annotate SNV/SNVMix2_source/SNVMix2-v0.12.1-rc1/samtools-0.1.6/ChangeLog @ 0:74f5ea818cea

Uploaded

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r451 | lh3lh3 | 2009-09-02 10:44:48 +0100 (Wed, 02 Sep 2009) | 4 lines
Changed paths:
   M /trunk/samtools/bam_md.c
   M /trunk/samtools/bam_rmdup.c
   M /trunk/samtools/bam_rmdupse.c
   M /trunk/samtools/bam_sort.c
   M /trunk/samtools/bamtk.c
   M /trunk/samtools/samtools.1

 * samtools-0.1.5-34 (r451)
 * applied the patch by John
 * improved the help message a little bit

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r450 | lh3lh3 | 2009-09-02 09:55:55 +0100 (Wed, 02 Sep 2009) | 3 lines
Changed paths:
   M /trunk/samtools/bam_color.c
   M /trunk/samtools/bamtk.c

 * samtools-0.1.5-33 (r450)
 * fixed a bug in bam_color.c (on behalf of Nils Homer)

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r449 | lh3lh3 | 2009-08-29 20:36:41 +0100 (Sat, 29 Aug 2009) | 4 lines
Changed paths:
   M /trunk/samtools/bam_import.c
   M /trunk/samtools/bam_md.c
   M /trunk/samtools/bamtk.c
   M /trunk/samtools/misc/samtools.pl

 * samtools-0.1.5-32 (r449)
 * fillmd: fixed a bug in modifying MD/NM tags
 * in import, give a warning if the read is aligned but there is no CIGAR.

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r448 | lh3lh3 | 2009-08-19 09:44:28 +0100 (Wed, 19 Aug 2009) | 3 lines
Changed paths:
   M /trunk/samtools/ChangeLog
   M /trunk/samtools/bam_pileup.c
   M /trunk/samtools/bamtk.c
   M /trunk/samtools/misc/wgsim_eval.pl

 * samtools-0.1.5-31 (r448)
 * fixed an issue when the last CIGAR is I or D

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r447 | lh3lh3 | 2009-08-17 09:34:57 +0100 (Mon, 17 Aug 2009) | 3 lines
Changed paths:
   M /trunk/samtools/bam_aux.c
   M /trunk/samtools/bamtk.c

 * samtools-0.1.5-30 (r447)
 * fixed a bug in bam_aux_get(): 'A' is not checked

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r446 | lh3lh3 | 2009-08-17 09:33:17 +0100 (Mon, 17 Aug 2009) | 2 lines
Changed paths:
   M /trunk/samtools/bam_aux.c
   M /trunk/samtools/bamtk.c

 * 

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r444 | lh3lh3 | 2009-08-11 10:02:36 +0100 (Tue, 11 Aug 2009) | 3 lines
Changed paths:
   M /trunk/samtools/bam_sort.c
   M /trunk/samtools/bamtk.c

 * samtools-0.1.5-28 (r444)
 * bug in "merge -n"

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r443 | lh3lh3 | 2009-08-11 09:29:11 +0100 (Tue, 11 Aug 2009) | 4 lines
Changed paths:
   M /trunk/samtools/bam.c
   M /trunk/samtools/bam_import.c
   M /trunk/samtools/bamtk.c

 * samtools-0.1.5-27 (r443)
 * SEQ and QUAL can be "*"
 * parse CIGAR "=" and "X" as "M"

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r442 | lh3lh3 | 2009-08-07 21:56:38 +0100 (Fri, 07 Aug 2009) | 4 lines
Changed paths:
   M /trunk/samtools/bam_pileup.c
   M /trunk/samtools/bamtk.c
   M /trunk/samtools/misc/md5.c
   M /trunk/samtools/misc/md5.h
   M /trunk/samtools/misc/md5fa.c

 * samtools-0.1.5-26 (r442)
 * replace RSA Inc md5.* with ones under permissive lincense
 * fixed a bug in detecting unsorted bam in pileup

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r441 | bhandsaker | 2009-08-05 14:41:28 +0100 (Wed, 05 Aug 2009) | 2 lines
Changed paths:
   M /trunk/samtools/bgzf.c
   M /trunk/samtools/bgzf.h
   M /trunk/samtools/bgzip.c

Change copyright notices now that MIT has approved open source distribution.

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r440 | lh3lh3 | 2009-08-05 10:44:24 +0100 (Wed, 05 Aug 2009) | 3 lines
Changed paths:
   M /trunk/samtools/bam_stat.c
   M /trunk/samtools/bamtk.c

 * samtools-0.1.5-25 (r436)
 * in flagstats, do not report singletons if both ends are unmapped

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r439 | lh3lh3 | 2009-08-04 22:16:51 +0100 (Tue, 04 Aug 2009) | 2 lines
Changed paths:
   M /trunk/samtools/misc/maq2sam.c

fixed a SERIOUS bug in setting 0x20 flag

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r438 | lh3lh3 | 2009-08-04 21:50:43 +0100 (Tue, 04 Aug 2009) | 2 lines
Changed paths:
   M /trunk/samtools/misc/samtools.pl

fixed two minor bugs (suggested by Tim M Storm)

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r437 | lh3lh3 | 2009-08-04 09:13:24 +0100 (Tue, 04 Aug 2009) | 3 lines
Changed paths:
   M /trunk/samtools/bamtk.c
   M /trunk/samtools/misc/samtools.pl
   M /trunk/samtools/sam_view.c

 * samtools-0.1.5-24 (r435)
 * fixed a typo

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r434 | lh3lh3 | 2009-08-03 10:40:42 +0100 (Mon, 03 Aug 2009) | 3 lines
Changed paths:
   M /trunk/samtools/bam_tview.c
   M /trunk/samtools/bamtk.c

 * samtools-0.1.5-23 (r434)
 * in tview, press 'r' to show read names rather than sequences

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r433 | lh3lh3 | 2009-08-02 19:13:35 +0100 (Sun, 02 Aug 2009) | 3 lines
Changed paths:
   M /trunk/samtools/knetfile.c

 * tried to fixed the buggy FTP random access in Windows. FAILED.
 * anyway, MinGW seems to have problem with "%lld".

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r432 | lh3lh3 | 2009-08-02 00:32:07 +0100 (Sun, 02 Aug 2009) | 5 lines
Changed paths:
   M /trunk/samtools/Makefile.mingw
   M /trunk/samtools/bamtk.c
   M /trunk/samtools/faidx.c
   M /trunk/samtools/razf.c
   A /trunk/samtools/win32/libcurses.a
   A /trunk/samtools/win32/xcurses.h

 * samtools-0.1.5-22 (r432)
 * faidx: fixed compitability issue with _WIN32
 * razf: fixed potential compitability issue with _WIN32
 * PDCurses support in Windows

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r431 | lh3lh3 | 2009-08-01 23:34:54 +0100 (Sat, 01 Aug 2009) | 2 lines
Changed paths:
   M /trunk/samtools/win32/libz.a

replace the GnuWin32 version of libz.a with my own build with MinGW.

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r430 | lh3lh3 | 2009-08-01 23:21:07 +0100 (Sat, 01 Aug 2009) | 2 lines
Changed paths:
   M /trunk/samtools/knetfile.c

add comments

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r429 | lh3lh3 | 2009-08-01 22:41:19 +0100 (Sat, 01 Aug 2009) | 3 lines
Changed paths:
   M /trunk/samtools/Makefile.mingw
   M /trunk/samtools/bamtk.c
   M /trunk/samtools/knetfile.c
   M /trunk/samtools/knetfile.h

 * samtools-0.1.5-21 (r428)
 * knetfile.c is now compatible with mingw-winsock

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r428 | lh3lh3 | 2009-08-01 00:39:07 +0100 (Sat, 01 Aug 2009) | 2 lines
Changed paths:
   M /trunk/samtools/Makefile.mingw

simplify MinGW Makefile

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r427 | lh3lh3 | 2009-08-01 00:30:54 +0100 (Sat, 01 Aug 2009) | 5 lines
Changed paths:
   A /trunk/samtools/Makefile.mingw
   M /trunk/samtools/bam_import.c
   M /trunk/samtools/bamtk.c
   A /trunk/samtools/win32
   A /trunk/samtools/win32/libz.a
   A /trunk/samtools/win32/zconf.h
   A /trunk/samtools/win32/zlib.h

 * samtools-0.1.5-20 (r427)
 * MinGW support. At least SAM<->BAM conversion is working. Other
   functionality are not tested at the moment.
 * zlib headers and Windows version of libz.a are included in win32/

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r426 | lh3lh3 | 2009-07-31 23:32:09 +0100 (Fri, 31 Jul 2009) | 3 lines
Changed paths:
   M /trunk/samtools/bamtk.c
   M /trunk/samtools/sam_view.c

 * samtools-0.1.5-19 (r426)
 * fixed a bug caused by recent modifications. Sorry.

