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ChangeLog.old
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ChangeLog.old
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------------------------------------------------------------------------
r108 | lh3lh3 | 2009-01-20 11:56:45 +0000 (Tue, 20 Jan 2009) | 2 lines
Changed paths:
M /branches/dev/samtools/examples/Makefile
made it a little more convenient
------------------------------------------------------------------------
r107 | lh3lh3 | 2009-01-20 11:53:30 +0000 (Tue, 20 Jan 2009) | 2 lines
Changed paths:
A /branches/dev/samtools/examples/Makefile
added a Makefile
------------------------------------------------------------------------
r106 | lh3lh3 | 2009-01-20 11:25:05 +0000 (Tue, 20 Jan 2009) | 2 lines
Changed paths:
M /branches/dev/samtools/misc/maq2sam.c
support RG tag
------------------------------------------------------------------------
r105 | lh3lh3 | 2009-01-18 17:37:20 +0000 (Sun, 18 Jan 2009) | 2 lines
Changed paths:
M /branches/dev/samtools/ChangeLog
update changelog
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r104 | lh3lh3 | 2009-01-18 17:31:21 +0000 (Sun, 18 Jan 2009) | 3 lines
Changed paths:
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
------------------------------------------------------------------------
r103 | lh3lh3 | 2009-01-18 16:34:03 +0000 (Sun, 18 Jan 2009) | 5 lines
Changed paths:
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
------------------------------------------------------------------------
r102 | lh3lh3 | 2009-01-17 19:46:49 +0000 (Sat, 17 Jan 2009) | 2 lines
Changed paths:
A /branches/dev/samtools/INSTALL
Instruction for compilation
------------------------------------------------------------------------
r101 | lh3lh3 | 2009-01-17 19:31:36 +0000 (Sat, 17 Jan 2009) | 3 lines
Changed paths:
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
------------------------------------------------------------------------
r100 | lh3lh3 | 2009-01-16 10:03:37 +0000 (Fri, 16 Jan 2009) | 3 lines
Changed paths:
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
------------------------------------------------------------------------
r99 | lh3lh3 | 2009-01-16 09:13:36 +0000 (Fri, 16 Jan 2009) | 4 lines
Changed paths:
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
------------------------------------------------------------------------
r98 | lh3lh3 | 2009-01-15 16:47:41 +0000 (Thu, 15 Jan 2009) | 3 lines
Changed paths:
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)
------------------------------------------------------------------------
r97 | lh3lh3 | 2009-01-15 16:38:47 +0000 (Thu, 15 Jan 2009) | 4 lines
Changed paths:
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
------------------------------------------------------------------------
r96 | lh3lh3 | 2009-01-14 21:46:14 +0000 (Wed, 14 Jan 2009) | 2 lines
Changed paths:
M /branches/dev/samtools/glf.c
fixed a typo
------------------------------------------------------------------------
r95 | lh3lh3 | 2009-01-14 21:44:53 +0000 (Wed, 14 Jan 2009) | 2 lines
Changed paths:
M /branches/dev/samtools/glf.c
added a main function for glf.c
------------------------------------------------------------------------
r94 | lh3lh3 | 2009-01-14 17:14:59 +0000 (Wed, 14 Jan 2009) | 4 lines
Changed paths:
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
------------------------------------------------------------------------
r93 | lh3lh3 | 2009-01-14 15:07:44 +0000 (Wed, 14 Jan 2009) | 4 lines
Changed paths:
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
------------------------------------------------------------------------
r92 | lh3lh3 | 2009-01-14 13:27:44 +0000 (Wed, 14 Jan 2009) | 3 lines
Changed paths:
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
------------------------------------------------------------------------
r91 | lh3lh3 | 2009-01-13 20:15:43 +0000 (Tue, 13 Jan 2009) | 2 lines
Changed paths:
M /branches/dev/samtools/examples/00README.txt
update README for typos
------------------------------------------------------------------------
r90 | lh3lh3 | 2009-01-13 19:57:50 +0000 (Tue, 13 Jan 2009) | 2 lines
Changed paths:
M /branches/dev/samtools/examples/ex1.sam.gz
update example
------------------------------------------------------------------------
r89 | lh3lh3 | 2009-01-13 17:21:38 +0000 (Tue, 13 Jan 2009) | 3 lines
