2009) | 3 lines
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M /branches/dev/samtools/bam_maqcns.c
M /branches/dev/samtools/bam_maqcns.h
M /branches/dev/samtools/bam_plcmd.c
M /branches/dev/samtools/bamtk.c

* samtools-0.1.1-1
* implemented a Bayesian indel caller

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r81 | lh3lh3 | 2009-01-09 09:54:28 +0000 (Fri, 09 Jan 2009) | 2 lines
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M /branches/dev/samtools/examples/00README.txt
D /branches/dev/samtools/examples/ex1.fa.fai

Let users generate ex1.fa.fai.

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r80 | lh3lh3 | 2009-01-08 16:10:08 +0000 (Thu, 08 Jan 2009) | 2 lines
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M /branches/dev/samtools/misc/bowtie2sam.pl

make the bowtie converter works for "-k 2"

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r78 | lh3lh3 | 2009-01-03 17:25:24 +0000 (Sat, 03 Jan 2009) | 2 lines
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M /branches/dev/samtools/misc/export2sam.pl

fixed a bug for "QC" reads

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r77 | lh3lh3 | 2009-01-01 18:32:06 +0000 (Thu, 01 Jan 2009) | 3 lines
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A /branches/dev/samtools/misc/bowtie2sam.pl
M /branches/dev/samtools/misc/soap2sam.pl

* soap2sam.pl: added NM tag
* bowtie2sam.pl: converter for bowtie

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r76 | lh3lh3 | 2008-12-31 23:24:24 +0000 (Wed, 31 Dec 2008) | 2 lines
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A /branches/dev/samtools/misc/soap2sam.pl

soap2sam.pl: convert soap output to SAM

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r75 | lh3lh3 | 2008-12-31 17:54:32 +0000 (Wed, 31 Dec 2008) | 3 lines
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M /branches/dev/samtools/misc/wgsim_eval.pl

* wgsim_eval.pl-0.1.1
* fixed a bug for a contig name like "NT_012345"

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r74 | lh3lh3 | 2008-12-31 16:38:21 +0000 (Wed, 31 Dec 2008) | 2 lines
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A /branches/dev/samtools/misc/wgsim_eval.pl

* evaluate alignment for reads generated by wgsim

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r73 | lh3lh3 | 2008-12-31 15:11:22 +0000 (Wed, 31 Dec 2008) | 2 lines
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M /branches/dev/samtools/misc/Makefile
M /branches/dev/samtools/misc/wgsim.c

fixed compiling warnings for wgsim

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r72 | lh3lh3 | 2008-12-31 13:40:51 +0000 (Wed, 31 Dec 2008) | 2 lines
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M /branches/dev/samtools/bam_tview.c

remove an unused variable (a compiler warning only)

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r71 | lh3lh3 | 2008-12-31 13:37:16 +0000 (Wed, 31 Dec 2008) | 2 lines
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M /branches/dev/samtools/misc/Makefile
A /branches/dev/samtools/misc/wgsim.c

wgsim: Paired-end reads simulator

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r70 | bhandsaker | 2008-12-29 20:27:16 +0000 (Mon, 29 Dec 2008) | 2 lines
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M /branches/dev/samtools/bam_maqcns.c
M /branches/dev/samtools/bam_tview.c

Move definition of bam_nt16_nt4_table so we can build without curses.

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r62 | lh3lh3 | 2008-12-22 15:55:13 +0000 (Mon, 22 Dec 2008) | 2 lines
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A /branches/dev/samtools/NEWS
M /branches/dev/samtools/bamtk.c
M /branches/dev/samtools/samtools.1

Release samtools-0.1.1

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r61 | lh3lh3 | 2008-12-22 15:46:08 +0000 (Mon, 22 Dec 2008) | 10 lines
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M /branches/dev/samtools/bam_aux.c
M /branches/dev/samtools/bam_index.c
M /branches/dev/samtools/bam_plcmd.c
M /branches/dev/samtools/bam_tview.c
M /branches/dev/samtools/bamtk.c
M /branches/dev/samtools/razf.c
M /branches/dev/samtools/samtools.1

* samtools-0.1.0-66
* fixed a bug in razf.c: reset z_eof when razf_seek() is called
* fixed a memory leak in parsing a region
* changed pileup a little bit when -s is in use: output ^ and $
* when a bam is not indexed, output more meaningful error message
* fixed a bug in indexing for small alignment
* fixed a bug in the viewer when we come to the end of a reference file
* updated documentation
* prepare to release 0.1.1

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r60 | lh3lh3 | 2008-12-22 15:10:16 +0000 (Mon, 22 Dec 2008) | 2 lines
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A /branches/dev/samtools/examples
A /branches/dev/samtools/examples/00README.txt
A /branches/dev/samtools/examples/ex1.fa
A /branches/dev/samtools/examples/ex1.fa.fai
A /branches/dev/samtools/examples/ex1.sam.gz

example

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r59 | lh3lh3 | 2008-12-22 09:38:15 +0000 (Mon, 22 Dec 2008) | 2 lines
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M /branches/dev/samtools/ChangeLog

update ChangeLog

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r58 | lh3lh3 | 2008-12-20 23:06:00 +0000 (Sat, 20 Dec 2008) | 3 lines
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7 changes: 7 additions & 0 deletions INSTALL
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Compiling samtools requires the zlib library <http://www.zlib.net/>;
compiling the alignment viewer further requires the GNU ncurses library
<http://www.gnu.org/software/ncurses/>. The default Makefile builds the
alignment viewer. If compilation fails due to errors in RAZF or the lack
of ncurses, you can compile with `make -f Makefile.lite'. However, the
alignment viewer will not be available; the FASTA indexer will not
support indexing compressed FASTA, either.
5 changes: 3 additions & 2 deletions Makefile
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Expand Up @@ -2,9 +2,10 @@ CC= gcc
CXX= g++
CFLAGS= -g -Wall -O2 -m64 #-arch ppc
CXXFLAGS= $(CFLAGS)
DFLAGS= -D_IOLIB=2 -D_FILE_OFFSET_BITS=64 -DHAVE_RAZF #-D_NO_CURSES
DFLAGS= -D_IOLIB=2 -D_FILE_OFFSET_BITS=64 #-D_NO_RAZF #-D_NO_CURSES
OBJS= bam.o bam_import.o bam_pileup.o bam_lpileup.o bam_sort.o bam_index.o \
razf.o bgzf.o faidx.o bam_tview.o bam_maqcns.o bam_aux.o bam_plcmd.o
razf.o bgzf.o faidx.o bam_tview.o bam_maqcns.o bam_aux.o bam_plcmd.o \
bam_mate.o bam_rmdup.o glf.o
PROG= razip bgzip samtools
INCLUDES=
LIBS= -lm -lz
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