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r425 | lh3lh3 | 2009-07-31 23:23:51 +0100 (Fri, 31 Jul 2009) | 2 lines
Changed paths:
   M /trunk/samtools/bgzf.c

compatible with Windows binary files

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r424 | lh3lh3 | 2009-07-31 10:19:59 +0100 (Fri, 31 Jul 2009) | 5 lines
Changed paths:
   M /trunk/samtools/bam_maqcns.c
   M /trunk/samtools/bam_maqcns.h
   M /trunk/samtools/bam_plcmd.c
   M /trunk/samtools/bam_tview.c
   M /trunk/samtools/bamtk.c
   M /trunk/samtools/misc/samtools.pl

 * samtools-0.1.5-18 (r423)
 * output additional information in pileup indel lines, for the purepose
   of debugging at the moment
 * in tview, optionally allow to treat reference skip as deletion

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r423 | lh3lh3 | 2009-07-30 22:00:36 +0100 (Thu, 30 Jul 2009) | 2 lines
Changed paths:
   A /trunk/samtools/misc/psl2sam.pl

convert BLAT psl to SAM.

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r422 | lh3lh3 | 2009-07-30 11:24:39 +0100 (Thu, 30 Jul 2009) | 6 lines
Changed paths:
   M /trunk/samtools/ChangeLog
   M /trunk/samtools/bam.c
   M /trunk/samtools/bamtk.c
   M /trunk/samtools/bgzf.c
   M /trunk/samtools/bgzf.h
   M /trunk/samtools/knetfile.c
   M /trunk/samtools/sam.c
   M /trunk/samtools/sam_view.c

 * samtools-0.1.5-17 (r422)
 * fixed a but in knetfile.c when seek type is not SEEK_SET
 * write an empty BGZF block to every BGZF file
 * check BGZF EOF marker in bam_header_read()
 * update ChangeLog

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r421 | lh3lh3 | 2009-07-30 10:03:39 +0100 (Thu, 30 Jul 2009) | 3 lines
Changed paths:
   M /trunk/samtools/bam_import.c
   M /trunk/samtools/bam_plcmd.c
   M /trunk/samtools/bamtk.c
   M /trunk/samtools/misc/samtools.pl
   M /trunk/samtools/sam.c
   M /trunk/samtools/sam.h
   M /trunk/samtools/sam_view.c

 * samtools-0.1.5-16 (r421)
 * in view and pileup, load header from FASTA index if the input is SAM.

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r420 | lh3lh3 | 2009-07-29 09:18:55 +0100 (Wed, 29 Jul 2009) | 2 lines
Changed paths:
   M /trunk/samtools/misc/maq2sam.c

do not set "read 1" if reads are not mapped in the PE mode of maq

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r419 | lh3lh3 | 2009-07-28 09:52:33 +0100 (Tue, 28 Jul 2009) | 5 lines
Changed paths:
   M /trunk/samtools/bam_import.c
   M /trunk/samtools/bamtk.c
   M /trunk/samtools/misc/samtools.pl
   M /trunk/samtools/misc/wgsim_eval.pl

 * samtools-0.1.5-15 (r419)
 * in sam_open(), return NULL when the file cannot be opened.
 * make wgsim_eval.pl more robust to imperfect SAM
 * add "unique" command to samtools.pl

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r418 | lh3lh3 | 2009-07-24 14:04:19 +0100 (Fri, 24 Jul 2009) | 2 lines
Changed paths:
   M /trunk/samtools/misc/wgsim_eval.pl

skip @header lines in SAM

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r417 | lh3lh3 | 2009-07-24 12:42:38 +0100 (Fri, 24 Jul 2009) | 3 lines
Changed paths:
   M /trunk/samtools/bamtk.c
   M /trunk/samtools/sam_view.c

 * samtools-0.1.5-14 (r417)
 * more help in "samtools view" due to the recent changes.

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r416 | lh3lh3 | 2009-07-24 12:34:30 +0100 (Fri, 24 Jul 2009) | 3 lines
Changed paths:
   M /trunk/samtools/bam.c
   M /trunk/samtools/bam.h
   M /trunk/samtools/bam_import.c
   M /trunk/samtools/bamtk.c
   M /trunk/samtools/sam.c
   M /trunk/samtools/sam.h
   M /trunk/samtools/sam_view.c

 * samtools-0.1.5-17 (r416)
 * support import/export SAM with string tags

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r415 | lh3lh3 | 2009-07-24 11:39:26 +0100 (Fri, 24 Jul 2009) | 3 lines
Changed paths:
   M /trunk/samtools/bam.c
   M /trunk/samtools/bam.h
   M /trunk/samtools/bam_import.c
   M /trunk/samtools/bamtk.c
   M /trunk/samtools/sam.c
   M /trunk/samtools/sam.h
   M /trunk/samtools/sam_view.c

 * samtools-0.1.5-12 (r415)
 * FLAG now can be in HEX

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r414 | lh3lh3 | 2009-07-22 22:03:49 +0100 (Wed, 22 Jul 2009) | 2 lines
Changed paths:
   M /trunk/samtools/kstring.h

fixed a compiling error (thank Ken for fixing it)

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r412 | lh3lh3 | 2009-07-21 22:19:40 +0100 (Tue, 21 Jul 2009) | 2 lines
Changed paths:
   M /trunk/samtools/kstring.c
   M /trunk/samtools/kstring.h

Implemented Boyer-Moore search in the kstring library.

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r409 | lh3lh3 | 2009-07-17 17:10:20 +0100 (Fri, 17 Jul 2009) | 2 lines
Changed paths:
   M /trunk/samtools/bam_index.c

do not include knetfile.h when _USE_KNETFILE is not defined

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r408 | lh3lh3 | 2009-07-17 15:29:21 +0100 (Fri, 17 Jul 2009) | 5 lines
Changed paths:
   M /trunk/samtools/bam_md.c
   M /trunk/samtools/bam_tview.c
   M /trunk/samtools/bamtk.c
   M /trunk/samtools/bgzf.c

 * samtools-0.1.5-11 (r408)
 * force to overwirte existing MD if it is different from the one calculated
   from fillmd.
 * bgzf.c: improved the compatibility with Windows headers

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r407 | lh3lh3 | 2009-07-17 14:46:56 +0100 (Fri, 17 Jul 2009) | 5 lines
Changed paths:
   M /trunk/samtools/bam.h
   M /trunk/samtools/bam_aux.c
   M /trunk/samtools/bam_md.c
   M /trunk/samtools/bamtk.c
   M /trunk/samtools/sam.h

 * samtools-0.1.5-10 (r407)
 * implemented bam_aux_del() to remove a tag
 * fillmd: generate the NM tag
 * fillmd: cmd interface improvement

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r406 | lh3lh3 | 2009-07-16 23:30:40 +0100 (Thu, 16 Jul 2009) | 2 lines
Changed paths:
   M /trunk/samtools/Makefile

Sorry. The old Makefile is for PDCurses...