Changed paths:
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
------------------------------------------------------------------------
r88 | lh3lh3 | 2009-01-13 10:48:23 +0000 (Tue, 13 Jan 2009) | 3 lines
Changed paths:
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
------------------------------------------------------------------------
r87 | lh3lh3 | 2009-01-12 22:12:12 +0000 (Mon, 12 Jan 2009) | 4 lines
Changed paths:
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
------------------------------------------------------------------------
r86 | lh3lh3 | 2009-01-12 21:16:48 +0000 (Mon, 12 Jan 2009) | 4 lines
Changed paths:
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
------------------------------------------------------------------------
r85 | lh3lh3 | 2009-01-12 20:47:51 +0000 (Mon, 12 Jan 2009) | 4 lines
Changed paths:
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
------------------------------------------------------------------------
r84 | lh3lh3 | 2009-01-12 09:22:35 +0000 (Mon, 12 Jan 2009) | 3 lines
Changed paths:
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
------------------------------------------------------------------------
r83 | lh3lh3 | 2009-01-11 15:18:01 +0000 (Sun, 11 Jan 2009) | 3 lines
Changed paths:
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
------------------------------------------------------------------------
r82 | lh3lh3 | 2009-01-10 23:34:31 +0000 (Sat, 10 Jan 2009) | 3 lines
Changed paths:
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
------------------------------------------------------------------------
r81 | lh3lh3 | 2009-01-09 09:54:28 +0000 (Fri, 09 Jan 2009) | 2 lines
Changed paths:
M /branches/dev/samtools/examples/00README.txt
D /branches/dev/samtools/examples/ex1.fa.fai
Let users generate ex1.fa.fai.
------------------------------------------------------------------------
r80 | lh3lh3 | 2009-01-08 16:10:08 +0000 (Thu, 08 Jan 2009) | 2 lines
Changed paths:
M /branches/dev/samtools/misc/bowtie2sam.pl
make the bowtie converter works for "-k 2"
------------------------------------------------------------------------
r78 | lh3lh3 | 2009-01-03 17:25:24 +0000 (Sat, 03 Jan 2009) | 2 lines
Changed paths:
M /branches/dev/samtools/misc/export2sam.pl
fixed a bug for "QC" reads
------------------------------------------------------------------------
r77 | lh3lh3 | 2009-01-01 18:32:06 +0000 (Thu, 01 Jan 2009) | 3 lines
Changed paths:
A /branches/dev/samtools/misc/bowtie2sam.pl
M /branches/dev/samtools/misc/soap2sam.pl
* soap2sam.pl: added NM tag
* bowtie2sam.pl: converter for bowtie
------------------------------------------------------------------------
r76 | lh3lh3 | 2008-12-31 23:24:24 +0000 (Wed, 31 Dec 2008) | 2 lines
Changed paths:
A /branches/dev/samtools/misc/soap2sam.pl
soap2sam.pl: convert soap output to SAM
------------------------------------------------------------------------
r75 | lh3lh3 | 2008-12-31 17:54:32 +0000 (Wed, 31 Dec 2008) | 3 lines
Changed paths:
M /branches/dev/samtools/misc/wgsim_eval.pl
* wgsim_eval.pl-0.1.1
* fixed a bug for a contig name like "NT_012345"
------------------------------------------------------------------------
r74 | lh3lh3 | 2008-12-31 16:38:21 +0000 (Wed, 31 Dec 2008) | 2 lines
Changed paths:
A /branches/dev/samtools/misc/wgsim_eval.pl
* evaluate alignment for reads generated by wgsim
------------------------------------------------------------------------
r73 | lh3lh3 | 2008-12-31 15:11:22 +0000 (Wed, 31 Dec 2008) | 2 lines
Changed paths:
M /branches/dev/samtools/misc/Makefile
M /branches/dev/samtools/misc/wgsim.c
fixed compiling warnings for wgsim
------------------------------------------------------------------------
r72 | lh3lh3 | 2008-12-31 13:40:51 +0000 (Wed, 31 Dec 2008) | 2 lines
Changed paths:
M /branches/dev/samtools/bam_tview.c
remove an unused variable (a compiler warning only)
------------------------------------------------------------------------
r71 | lh3lh3 | 2008-12-31 13:37:16 +0000 (Wed, 31 Dec 2008) | 2 lines
Changed paths:
M /branches/dev/samtools/misc/Makefile
A /branches/dev/samtools/misc/wgsim.c
wgsim: Paired-end reads simulator
------------------------------------------------------------------------
r70 | bhandsaker | 2008-12-29 20:27:16 +0000 (Mon, 29 Dec 2008) | 2 lines
Changed paths:
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.