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r405 | lh3lh3 | 2009-07-16 23:30:11 +0100 (Thu, 16 Jul 2009) | 3 lines
Changed paths:
   M /trunk/samtools/Makefile
   M /trunk/samtools/bam_tview.c
   M /trunk/samtools/bamtk.c

 * samtools-0.1.5-9 (r405)
 * improved the compatibility with PDCurses a little bit

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r404 | lh3lh3 | 2009-07-16 23:23:52 +0100 (Thu, 16 Jul 2009) | 3 lines
Changed paths:
   M /trunk/samtools/Makefile
   M /trunk/samtools/bam_tview.c
   M /trunk/samtools/bamtk.c

 * samtools-0.1.5-8 (r404)
 * compatible with PDCurses

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r403 | lh3lh3 | 2009-07-16 22:39:39 +0100 (Thu, 16 Jul 2009) | 3 lines
Changed paths:
   M /trunk/samtools/bamtk.c
   M /trunk/samtools/kseq.h

 * samtools-0.1.5-7 (r403)
 * fixed a bug in kseq.h for binary files (text files are fine)

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r402 | lh3lh3 | 2009-07-16 11:49:53 +0100 (Thu, 16 Jul 2009) | 4 lines
Changed paths:
   M /trunk/samtools/bam_import.c
   M /trunk/samtools/bam_index.c
   M /trunk/samtools/bamtk.c
   M /trunk/samtools/bgzf.c

 * samtools-0.1.5-6 (r402)
 * fixed compiling error when "-D_USE_NETFILE" is not applied
 * improve portability to MinGW

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r398 | lh3lh3 | 2009-07-13 10:21:36 +0100 (Mon, 13 Jul 2009) | 3 lines
Changed paths:
   A /trunk/bam-lite/bam.h (from /trunk/samtools/bam.h:395)
   A /trunk/bam-lite/bam_lite.c (from /trunk/samtools/bam_lite.c:395)
   D /trunk/samtools/bam_lite.c

 * move bam_lite.c to bam-lite
 * copy bam.h to bam-lite

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r395 | lh3lh3 | 2009-07-13 10:12:57 +0100 (Mon, 13 Jul 2009) | 3 lines
Changed paths:
   M /trunk/samtools/bam.h
   M /trunk/samtools/bam_lite.c
   M /trunk/samtools/bam_lpileup.c
   M /trunk/samtools/bam_pileup.c
   M /trunk/samtools/bamtk.c

 * samtools-0.1.5-5 (r395)
 * added bam_pileup_file() and removed bam_lpileup_file()

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r394 | lh3lh3 | 2009-07-13 00:35:10 +0100 (Mon, 13 Jul 2009) | 3 lines
Changed paths:
   M /trunk/samtools/bamtk.c
   M /trunk/samtools/knetfile.c
   M /trunk/samtools/knetfile.h

 * samtools-0.1.5-4 (r394)
 * http_proxy support in knetfile library (check http_proxy ENV)

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r393 | lh3lh3 | 2009-07-12 23:57:07 +0100 (Sun, 12 Jul 2009) | 5 lines
Changed paths:
   M /trunk/samtools/bam_index.c
   M /trunk/samtools/bam_tview.c
   M /trunk/samtools/bamtk.c
   M /trunk/samtools/knetfile.c
   M /trunk/samtools/knetfile.h

 * samtools-0.1.5-3 (r393)
 * knetfile now supports HTTP (no proxy at the moment)
 * fixed a potential issue in knetfile on opening ordinary file, although I have
   not seen the sideeffect so far.

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r392 | lh3lh3 | 2009-07-12 18:50:55 +0100 (Sun, 12 Jul 2009) | 2 lines
Changed paths:
   M /trunk/samtools/samtools.1

Remove the warning in tview

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r391 | lh3lh3 | 2009-07-12 18:42:43 +0100 (Sun, 12 Jul 2009) | 3 lines
Changed paths:
   M /trunk/samtools/bam_tview.c
   M /trunk/samtools/bamtk.c

 * samtools-0.1.5-2 (r391)
 * do not show a blank screen when no reads mapped

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r390 | lh3lh3 | 2009-07-09 14:01:42 +0100 (Thu, 09 Jul 2009) | 4 lines
Changed paths:
   M /trunk/samtools/bam.h
   A /trunk/samtools/bam_lite.c
   M /trunk/samtools/bamtk.c

 * samtools-0.1.5-1 (r390)
 * removed useless _IOLIB in bam.h. This should cause no change at all.
 * added bam_lite.c for light-weight BAM reading

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r385 | lh3lh3 | 2009-07-07 16:53:29 +0100 (Tue, 07 Jul 2009) | 2 lines
Changed paths:
   M /trunk/samtools/bamtk.c
   M /trunk/samtools/knetfile.c

Release samtools-0.1.5c (fixed a bug in piping)

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r383 | lh3lh3 | 2009-07-07 11:39:55 +0100 (Tue, 07 Jul 2009) | 2 lines
Changed paths:
   M /trunk/samtools/bamtk.c
   M /trunk/samtools/sam.c

Release samtools-0.1.5b (BUG! so embarrassing!)

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r381 | lh3lh3 | 2009-07-07 11:20:06 +0100 (Tue, 07 Jul 2009) | 2 lines
Changed paths:
   M /trunk/samtools/Makefile
   M /trunk/samtools/bam.h
   M /trunk/samtools/bam_aux.c
   M /trunk/samtools/bamtk.c

Release samtools-0.1.5a (for compatibility with Bio::DB::Sam)

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r373 | lh3lh3 | 2009-07-07 10:26:57 +0100 (Tue, 07 Jul 2009) | 2 lines
Changed paths:
   M /trunk/samtools/ChangeLog
   M /trunk/samtools/NEWS
   M /trunk/samtools/bamtk.c
   M /trunk/samtools/samtools.1

Release samtools-0.1.5

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r372 | lh3lh3 | 2009-07-07 09:49:27 +0100 (Tue, 07 Jul 2009) | 3 lines
Changed paths:
   M /trunk/samtools/bamtk.c
   M /trunk/samtools/sam.c

 * samtools-0.1.4-23 (r372)
 * keep header text if "view -t" is used (by Gerton)

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r371 | lh3lh3 | 2009-07-07 01:13:32 +0100 (Tue, 07 Jul 2009) | 2 lines
Changed paths:
   M /trunk/samtools/samtools.1

update documentation

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r370 | bhandsaker | 2009-07-02 22:24:34 +0100 (Thu, 02 Jul 2009) | 2 lines
Changed paths:
   M /trunk/samtools/Makefile

Introduced LIBPATH variable so this could be overridden to allow samtools to build correct at the Broad.

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r369 | lh3lh3 | 2009-07-02 13:36:53 +0100 (Thu, 02 Jul 2009) | 4 lines
Changed paths:
   M /trunk/samtools/ChangeLog
   M /trunk/samtools/bam_aux.c
   M /trunk/samtools/bam_plcmd.c
   M /trunk/samtools/bamtk.c

 * samtools-0.1.4-22 (r369)
 * in pileup, optionally print E2 and U2
 * remove the debugging code in bam_aux_get() (Drat!)

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r368 | lh3lh3 | 2009-07-02 11:32:26 +0100 (Thu, 02 Jul 2009) | 6 lines
Changed paths:
   M /trunk/samtools/bam.c
   M /trunk/samtools/bam.h
   M /trunk/samtools/bam_aux.c
   M /trunk/samtools/bam_index.c
   M /trunk/samtools/bam_lpileup.c
   M /trunk/samtools/bam_md.c
   M /trunk/samtools/bam_pileup.c
   M /trunk/samtools/bam_rmdup.c
   M /trunk/samtools/bam_stat.c
   M /trunk/samtools/bam_tview.c
   M /trunk/samtools/bamtk.c
   M /trunk/samtools/faidx.c
   M /trunk/samtools/faidx.h
   M /trunk/samtools/glf.c

 * samtools-0.1.4-21 (r368)
 * propagate errors rather than exit or complain assertion failure. Assertion
   should be only used for checking internal bugs, but not for external input
   inconsistency. I was just a bit lazy.
 * small memory leak may be present on failure, though

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r367 | lh3lh3 | 2009-06-30 16:18:42 +0100 (Tue, 30 Jun 2009) | 2 lines
Changed paths:
   M /trunk/samtools/knetfile.c

reduce the chance of blocking in FTP connection

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r366 | lh3lh3 | 2009-06-30 15:35:21 +0100 (Tue, 30 Jun 2009) | 2 lines
Changed paths:
   M /trunk/samtools/knetfile.c

minor changes to knetfile: invalid fd equals -1 rather than 0

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r365 | lh3lh3 | 2009-06-30 14:04:30 +0100 (Tue, 30 Jun 2009) | 3 lines
Changed paths:
   M /trunk/samtools/bam_index.c
   M /trunk/samtools/bamtk.c
   M /trunk/samtools/knetfile.c
   M /trunk/samtools/knetfile.h

 * samtools-0.1.4-20 (r365)
 * download the BAM index file if it is not found in the current working directory.