------------------------------------------------------------------------
r62 | lh3lh3 | 2008-12-22 15:55:13 +0000 (Mon, 22 Dec 2008) | 2 lines
Changed paths:
A /branches/dev/samtools/NEWS
M /branches/dev/samtools/bamtk.c
M /branches/dev/samtools/samtools.1
Release samtools-0.1.1
------------------------------------------------------------------------
r61 | lh3lh3 | 2008-12-22 15:46:08 +0000 (Mon, 22 Dec 2008) | 10 lines
Changed paths:
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
------------------------------------------------------------------------
r60 | lh3lh3 | 2008-12-22 15:10:16 +0000 (Mon, 22 Dec 2008) | 2 lines
Changed paths:
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
------------------------------------------------------------------------
r59 | lh3lh3 | 2008-12-22 09:38:15 +0000 (Mon, 22 Dec 2008) | 2 lines
Changed paths:
M /branches/dev/samtools/ChangeLog
update ChangeLog
------------------------------------------------------------------------
r58 | lh3lh3 | 2008-12-20 23:06:00 +0000 (Sat, 20 Dec 2008) | 3 lines
Changed paths:
M /branches/dev/samtools/misc/export2sam.pl
* added comments
* fixed several bugs
------------------------------------------------------------------------
r57 | lh3lh3 | 2008-12-20 15:44:20 +0000 (Sat, 20 Dec 2008) | 2 lines
Changed paths:
A /branches/dev/samtools/misc/export2sam.pl
convert Export format to SAM; not thoroughly tested
------------------------------------------------------------------------
r56 | lh3lh3 | 2008-12-19 22:13:28 +0000 (Fri, 19 Dec 2008) | 6 lines
Changed paths:
M /branches/dev/samtools/bam_import.c
M /branches/dev/samtools/bam_plcmd.c
M /branches/dev/samtools/bam_tview.c
M /branches/dev/samtools/bamtk.c
A /branches/dev/samtools/source.dot
* samtools-0.1.0-65
* pileup: generate maq-like simple output
* pileup: allow to output pileup at required sites
* source.dot: source file relationship graph
* tview: fixed a minor bug
------------------------------------------------------------------------
r55 | lh3lh3 | 2008-12-19 20:10:26 +0000 (Fri, 19 Dec 2008) | 2 lines
Changed paths:
D /branches/dev/samtools/misc/all2sam.pl
remove all2sam.pl
------------------------------------------------------------------------
r54 | lh3lh3 | 2008-12-16 22:34:25 +0000 (Tue, 16 Dec 2008) | 2 lines
Changed paths:
A /branches/dev/samtools/COPYING
M /branches/dev/samtools/bam.h
M /branches/dev/samtools/faidx.h
M /branches/dev/samtools/khash.h
M /branches/dev/samtools/kseq.h
M /branches/dev/samtools/ksort.h
M /branches/dev/samtools/samtools.1
Added copyright information and a bit more documentation. No code change.