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r364 | lh3lh3 | 2009-06-30 12:39:07 +0100 (Tue, 30 Jun 2009) | 3 lines
Changed paths:
   M /trunk/samtools/bamtk.c
   M /trunk/samtools/knetfile.c

 * samtools-0.1.4-19 (r364)
 * knetfile: report error when the file is not present on FTP

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r363 | lh3lh3 | 2009-06-29 23:23:32 +0100 (Mon, 29 Jun 2009) | 4 lines
Changed paths:
   M /trunk/samtools/bam_tview.c
   M /trunk/samtools/bamtk.c
   M /trunk/samtools/bgzf.c
   M /trunk/samtools/bgzf.h
   M /trunk/samtools/knetfile.c
   M /trunk/samtools/knetfile.h

 * samtools-0.1.4-18 (r363)
 * knetfile: do not trigger network communication in FTP seek (lazy seek)
 * bgzf: cache recent blocks (disabled by default)

------------------------------------------------------------------------
r362 | lh3lh3 | 2009-06-25 21:04:34 +0100 (Thu, 25 Jun 2009) | 2 lines
Changed paths:
   M /trunk/samtools/bgzf.c

write changelog

------------------------------------------------------------------------
r361 | lh3lh3 | 2009-06-25 21:03:10 +0100 (Thu, 25 Jun 2009) | 3 lines
Changed paths:
   M /trunk/samtools/bam_index.c
   M /trunk/samtools/bamtk.c

 * samtools-0.1.4-17 (r361)
 * if a file is given on FTP, search locally for the BAM index

------------------------------------------------------------------------
r360 | lh3lh3 | 2009-06-25 20:44:52 +0100 (Thu, 25 Jun 2009) | 5 lines
Changed paths:
   M /trunk/samtools/Makefile
   M /trunk/samtools/bam_import.c
   M /trunk/samtools/bam_index.c
   M /trunk/samtools/bamtk.c
   M /trunk/samtools/bgzf.c
   M /trunk/samtools/bgzf.h
   M /trunk/samtools/knetfile.c
   M /trunk/samtools/knetfile.h

 * samtools-0.1.4-16 (r360)
 * report more information in index when the input is not sorted
 * change the behaviour of knet_seek() such that it returns 0 on success
 * support knetfile library in BGZF

------------------------------------------------------------------------
r359 | lh3lh3 | 2009-06-25 17:10:55 +0100 (Thu, 25 Jun 2009) | 2 lines
Changed paths:
   M /trunk/samtools/knetfile.c
   M /trunk/samtools/knetfile.h

fixed bugs in knetfile.*

------------------------------------------------------------------------
r358 | lh3lh3 | 2009-06-25 13:53:19 +0100 (Thu, 25 Jun 2009) | 2 lines
Changed paths:
   A /trunk/samtools/knetfile.h

this is the header file

------------------------------------------------------------------------
r357 | lh3lh3 | 2009-06-25 13:52:03 +0100 (Thu, 25 Jun 2009) | 3 lines
Changed paths:
   A /trunk/samtools/knetfile.c

 * open a file at FTP
 * preliminary version

------------------------------------------------------------------------
r354 | lh3lh3 | 2009-06-24 14:02:25 +0100 (Wed, 24 Jun 2009) | 3 lines
Changed paths:
   M /trunk/samtools/bam.c
   M /trunk/samtools/bamtk.c

 * samtools-0.1.4-15 (r354)
 * fixed a memory leak in bam_view1(), although samtools is not using this routine.

------------------------------------------------------------------------
r351 | lh3lh3 | 2009-06-18 00:16:26 +0100 (Thu, 18 Jun 2009) | 4 lines
Changed paths:
   M /trunk/samtools/bamtk.c
   M /trunk/samtools/faidx.c

 * samtools-0.1.4-13 (r351)
 * make faidx more tolerant to empty lines right before or after > lines
 * hope this does not introduce new bugs...

------------------------------------------------------------------------
r350 | lh3lh3 | 2009-06-16 14:37:01 +0100 (Tue, 16 Jun 2009) | 3 lines
Changed paths:
   M /trunk/samtools/bam_plcmd.c
   M /trunk/samtools/bamtk.c

 * samtools-0.1.4-13 (r350)
 * fixed a small memory leak in pileup, caused by recent modifications

------------------------------------------------------------------------
r347 | lh3lh3 | 2009-06-13 21:20:49 +0100 (Sat, 13 Jun 2009) | 3 lines
Changed paths:
   M /trunk/samtools/bam_plcmd.c
   M /trunk/samtools/bamtk.c
   M /trunk/samtools/sam_view.c

 * samtools-0.1.4-12 (r347)
 * added `-S' to pileup, similar to `view -S' 

------------------------------------------------------------------------
r346 | lh3lh3 | 2009-06-13 17:52:31 +0100 (Sat, 13 Jun 2009) | 3 lines
Changed paths:
   M /trunk/samtools/Makefile
   M /trunk/samtools/bamtk.c
   M /trunk/samtools/sam_view.c
   M /trunk/samtools/samtools.1

 * samtools-0.1.4-11 (r346)
 * allow to select a read group at view command-line

------------------------------------------------------------------------
r344 | lh3lh3 | 2009-06-13 14:06:24 +0100 (Sat, 13 Jun 2009) | 2 lines
Changed paths:
   M /trunk/samtools/examples/calDepth.c

added more comments

------------------------------------------------------------------------
r343 | lh3lh3 | 2009-06-13 14:01:22 +0100 (Sat, 13 Jun 2009) | 2 lines
Changed paths:
   M /trunk/samtools/examples/calDepth.c

nothing really

------------------------------------------------------------------------
r342 | lh3lh3 | 2009-06-13 13:58:48 +0100 (Sat, 13 Jun 2009) | 2 lines
Changed paths:
   M /trunk/samtools/examples/Makefile
   A /trunk/samtools/examples/calDepth.c

added an example of calculating read depth

------------------------------------------------------------------------
r341 | lh3lh3 | 2009-06-13 13:00:08 +0100 (Sat, 13 Jun 2009) | 6 lines
Changed paths:
   M /trunk/samtools/Makefile
   M /trunk/samtools/bam.h
   M /trunk/samtools/bam_aux.c
   A /trunk/samtools/bam_color.c
   M /trunk/samtools/bam_plcmd.c
   M /trunk/samtools/bam_sort.c
   M /trunk/samtools/bam_tview.c
   M /trunk/samtools/bamtk.c
   M /trunk/samtools/sam.c
   M /trunk/samtools/sam.h

 * samtools-0.1.4-10 (r341)
 * only include key APIs in libbam.a
 * move color-specific routines to bam_color.c
 * update documentations
 * remove the support of -q in pileup

------------------------------------------------------------------------
r340 | lh3lh3 | 2009-06-13 11:17:14 +0100 (Sat, 13 Jun 2009) | 6 lines
Changed paths:
   M /trunk/samtools/INSTALL
   M /trunk/samtools/Makefile
   M /trunk/samtools/bam_aux.c
   M /trunk/samtools/bam_import.c
   M /trunk/samtools/bam_tview.c
   M /trunk/samtools/bamtk.c
   M /trunk/samtools/razf.c
   M /trunk/samtools/sam_view.c