------------------------------------------------------------------------
r53 | lh3lh3 | 2008-12-16 13:40:18 +0000 (Tue, 16 Dec 2008) | 3 lines
Changed paths:
M /branches/dev/samtools/bam.c
M /branches/dev/samtools/bam.h
M /branches/dev/samtools/bam_index.c
M /branches/dev/samtools/bam_maqcns.c
M /branches/dev/samtools/bamtk.c
* samtools-0.1.0-64
* improved efficiency of the indel caller for spliced alignments
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r52 | lh3lh3 | 2008-12-16 10:28:20 +0000 (Tue, 16 Dec 2008) | 3 lines
Changed paths:
M /branches/dev/samtools/bam.c
M /branches/dev/samtools/bam.h
M /branches/dev/samtools/bam_aux.c
M /branches/dev/samtools/bam_index.c
M /branches/dev/samtools/bamtk.c
* samtools-0.1.0-63
* a bit code cleanup: reduce the dependency between source files
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r51 | lh3lh3 | 2008-12-15 14:29:32 +0000 (Mon, 15 Dec 2008) | 3 lines
Changed paths:
M /branches/dev/samtools/bam_maqcns.c
M /branches/dev/samtools/bam_plcmd.c
M /branches/dev/samtools/bamtk.c
* samtools-0.1.0-62
* fixed a memory leak
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r50 | lh3lh3 | 2008-12-15 14:00:13 +0000 (Mon, 15 Dec 2008) | 2 lines
Changed paths:
M /branches/dev/samtools/ChangeLog
M /branches/dev/samtools/bam.h
M /branches/dev/samtools/samtools.1
update documentation, ChangeLog and a comment
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r49 | lh3lh3 | 2008-12-15 13:36:43 +0000 (Mon, 15 Dec 2008) | 6 lines
Changed paths:
M /branches/dev/samtools/Makefile
M /branches/dev/samtools/bam.h
M /branches/dev/samtools/bam_maqcns.c
M /branches/dev/samtools/bam_maqcns.h
M /branches/dev/samtools/bam_pileup.c
A /branches/dev/samtools/bam_plcmd.c
M /branches/dev/samtools/bamtk.c
M /branches/dev/samtools/samtools.1
* samtools-0.1.0-61
* moved pileup command to a separate source file
* added indel caller
* added bam_cal_segend(). (NOT WORKING for spliced alignment!!!)
* updated documentation
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r48 | lh3lh3 | 2008-12-12 13:55:36 +0000 (Fri, 12 Dec 2008) | 3 lines
Changed paths:
M /branches/dev/samtools/bam_maqcns.c
M /branches/dev/samtools/bamtk.c
* samtools-0.1.0-60
* fixed another bug in maqcns when there is a nearby deletion
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r47 | lh3lh3 | 2008-12-12 13:42:16 +0000 (Fri, 12 Dec 2008) | 5 lines
Changed paths:
M /branches/dev/samtools/bam_maqcns.c
M /branches/dev/samtools/bam_pileup.c
M /branches/dev/samtools/bamtk.c
* samtools-0.1.0-59
* pileup: outputing consensus is now optional
* fixed a bug in glfgen. This bug also exists in maq's glfgen. However,
I am not quite sure why the previous version may have problem.
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r46 | lh3lh3 | 2008-12-12 11:44:56 +0000 (Fri, 12 Dec 2008) | 6 lines
Changed paths:
M /branches/dev/samtools/bam_pileup.c
M /branches/dev/samtools/bamtk.c
* samtools-0.1.0-58
* add maq consensus to pileup. However, I will move this part to a new
command as strictly speaking, consensus callin is not part of pileup,
and imposing it would make it harder to generate for other language
bindings.
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r45 | bhandsaker | 2008-12-11 20:43:56 +0000 (Thu, 11 Dec 2008) | 2 lines
Changed paths:
M /branches/dev/samtools/bgzf.c
Fix bug in tell() after reads that consume to the exact end of a block.
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r44 | lh3lh3 | 2008-12-11 09:36:53 +0000 (Thu, 11 Dec 2008) | 2 lines
Changed paths:
M /branches/dev/samtools/samtools.1
update manual
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r43 | lh3lh3 | 2008-12-11 09:25:36 +0000 (Thu, 11 Dec 2008) | 4 lines
Changed paths:
M /branches/dev/samtools/bam_import.c
M /branches/dev/samtools/bamtk.c
* samtools-0.1.0-57
* fixed a bug in parser when there is auxiliary fields
* made the parser a bit more robust
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r42 | lh3lh3 | 2008-12-10 14:57:29 +0000 (Wed, 10 Dec 2008) | 5 lines
Changed paths:
M /branches/dev/samtools/bam_index.c
M /branches/dev/samtools/bamtk.c
M /branches/dev/samtools/bgzf.c
* samtools-0.1.0-56
* fixed a bug in bgzf (only reading is affected)
* fixed a typo in bam_index.c
* in bam_index.c, check potential bugs in the underlying I/O library
------------------------------------------------------------------------
r41 | lh3lh3 | 2008-12-10 12:53:08 +0000 (Wed, 10 Dec 2008) | 2 lines
Changed paths:
M /branches/dev/samtools/samtools.1
update manual
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r40 | lh3lh3 | 2008-12-10 11:52:10 +0000 (Wed, 10 Dec 2008) | 5 lines
Changed paths:
M /branches/dev/samtools/bam.h
M /branches/dev/samtools/bam_pileup.c
M /branches/dev/samtools/bamtk.c
* samtools-0.1.0-55
* tried to make pileup work with clipping (previously not), though NOT tested
* removed -v from pileup
* made pileup take the reference sequence
------------------------------------------------------------------------
r39 | lh3lh3 | 2008-12-09 11:59:28 +0000 (Tue, 09 Dec 2008) | 4 lines
Changed paths:
M /branches/dev/samtools/bam_import.c
M /branches/dev/samtools/bamtk.c
M /branches/dev/samtools/samtools.1
* samtools-0.1.0-54
* in parser, recognize "=", rather than ",", as a match
* in parser, correctl parse "=" at the MRNM field.
------------------------------------------------------------------------
r38 | lh3lh3 | 2008-12-09 11:39:07 +0000 (Tue, 09 Dec 2008) | 2 lines
Changed paths:
M /branches/dev/samtools/misc/maq2sam.c
fixed a bug in handling maq flag 64 and 192
------------------------------------------------------------------------
r37 | lh3lh3 | 2008-12-09 09:53:46 +0000 (Tue, 09 Dec 2008) | 2 lines
Changed paths:
M /branches/dev/samtools/misc/md5fa.c
also calculate unordered md5sum check
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r36 | lh3lh3 | 2008-12-09 09:46:21 +0000 (Tue, 09 Dec 2008) | 2 lines
Changed paths:
M /branches/dev/samtools/misc/md5fa.c
fixed a minor bug when there are space in the sequence
------------------------------------------------------------------------
r35 | lh3lh3 | 2008-12-09 09:40:45 +0000 (Tue, 09 Dec 2008) | 2 lines
Changed paths:
M /branches/dev/samtools/misc/md5fa.c
fixed a potential memory leak
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r34 | lh3lh3 | 2008-12-08 14:52:17 +0000 (Mon, 08 Dec 2008) | 2 lines
Changed paths:
M /branches/dev/samtools/bam_import.c
M /branches/dev/samtools/bam_index.c
M /branches/dev/samtools/bamtk.c
* fixed a bug in import: bin is wrongly calculated
------------------------------------------------------------------------
r33 | lh3lh3 | 2008-12-08 14:08:01 +0000 (Mon, 08 Dec 2008) | 2 lines
Changed paths:
M /branches/dev/samtools/misc/all2sam.pl
nothing, really
------------------------------------------------------------------------
r32 | lh3lh3 | 2008-12-08 12:56:02 +0000 (Mon, 08 Dec 2008) | 3 lines
Changed paths:
M /branches/dev/samtools/Makefile
M /branches/dev/samtools/kseq.h
M /branches/dev/samtools/misc/Makefile
A /branches/dev/samtools/misc/md5.c
A /branches/dev/samtools/misc/md5.h
A /branches/dev/samtools/misc/md5fa.c
* fixed two warnings in kseq.h
* added md5sum utilities
------------------------------------------------------------------------
r31 | lh3lh3 | 2008-12-08 11:35:29 +0000 (Mon, 08 Dec 2008) | 5 lines
Changed paths:
M /branches/dev/samtools/Makefile
M /branches/dev/samtools/bam_import.c
M /branches/dev/samtools/bamtk.c
A /branches/dev/samtools/kseq.h
D /branches/dev/samtools/kstream.h
* samtools-0.1.0-52
* replace kstream with kseq. kseq is a superset of kstream. I need the
extra functions in kseq.h.