 * samtools-0.1.4-9 (r340)
 * added a warning to razf.c if zlib<1.2.2.1
 * fixed a compilation warning
 * fixed a segfault caused by @RG parsing
 * detect NCURSES in bam_tview.c

------------------------------------------------------------------------
r339 | lh3lh3 | 2009-06-13 10:35:19 +0100 (Sat, 13 Jun 2009) | 2 lines
Changed paths:
   M /trunk/samtools/INSTALL

update INSTALL

------------------------------------------------------------------------
r338 | lh3lh3 | 2009-06-13 00:15:24 +0100 (Sat, 13 Jun 2009) | 4 lines
Changed paths:
   M /trunk/samtools/bam.c
   M /trunk/samtools/bam.h
   M /trunk/samtools/bam_aux.c
   M /trunk/samtools/bam_import.c
   M /trunk/samtools/bamtk.c
   M /trunk/samtools/kstring.h
   M /trunk/samtools/sam.c
   M /trunk/samtools/sam_view.c

 * samtools-0.1.4-8 (r338)
 * parse the @RG header lines and allow to choose library at the "samtools view"
   command line

------------------------------------------------------------------------
r337 | lh3lh3 | 2009-06-12 21:25:50 +0100 (Fri, 12 Jun 2009) | 4 lines
Changed paths:
   M /trunk/samtools/bamtk.c
   M /trunk/samtools/bgzf.c
   M /trunk/samtools/bgzf.h
   M /trunk/samtools/sam.c
   M /trunk/samtools/sam_view.c

 * samtools-0.1.4-7 (r337)
 * bgzf.c: support mode string "wu": uncompressed output
 * "samtools view" support "-u" command-line option

------------------------------------------------------------------------
r336 | lh3lh3 | 2009-06-12 17:20:12 +0100 (Fri, 12 Jun 2009) | 5 lines
Changed paths:
   M /trunk/samtools/Makefile
   M /trunk/samtools/misc/Makefile
   M /trunk/samtools/razf.c
   M /trunk/samtools/razf.h
   M /trunk/samtools/razip.c

 * no changes to samtools itself
 * remove zlib source codes
 * make RAZF reading compatible with old version of zlib
 * on old version of zlib, writing is not available

------------------------------------------------------------------------
r335 | lh3lh3 | 2009-06-12 16:47:33 +0100 (Fri, 12 Jun 2009) | 2 lines
Changed paths:
   D /trunk/samtools/zlib

remove zlib for simplification...

------------------------------------------------------------------------
r334 | lh3lh3 | 2009-06-12 15:43:36 +0100 (Fri, 12 Jun 2009) | 5 lines
Changed paths:
   M /trunk/samtools/bam.h
   M /trunk/samtools/bam_aux.c
   M /trunk/samtools/bamtk.c

 * samtools-0.1.4-6 (r334)
 * do not export bam_aux_get_core() for Bio::DB::Sam because it has already
   been implemented in that.
 * this version works with the latest Bio::DB::Sam (20090612)

------------------------------------------------------------------------
r333 | lh3lh3 | 2009-06-12 15:33:42 +0100 (Fri, 12 Jun 2009) | 2 lines
Changed paths:
   M /trunk/samtools/ChangeLog

update ChangeLog

------------------------------------------------------------------------
r332 | lh3lh3 | 2009-06-12 15:21:21 +0100 (Fri, 12 Jun 2009) | 2 lines
Changed paths:
   M /trunk/samtools/AUTHORS
   M /trunk/samtools/Makefile
   M /trunk/samtools/misc/Makefile

fixed minor things in Makefile

------------------------------------------------------------------------
r331 | lh3lh3 | 2009-06-12 15:07:05 +0100 (Fri, 12 Jun 2009) | 4 lines
Changed paths:
   M /trunk/samtools/bamtk.c

 * samtools-0.1.4-5 (r3310
 * no change to samtools itself. Version number is increased to reflect the
   changes in the Makefile building system.

------------------------------------------------------------------------
r330 | lh3lh3 | 2009-06-12 15:03:38 +0100 (Fri, 12 Jun 2009) | 2 lines
Changed paths:
   M /trunk/samtools/AUTHORS
   D /trunk/samtools/README

update information...

------------------------------------------------------------------------
r329 | lh3lh3 | 2009-06-12 14:52:21 +0100 (Fri, 12 Jun 2009) | 3 lines
Changed paths:
   M /trunk/samtools/misc/novo2sam.pl

 * updated novoalign converter by Colin Hercus et al.
 * this version works with indels

------------------------------------------------------------------------
r328 | lh3lh3 | 2009-06-12 14:50:53 +0100 (Fri, 12 Jun 2009) | 3 lines
Changed paths:
   M /trunk/samtools/INSTALL
   M /trunk/samtools/Makefile
   M /trunk/samtools/misc/Makefile
   M /trunk/samtools/zlib/Makefile

 * update Makefile
 * update INSTALL instruction

------------------------------------------------------------------------
r327 | lh3lh3 | 2009-06-12 14:18:29 +0100 (Fri, 12 Jun 2009) | 4 lines
Changed paths:
   A /trunk/samtools/Makefile (from /trunk/samtools/Makefile.generic:325)
   D /trunk/samtools/Makefile.am
   D /trunk/samtools/Makefile.generic
   D /trunk/samtools/Makefile.lite
   D /trunk/samtools/autogen.sh
   D /trunk/samtools/cleanup.sh
   D /trunk/samtools/configure.ac
   A /trunk/samtools/misc/Makefile (from /trunk/samtools/misc/Makefile.generic:305)
   D /trunk/samtools/misc/Makefile.am
   D /trunk/samtools/misc/Makefile.generic
   M /trunk/samtools/razf.c
   A /trunk/samtools/zlib
   A /trunk/samtools/zlib/Makefile
   A /trunk/samtools/zlib/adler32.c
   A /trunk/samtools/zlib/compress.c
   A /trunk/samtools/zlib/crc32.c
   A /trunk/samtools/zlib/crc32.h
   A /trunk/samtools/zlib/deflate.c
   A /trunk/samtools/zlib/deflate.h
   A /trunk/samtools/zlib/gzio.c
   A /trunk/samtools/zlib/infback.c
   A /trunk/samtools/zlib/inffast.c
   A /trunk/samtools/zlib/inffast.h
   A /trunk/samtools/zlib/inffixed.h
   A /trunk/samtools/zlib/inflate.c
   A /trunk/samtools/zlib/inflate.h
   A /trunk/samtools/zlib/inftrees.c
   A /trunk/samtools/zlib/inftrees.h
   A /trunk/samtools/zlib/trees.c
   A /trunk/samtools/zlib/trees.h
   A /trunk/samtools/zlib/uncompr.c
   A /trunk/samtools/zlib/zconf.h
   A /trunk/samtools/zlib/zlib.h
   A /trunk/samtools/zlib/zutil.c
   A /trunk/samtools/zlib/zutil.h
   D /trunk/samtools/zutil.h

 * added zlib-1.2.3 as razip requires that
 * prepare to changed back to the Makefile building system
 * unfinished! (will be soon)

------------------------------------------------------------------------
r326 | lh3lh3 | 2009-06-12 14:12:03 +0100 (Fri, 12 Jun 2009) | 2 lines
Changed paths:
   M /trunk/samtools/misc/samtools.pl

Unfinished

------------------------------------------------------------------------
r325 | lh3lh3 | 2009-06-10 16:27:59 +0100 (Wed, 10 Jun 2009) | 3 lines
Changed paths:
   M /trunk/samtools/bam_maqcns.c
   M /trunk/samtools/bamtk.c

 * samtools-0.1.4-4 (r325)
 * further avoid wrong consensus calls in repetitive regions.

------------------------------------------------------------------------
r324 | lh3lh3 | 2009-06-10 15:56:17 +0100 (Wed, 10 Jun 2009) | 4 lines
Changed paths:
   M /trunk/samtools/bam_maqcns.c
   M /trunk/samtools/bam_plcmd.c
   M /trunk/samtools/bamtk.c
   M /trunk/samtools/sam.c
   M /trunk/samtools/sam.h

 * samtools-0.1.4-3 (r324)
 * make maqcns generate the correct call in repetitive regions.
 * allow filtering on mapQ at the pileup command line

------------------------------------------------------------------------
r323 | lh3lh3 | 2009-06-10 10:04:21 +0100 (Wed, 10 Jun 2009) | 3 lines
Changed paths:
   M /trunk/samtools/misc/samtools.pl

 * samtools.pl-0.3.2 (r322)
 * indels and SNPs use different mapping quality threshold

------------------------------------------------------------------------
r322 | lh3lh3 | 2009-06-10 10:03:22 +0100 (Wed, 10 Jun 2009) | 2 lines
Changed paths:
   M /trunk/samtools/misc/export2sam.pl

fixed a typo

------------------------------------------------------------------------
r321 | lh3lh3 | 2009-06-09 09:21:48 +0100 (Tue, 09 Jun 2009) | 2 lines
Changed paths:
   M /trunk/samtools/misc/samtools.pl

just typo. no real change

------------------------------------------------------------------------
r320 | lh3lh3 | 2009-06-08 14:32:51 +0100 (Mon, 08 Jun 2009) | 2 lines
Changed paths:
   M /trunk/samtools/misc/samtools.pl

a little bit code cleanup

------------------------------------------------------------------------
r319 | lh3lh3 | 2009-06-08 14:22:33 +0100 (Mon, 08 Jun 2009) | 4 lines
Changed paths:
   M /trunk/samtools/misc/samtools.pl

 * samtools.pl-0.3.1
 * change default parameters
 * optionally print filtered variants

------------------------------------------------------------------------
r318 | lh3lh3 | 2009-06-08 14:14:26 +0100 (Mon, 08 Jun 2009) | 3 lines
Changed paths:
   M /trunk/samtools/misc/samtools.pl

 * samtools.pl-0.3.0
 * combine snpFilter and indelFilter

------------------------------------------------------------------------
r317 | lh3lh3 | 2009-06-08 11:31:42 +0100 (Mon, 08 Jun 2009) | 3 lines
Changed paths:
   M /trunk/samtools/misc/samtools.pl

 * samtools.pl-0.2.3
 * change a default parameter

------------------------------------------------------------------------
r316 | lh3lh3 | 2009-06-08 11:11:06 +0100 (Mon, 08 Jun 2009) | 5 lines
Changed paths:
   M /trunk/samtools/bam_maqcns.c
   M /trunk/samtools/bam_maqcns.h
   M /trunk/samtools/bam_plcmd.c
   M /trunk/samtools/bamtk.c
   M /trunk/samtools/sam.c

 * samtools-0.1.4-2 (r316)
 * pileup: cap mapping quality at 60 (by default)
 * pileup: always calculate RMS mapq
 * pileup: allow to output variant sites only

------------------------------------------------------------------------
r312 | lh3lh3 | 2009-06-04 13:01:10 +0100 (Thu, 04 Jun 2009) | 3 lines
Changed paths:
   M /trunk/samtools/misc/samtools.pl

 * samtools.pl-0.2.2
 * added pileup2fq

------------------------------------------------------------------------
r311 | lh3lh3 | 2009-06-03 09:40:40 +0100 (Wed, 03 Jun 2009) | 2 lines
Changed paths:
   M /trunk/samtools/misc/samtools.pl

 * in snpFilter, suppress non-SNP sites

------------------------------------------------------------------------
r310 | lh3lh3 | 2009-06-01 14:35:13 +0100 (Mon, 01 Jun 2009) | 3 lines
Changed paths:
   M /trunk/samtools/misc/samtools.pl

 * samtools.pl-0.2.1
 * fixed a typo

------------------------------------------------------------------------
r309 | lh3lh3 | 2009-06-01 14:04:39 +0100 (Mon, 01 Jun 2009) | 3 lines
Changed paths:
   M /trunk/samtools/misc/samtools.pl

 * samtools.pl-0.2.0
 * snpFilter

------------------------------------------------------------------------
r306 | lh3lh3 | 2009-05-28 11:49:35 +0100 (Thu, 28 May 2009) | 3 lines
Changed paths:
   M /trunk/samtools/bgzf.c

 * minor changes to bgzf: return NULL if fd == -1
 * suggested by {kdj,jm18}@sanger.ac.uk

------------------------------------------------------------------------
r305 | lh3lh3 | 2009-05-28 11:16:08 +0100 (Thu, 28 May 2009) | 2 lines
Changed paths:
   A /trunk/samtools/misc/interpolate_sam.pl

Script for paired-end pileup, contributed by Stephen Montgomery.

------------------------------------------------------------------------
r304 | lh3lh3 | 2009-05-28 11:08:49 +0100 (Thu, 28 May 2009) | 3 lines
Changed paths:
   M /trunk/samtools/bamtk.c
   M /trunk/samtools/sam.c

 * samtools-0.1.4-1 (r304)
 * fixed a minor bug in printing headers

------------------------------------------------------------------------
r297 | lh3lh3 | 2009-05-21 16:06:16 +0100 (Thu, 21 May 2009) | 2 lines
Changed paths:
   M /trunk/samtools/ChangeLog
   M /trunk/samtools/NEWS
   M /trunk/samtools/bam_plcmd.c
   M /trunk/samtools/bamtk.c
   M /trunk/samtools/misc/maq2sam.c
   M /trunk/samtools/samtools.1

Release samtools-0.1.4

------------------------------------------------------------------------
r296 | lh3lh3 | 2009-05-21 12:53:14 +0100 (Thu, 21 May 2009) | 3 lines
Changed paths:
   M /trunk/samtools/bam_maqcns.c
   M /trunk/samtools/bamtk.c

 * samtools-0.1.3-24 (r296)
 * another similar bug in the indel caller

------------------------------------------------------------------------
r295 | lh3lh3 | 2009-05-21 12:50:28 +0100 (Thu, 21 May 2009) | 3 lines
Changed paths:
   M /trunk/samtools/bam_maqcns.c
   M /trunk/samtools/bamtk.c

 * samtools-0.1.3-23 (r295)
 * fixed a critical bug in the indel caller

------------------------------------------------------------------------
r294 | lh3lh3 | 2009-05-20 13:00:20 +0100 (Wed, 20 May 2009) | 2 lines
Changed paths:
   M /trunk/samtools/bam_stat.c

added a missing header file

------------------------------------------------------------------------
r293 | lh3lh3 | 2009-05-19 23:44:25 +0100 (Tue, 19 May 2009) | 3 lines
Changed paths:
   M /trunk/samtools/bam_tview.c
   M /trunk/samtools/bamtk.c

 * samtools-0.1.3-22 (r293)
 * open tview in the dot-view mode by default

------------------------------------------------------------------------
r292 | lh3lh3 | 2009-05-18 21:01:23 +0100 (Mon, 18 May 2009) | 6 lines
Changed paths:
   M /trunk/samtools/samtools.1

Added a note to the manual. Currently SAMtools used unaligned words in
several places. Although this does not cause bus errors to me, it may
affect portability. Please see the "Bus error" wiki page for more
information. Also thank James Bonfields for pointing this out.