* also compile stand-alone faidx
------------------------------------------------------------------------
r30 | lh3lh3 | 2008-12-08 11:17:04 +0000 (Mon, 08 Dec 2008) | 3 lines
Changed paths:
M /branches/dev/samtools/bam.h
M /branches/dev/samtools/bam_sort.c
M /branches/dev/samtools/bamtk.c
* samtools-0.1.0-51
* sorting by read names is available
------------------------------------------------------------------------
r29 | lh3lh3 | 2008-12-08 10:29:02 +0000 (Mon, 08 Dec 2008) | 3 lines
Changed paths:
M /branches/dev/samtools/bam.c
M /branches/dev/samtools/bam.h
M /branches/dev/samtools/bam_import.c
M /branches/dev/samtools/bam_maqcns.c
M /branches/dev/samtools/bam_pileup.c
M /branches/dev/samtools/bam_sort.c
M /branches/dev/samtools/bam_tview.c
M /branches/dev/samtools/bamtk.c
M /branches/dev/samtools/misc/maq2sam.c
* samtools-0.1.0-50
* format change to meet the latest specification
------------------------------------------------------------------------
r28 | lh3lh3 | 2008-12-04 16:09:21 +0000 (Thu, 04 Dec 2008) | 3 lines
Changed paths:
M /branches/dev/samtools/bam_maqcns.c
M /branches/dev/samtools/misc/maq2sam.c
* minor change in maqcns: special care when n==0
* change maq2sam to meet the latest specification
------------------------------------------------------------------------
r27 | lh3lh3 | 2008-12-04 15:55:44 +0000 (Thu, 04 Dec 2008) | 2 lines
Changed paths:
M /branches/dev/samtools/razf.c
M /branches/dev/samtools/razf.h
considerable code clean up in razf
------------------------------------------------------------------------
r26 | lh3lh3 | 2008-12-04 15:08:18 +0000 (Thu, 04 Dec 2008) | 2 lines
Changed paths:
M /branches/dev/samtools/ChangeLog
M /branches/dev/samtools/Makefile
M /branches/dev/samtools/faidx.c
make RAZF optional in faidx.c
------------------------------------------------------------------------
r25 | lh3lh3 | 2008-12-01 15:27:22 +0000 (Mon, 01 Dec 2008) | 3 lines
Changed paths:
M /branches/dev/samtools/Makefile
M /branches/dev/samtools/bam.h
M /branches/dev/samtools/bam_aux.c
M /branches/dev/samtools/bamtk.c
M /branches/dev/samtools/samtools.1
* samtools-0.1.0-49
* added routines for retrieving aux data, NOT TESTED YET!
------------------------------------------------------------------------
r24 | lh3lh3 | 2008-12-01 14:29:43 +0000 (Mon, 01 Dec 2008) | 5 lines
Changed paths:
M /branches/dev/samtools/bam.c
M /branches/dev/samtools/bam_import.c
M /branches/dev/samtools/bam_maqcns.c
M /branches/dev/samtools/bamtk.c
M /branches/dev/samtools/bgzf.c
M /branches/dev/samtools/samtools.1
* samtools-0.1.0-48
* bgzf: fixed a potential integer overflow on 32-it machines
* maqcns: set the minimum combined quality as 0
* supporting hex strings
------------------------------------------------------------------------
r23 | lh3lh3 | 2008-11-27 17:14:37 +0000 (Thu, 27 Nov 2008) | 3 lines
Changed paths:
M /branches/dev/samtools/bam_maqcns.c
M /branches/dev/samtools/bamtk.c
* samtools-0.1.0-47
* fixed the bug in maqcns
------------------------------------------------------------------------
r22 | lh3lh3 | 2008-11-27 17:08:11 +0000 (Thu, 27 Nov 2008) | 3 lines
Changed paths:
M /branches/dev/samtools/Makefile
M /branches/dev/samtools/bam.h
A /branches/dev/samtools/bam_maqcns.c
A /branches/dev/samtools/bam_maqcns.h
M /branches/dev/samtools/bam_tview.c
M /branches/dev/samtools/bamtk.c
A /branches/dev/samtools/glf.h
* samtools-0.1.0-46
* add MAQ consensus caller, currently BUGGY!
------------------------------------------------------------------------
r21 | lh3lh3 | 2008-11-27 13:51:28 +0000 (Thu, 27 Nov 2008) | 4 lines
Changed paths:
M /branches/dev/samtools/bam_pileup.c
M /branches/dev/samtools/bam_tview.c
M /branches/dev/samtools/bamtk.c
* samtools-0.1.0-45
* tview: display padded alignment (but not P operation)
* better coordinates and reference sequence
------------------------------------------------------------------------
r19 | lh3lh3 | 2008-11-27 09:26:05 +0000 (Thu, 27 Nov 2008) | 2 lines
Changed paths:
A /branches/dev/samtools/ChangeLog
new ChangeLog
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r18 | lh3lh3 | 2008-11-27 09:24:45 +0000 (Thu, 27 Nov 2008) | 3 lines
Changed paths:
D /branches/dev/samtools/ChangeLog
A /branches/dev/samtools/ChangeLog.old (from /branches/dev/samtools/ChangeLog:6)
Rename ChangeLog to ChangeLog.old. This old ChangeLog is generated from
the log of my personal SVN repository.