------------------------------------------------------------------------
r286 | lh3lh3 | 2009-05-14 15:23:13 +0100 (Thu, 14 May 2009) | 3 lines
Changed paths:
   M /trunk/samtools/bam.h
   M /trunk/samtools/bam_aux.c
   M /trunk/samtools/bamtk.c

 * samtools-0.1.3-21 (286)
 * declare bam_aux_get_core() in bam.h

------------------------------------------------------------------------
r276 | lh3lh3 | 2009-05-13 10:07:55 +0100 (Wed, 13 May 2009) | 5 lines
Changed paths:
   M /trunk/samtools/bam.h
   M /trunk/samtools/bam_index.c
   M /trunk/samtools/bamtk.c

 * samtools-0.1.3-20 (r276)
 * remove bam1_t::hash again. We need to modify the Perl API anyway to
   make it work with the latest SVN.
 * As is suggested by Tim, scan "{base}.bai" and "{base}.bam.bai" for index

------------------------------------------------------------------------
r275 | lh3lh3 | 2009-05-12 21:14:10 +0100 (Tue, 12 May 2009) | 4 lines
Changed paths:
   M /trunk/samtools/ChangeLog
   M /trunk/samtools/bam.h
   M /trunk/samtools/bamtk.c

 * samtools-0.1.3-19 (r275)
 * a minor change to the bam1_t struct: added back "void *hash" for the
   backward compatibility with Bio::DB::Sam

------------------------------------------------------------------------
r273 | lh3lh3 | 2009-05-12 14:28:39 +0100 (Tue, 12 May 2009) | 3 lines
Changed paths:
   M /trunk/samtools/bam_rmdupse.c
   M /trunk/samtools/bamtk.c

 * samtools-0.1.3-18 (r273)
 * rmdupse: do not remove unmapped reads

------------------------------------------------------------------------
r272 | lh3lh3 | 2009-05-12 14:20:00 +0100 (Tue, 12 May 2009) | 2 lines
Changed paths:
   M /trunk/samtools/bam_rmdupse.c

change a parameter. It does nothing

------------------------------------------------------------------------
r271 | lh3lh3 | 2009-05-12 14:17:58 +0100 (Tue, 12 May 2009) | 3 lines
Changed paths:
   M /trunk/samtools/Makefile.am
   M /trunk/samtools/Makefile.generic
   M /trunk/samtools/Makefile.lite
   A /trunk/samtools/bam_rmdupse.c
   M /trunk/samtools/bamtk.c
   M /trunk/samtools/configure.ac

 * samtools-0.1.3-17 (r271)
 * added 'rmdupse' command

------------------------------------------------------------------------
r267 | lh3lh3 | 2009-05-05 22:31:41 +0100 (Tue, 05 May 2009) | 3 lines
Changed paths:
   M /trunk/samtools/bamtk.c
   M /trunk/samtools/sam_view.c

 * samtools-0.1.3-16 (r267)
 * in sam_view.c, changed g_flag_on based on the suggestion by Angie Hinrichs

------------------------------------------------------------------------
r266 | lh3lh3 | 2009-05-05 22:23:27 +0100 (Tue, 05 May 2009) | 3 lines
Changed paths:
   M /trunk/samtools/bam_import.c
   M /trunk/samtools/bamtk.c

 * samtools-0.1.3-15 (r266)
 * report an error if a non-* reference is present while @SQ is absent

------------------------------------------------------------------------
r265 | lh3lh3 | 2009-05-05 22:09:00 +0100 (Tue, 05 May 2009) | 3 lines
Changed paths:
   M /trunk/samtools/bam.h
   M /trunk/samtools/bam_import.c
   M /trunk/samtools/bamtk.c
   M /trunk/samtools/sam.c
   M /trunk/samtools/sam_view.c

 * samtools-0.1.3-14 (r262)
 * make samopen() recognize @SQ header lines

------------------------------------------------------------------------
r261 | lh3lh3 | 2009-05-05 15:10:30 +0100 (Tue, 05 May 2009) | 3 lines
Changed paths:
   M /trunk/samtools/bam_plcmd.c
   M /trunk/samtools/bamtk.c
   M /trunk/samtools/bgzf.c
   M /trunk/samtools/sam.c
   M /trunk/samtools/sam_view.c

 * samtools-0.1.3-13 (r260)
 * report error for file I/O error

------------------------------------------------------------------------
r260 | lh3lh3 | 2009-05-05 15:01:16 +0100 (Tue, 05 May 2009) | 2 lines
Changed paths:
   M /trunk/samtools/Makefile.am

update Makefile.am

------------------------------------------------------------------------
r259 | lh3lh3 | 2009-05-05 14:52:25 +0100 (Tue, 05 May 2009) | 3 lines
Changed paths:
   M /trunk/samtools/bam.h
   M /trunk/samtools/bam_pileup.c
   M /trunk/samtools/bam_plcmd.c
   M /trunk/samtools/bamtk.c
   M /trunk/samtools/sam.c
   M /trunk/samtools/sam.h

 * samtools-0.1.3-12 (r259)
 * use the new I/O interface in pileup

------------------------------------------------------------------------
r258 | lh3lh3 | 2009-05-05 14:33:22 +0100 (Tue, 05 May 2009) | 3 lines
Changed paths:
   M /trunk/samtools/Makefile.generic
   M /trunk/samtools/Makefile.lite
   M /trunk/samtools/bam.c
   M /trunk/samtools/bam.h
   M /trunk/samtools/bam_import.c
   M /trunk/samtools/bamtk.c
   A /trunk/samtools/sam.c
   A /trunk/samtools/sam.h
   A /trunk/samtools/sam_view.c

 * samtools-0.1.3-11 (r258)
 * unify the interface to BAM and SAM I/O

------------------------------------------------------------------------
r257 | lh3lh3 | 2009-05-05 09:53:35 +0100 (Tue, 05 May 2009) | 3 lines
Changed paths:
   M /trunk/samtools/Makefile.lite
   M /trunk/samtools/bam_plcmd.c
   M /trunk/samtools/bamtk.c

 * samtools-0.1.3-10 (r257)
 * allow hex with "pileup -m"

------------------------------------------------------------------------
r256 | lh3lh3 | 2009-05-04 19:16:50 +0100 (Mon, 04 May 2009) | 4 lines
Changed paths:
   M /trunk/samtools/bam_lpileup.c
   M /trunk/samtools/bamtk.c

 * samtools-0.1.3-9 (r256)
 * fixed a bug in bam_lpileup.c
 * I do not know if this also fixes the bug causing assertion failure in the tview

------------------------------------------------------------------------
r251 | lh3lh3 | 2009-04-28 13:53:23 +0100 (Tue, 28 Apr 2009) | 3 lines
Changed paths:
   M /trunk/samtools/bam_pileup.c
   M /trunk/samtools/bamtk.c

 * samtools-0.1.3-8 (r251)
 * fixed a bug when there are reads without coordinates

------------------------------------------------------------------------
r250 | lh3lh3 | 2009-04-28 13:43:33 +0100 (Tue, 28 Apr 2009) | 2 lines
Changed paths:
   A /trunk/samtools/AUTHORS
   A /trunk/samtools/README
   M /trunk/samtools/cleanup.sh

added missing files

------------------------------------------------------------------------
r249 | lh3lh3 | 2009-04-28 13:37:16 +0100 (Tue, 28 Apr 2009) | 2 lines
Changed paths:
   M /trunk/samtools/Makefile.generic
   M /trunk/samtools/Makefile.lite
   M /trunk/samtools/configure.ac
   M /trunk/samtools/misc/Makefile.generic

improve large file support in compilation

------------------------------------------------------------------------
r248 | lh3lh3 | 2009-04-28 13:33:24 +0100 (Tue, 28 Apr 2009) | 2 lines
Changed paths:
   M /trunk/samtools/INSTALL

update INSTALL

------------------------------------------------------------------------
r247 | lh3lh3 | 2009-04-28 13:28:50 +0100 (Tue, 28 Apr 2009) | 2 lines
Changed paths:
   M /trunk/samtools/Makefile.am
   M /trunk/samtools/autogen.sh
   M /trunk/samtools/cleanup.sh
   M /trunk/samtools/configure.ac
   A /trunk/samtools/misc/Makefile.am

fixed various issues about the GNU building scripts

------------------------------------------------------------------------
r246 | lh3lh3 | 2009-04-28 13:10:23 +0100 (Tue, 28 Apr 2009) | 4 lines
Changed paths:
   M /trunk/samtools/ChangeLog
   D /trunk/samtools/Makefile
   A /trunk/samtools/Makefile.am
   A /trunk/samtools/Makefile.generic
   A /trunk/samtools/autogen.sh
   M /trunk/samtools/bam.h
   M /trunk/samtools/bam_aux.c
   M /trunk/samtools/bam_tview.c
   M /trunk/samtools/bamtk.c
   A /trunk/samtools/cleanup.sh
   A /trunk/samtools/configure.ac
   D /trunk/samtools/misc/Makefile
   A /trunk/samtools/misc/Makefile.generic (from /trunk/samtools/misc/Makefile:245)