------------------------------------------------------------------------
r17 | lh3lh3 | 2008-11-27 09:22:55 +0000 (Thu, 27 Nov 2008) | 6 lines
Changed paths:
M /branches/dev/samtools/Makefile
M /branches/dev/samtools/bamtk.c
M /branches/dev/samtools/bgzf.c
* samtools-0.1.0-44
* declare fseeko and ftello as some Linux may not do this by default and
missing these declarations will make bgzf buggy
* get rid of some harmless warings
* use BGZF by default, now
------------------------------------------------------------------------
r16 | lh3lh3 | 2008-11-26 21:19:11 +0000 (Wed, 26 Nov 2008) | 4 lines
Changed paths:
M /branches/dev/samtools/bam_index.c
M /branches/dev/samtools/bamtk.c
M /branches/dev/samtools/razf.c
* samtools-0.1.0-43
* fixed a bug in razf_read()
* give more warnings when the file is truncated (or due to bugs in I/O library)
------------------------------------------------------------------------
r15 | lh3lh3 | 2008-11-26 20:41:39 +0000 (Wed, 26 Nov 2008) | 2 lines
Changed paths:
M /branches/dev/samtools/bgzf.c
fixed a bug in bgzf.c at the end of the file
------------------------------------------------------------------------
r14 | lh3lh3 | 2008-11-26 17:05:18 +0000 (Wed, 26 Nov 2008) | 4 lines
Changed paths:
M /branches/dev/samtools/bamtk.c
* samtools-0.1.0-42
* a lot happened to RAZF, although samtools itself is untouched. Better
also update the version number anyway to avoid confusion
------------------------------------------------------------------------
r13 | lh3lh3 | 2008-11-26 17:03:48 +0000 (Wed, 26 Nov 2008) | 2 lines
Changed paths:
M /branches/dev/samtools/razf.c
a change from Jue, but I think it should not matter
------------------------------------------------------------------------
r12 | lh3lh3 | 2008-11-26 16:48:14 +0000 (Wed, 26 Nov 2008) | 3 lines
Changed paths:
M /branches/dev/samtools/razf.c
fixed a potential bug in razf. However, it seems still buggy, just
rarely happens, very rarely.
------------------------------------------------------------------------
r11 | lh3lh3 | 2008-11-26 14:02:56 +0000 (Wed, 26 Nov 2008) | 2 lines
Changed paths:
M /branches/dev/samtools/razf.c
fixed a bug in razf, with the help of Jue
------------------------------------------------------------------------
r10 | lh3lh3 | 2008-11-26 11:55:32 +0000 (Wed, 26 Nov 2008) | 2 lines
Changed paths:
M /branches/dev/samtools/bam_index.c
remove a comment
------------------------------------------------------------------------
r9 | lh3lh3 | 2008-11-26 11:37:05 +0000 (Wed, 26 Nov 2008) | 2 lines
Changed paths:
M /branches/dev/samtools/Makefile
M /branches/dev/samtools/bam.h
M /branches/dev/samtools/razf.c
M /branches/dev/samtools/razf.h
* Jue has updated razf to realize Bob's scheme
------------------------------------------------------------------------
r7 | lh3lh3 | 2008-11-25 20:37:37 +0000 (Tue, 25 Nov 2008) | 2 lines
Changed paths:
A /branches/dev/samtools/samtools.1
the manual page
------------------------------------------------------------------------
r6 | lh3lh3 | 2008-11-25 20:37:16 +0000 (Tue, 25 Nov 2008) | 3 lines
Changed paths:
A /branches/dev/samtools/ChangeLog
A /branches/dev/samtools/Makefile
A /branches/dev/samtools/bam.c
A /branches/dev/samtools/bam.h
A /branches/dev/samtools/bam_aux.c
A /branches/dev/samtools/bam_endian.h
A /branches/dev/samtools/bam_import.c
A /branches/dev/samtools/bam_index.c
A /branches/dev/samtools/bam_lpileup.c
A /branches/dev/samtools/bam_pileup.c
A /branches/dev/samtools/bam_sort.c
A /branches/dev/samtools/bam_tview.c
A /branches/dev/samtools/bamtk.c
A /branches/dev/samtools/bgzf.c
A /branches/dev/samtools/bgzf.h
A /branches/dev/samtools/bgzip.c
A /branches/dev/samtools/faidx.c
A /branches/dev/samtools/faidx.h
A /branches/dev/samtools/khash.h
A /branches/dev/samtools/ksort.h
A /branches/dev/samtools/kstream.h
A /branches/dev/samtools/misc
A /branches/dev/samtools/misc/Makefile
A /branches/dev/samtools/misc/all2sam.pl
A /branches/dev/samtools/misc/maq2sam.c
A /branches/dev/samtools/razf.c
A /branches/dev/samtools/razf.h
A /branches/dev/samtools/razip.c
A /branches/dev/samtools/zutil.h
The initial version of samtools, replicated from my local SVN repository.
The current version is: 0.1.0-42. All future development will happen here.
------------------------------------------------------------------------
r5 | lh3lh3 | 2008-11-25 20:30:49 +0000 (Tue, 25 Nov 2008) | 2 lines
Changed paths:
A /branches/dev/samtools
samtools (C version)
------------------------------------------------------------------------
------------------------------------------------------------------------
r703 | lh3 | 2008-11-25 20:20:02 +0000 (Tue, 25 Nov 2008) | 2 lines
Changed paths:
M /branches/prog/bam/samtools.1
rename bamtk to samtools
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r702 | lh3 | 2008-11-25 20:15:09 +0000 (Tue, 25 Nov 2008) | 2 lines
Changed paths:
D /branches/prog/bam/bamtk.1
A /branches/prog/bam/samtools.1 (from /branches/prog/bam/bamtk.1:679)
rename bamtk.1 to samtools.1
------------------------------------------------------------------------
r701 | lh3 | 2008-11-25 13:29:10 +0000 (Tue, 25 Nov 2008) | 3 lines
Changed paths:
M /branches/prog/bam/Makefile
M /branches/prog/bam/bam.c
M /branches/prog/bam/bam.h
M /branches/prog/bam/bam_import.c
M /branches/prog/bam/bam_index.c
M /branches/prog/bam/bam_pileup.c
M /branches/prog/bam/bamtk.c
M /branches/prog/bam/misc/Makefile
* samtools-0.1.0-41
* small (but a bit dangerous) changes to meet the latest specification
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r700 | lh3 | 2008-11-25 13:15:11 +0000 (Tue, 25 Nov 2008) | 2 lines
Changed paths:
A /branches/prog/bam/misc/all2sam.pl (from /branches/prog/bam/misc/all2tam.pl:649)
D /branches/prog/bam/misc/all2tam.pl
A /branches/prog/bam/misc/maq2sam.c (from /branches/prog/bam/misc/maq2tam.c:699)
D /branches/prog/bam/misc/maq2tam.c
rename tam to sam
------------------------------------------------------------------------
r699 | lh3 | 2008-11-25 13:14:49 +0000 (Tue, 25 Nov 2008) | 2 lines
Changed paths:
M /branches/prog/bam/misc/maq2tam.c
change for the new specification
------------------------------------------------------------------------
r698 | lh3 | 2008-11-24 13:15:20 +0000 (Mon, 24 Nov 2008) | 3 lines
Changed paths:
M /branches/prog/bam/bam.h
M /branches/prog/bam/razf.c
M /branches/prog/bam/razf.h
* add a fake BGZF mode to razf. It is fake in that it loads razf index into
memory but gives BGZF like virtual offset
------------------------------------------------------------------------
r697 | lh3 | 2008-11-24 09:53:44 +0000 (Mon, 24 Nov 2008) | 2 lines
Changed paths:
A /branches/prog/bam/ChangeLog
change log
------------------------------------------------------------------------
r696 | lh3 | 2008-11-24 09:53:23 +0000 (Mon, 24 Nov 2008) | 2 lines
Changed paths:
M /branches/prog/bam/bgzf.c