 * samtools-0.1.3-7 (r246)
 * incorporated revisions from Nils Homer
 * enhanced support of displaying color-space reads

------------------------------------------------------------------------
r244 | lh3lh3 | 2009-04-25 11:49:40 +0100 (Sat, 25 Apr 2009) | 3 lines
Changed paths:
   M /trunk/samtools/bam_md.c
   M /trunk/samtools/bamtk.c

 * samtools-0.1.3-6 (r244)
 * fixed segfault for unmapped reads

------------------------------------------------------------------------
r243 | lh3lh3 | 2009-04-24 21:27:26 +0100 (Fri, 24 Apr 2009) | 5 lines
Changed paths:
   M /trunk/samtools/bam.h
   M /trunk/samtools/bam_maqcns.c
   M /trunk/samtools/bam_md.c
   M /trunk/samtools/bamtk.c

 * samtools-0.1.3-5 (r243)
 * fixed a long existing bug which may cause memory leak
 * check MD
 * consensus calling now works with "=", but indel calling not

------------------------------------------------------------------------
r242 | lh3lh3 | 2009-04-24 20:44:46 +0100 (Fri, 24 Apr 2009) | 3 lines
Changed paths:
   M /trunk/samtools/bam_md.c
   M /trunk/samtools/bamtk.c

 * samtools-0.1.3-4 (r242)
 * fixed a memory leak

------------------------------------------------------------------------
r240 | lh3lh3 | 2009-04-24 16:40:18 +0100 (Fri, 24 Apr 2009) | 5 lines
Changed paths:
   M /trunk/samtools/Makefile
   M /trunk/samtools/Makefile.lite
   M /trunk/samtools/bam.h
   M /trunk/samtools/bam_aux.c
   A /trunk/samtools/bam_md.c
   M /trunk/samtools/bam_plcmd.c
   M /trunk/samtools/bamtk.c

 * samtools-0.1.3-3 (r240)
 * generate MD tag
 * generate "=" bases
 * the plain pileup now support "=" bases, but consensus calling and glfgen may fail

------------------------------------------------------------------------
r239 | lh3lh3 | 2009-04-24 12:08:20 +0100 (Fri, 24 Apr 2009) | 5 lines
Changed paths:
   M /trunk/samtools/bam.h
   M /trunk/samtools/bam_aux.c
   M /trunk/samtools/bamtk.c

 * samtools-0.1.3-2 (r239)
 * fixed bugs in bam_aux.c (these functions nevered used by samtools)
 * removed bam_aux_init()/bam_aux_destroy()
 * added tagview for testing bam_aux

------------------------------------------------------------------------
r235 | lh3lh3 | 2009-04-21 23:17:39 +0100 (Tue, 21 Apr 2009) | 3 lines
Changed paths:
   M /trunk/samtools/bam_pileup.c
   M /trunk/samtools/bamtk.c

 * samtools-0.1.3-1
 * fixed a bug in pileup: the first read in a chromosome may not be printed

------------------------------------------------------------------------
r232 | lh3lh3 | 2009-04-16 15:25:43 +0100 (Thu, 16 Apr 2009) | 2 lines
Changed paths:
   M /trunk/samtools/Makefile.lite

a missing file in Makefile.lite

------------------------------------------------------------------------
r227 | lh3lh3 | 2009-04-15 22:02:53 +0100 (Wed, 15 Apr 2009) | 2 lines
Changed paths:
   M /trunk/samtools/NEWS
   M /trunk/samtools/bamtk.c

Release samtools-0.1.3

------------------------------------------------------------------------
r223 | lh3lh3 | 2009-04-15 14:31:32 +0100 (Wed, 15 Apr 2009) | 3 lines
Changed paths:
   M /trunk/samtools/bam_plcmd.c
   M /trunk/samtools/bamtk.c

 * samtools-0.1.2-28
 * make samtools more robust to weird input such as empty file

------------------------------------------------------------------------
r222 | lh3lh3 | 2009-04-15 14:05:33 +0100 (Wed, 15 Apr 2009) | 2 lines
Changed paths:
   M /trunk/samtools/ChangeLog
   M /trunk/samtools/NEWS
   M /trunk/samtools/samtools.1

prepare for release 0.1.3

------------------------------------------------------------------------
r221 | lh3lh3 | 2009-04-15 13:32:14 +0100 (Wed, 15 Apr 2009) | 2 lines
Changed paths:
   A /trunk/samtools/misc/blast2sam.pl

convert NCBI-BLASTN to SAM

------------------------------------------------------------------------
r220 | lh3lh3 | 2009-04-15 13:18:19 +0100 (Wed, 15 Apr 2009) | 3 lines
Changed paths:
   M /trunk/samtools/bam_lpileup.c
   M /trunk/samtools/bamtk.c

 * samtools-0.1.2-27
 * fixed a small memory leak in tview

------------------------------------------------------------------------
r219 | lh3lh3 | 2009-04-15 13:00:08 +0100 (Wed, 15 Apr 2009) | 3 lines
Changed paths:
   M /trunk/samtools/bam_rmdup.c
   M /trunk/samtools/bamtk.c

 * samtools-0.1.2-26
 * fixed a bug in rmdup when there are unmapped reads

------------------------------------------------------------------------
r218 | lh3lh3 | 2009-04-14 22:28:58 +0100 (Tue, 14 Apr 2009) | 2 lines
Changed paths:
   M /trunk/samtools/ChangeLog
   M /trunk/samtools/NEWS

proposed NEWS for the new release (have not yet)

------------------------------------------------------------------------
r216 | lh3lh3 | 2009-04-14 22:10:46 +0100 (Tue, 14 Apr 2009) | 4 lines
Changed paths:
   M /trunk/samtools/misc/samtools.pl

 * samtools.pl-0.1.1
 * improve indelFilter to avoid filtering true indels. The new filter relies
   on the new pileup indel line implemented in samtools-0.1.2-25

------------------------------------------------------------------------
r215 | lh3lh3 | 2009-04-14 22:04:19 +0100 (Tue, 14 Apr 2009) | 4 lines
Changed paths:
   M /trunk/samtools/bam_maqcns.c
   M /trunk/samtools/bam_plcmd.c
   M /trunk/samtools/bamtk.c
   M /trunk/samtools/samtools.1

 * samtools-0.1.2-25
 * change the pileup indel line to shows the number of alignments actually
   containing indels

------------------------------------------------------------------------
r211 | lh3lh3 | 2009-04-13 12:07:13 +0100 (Mon, 13 Apr 2009) | 2 lines
Changed paths:
   M /trunk/samtools/ChangeLog

update ChangeLog from "svn log"

------------------------------------------------------------------------
r210 | lh3lh3 | 2009-04-12 20:57:05 +0100 (Sun, 12 Apr 2009) | 4 lines
Changed paths:
   M /trunk/samtools/bam.c
   M /trunk/samtools/bam_import.c
   M /trunk/samtools/bam_sort.c
   M /trunk/samtools/bamtk.c
   M /trunk/samtools/kseq.h

 * samtools-0.1.2-24
 * in merge, gives a warning rather than error if the target sequence length is different
 * allow empty header

------------------------------------------------------------------------
r209 | lh3lh3 | 2009-04-12 20:32:44 +0100 (Sun, 12 Apr 2009) | 3 lines
Changed paths:
   M /trunk/samtools/bam.c
   M /trunk/samtools/bam_import.c
   M /trunk/samtools/bamtk.c

 * samtools-0.1.2-23
 * recognize '*' at the QUAL field

------------------------------------------------------------------------
r208 | lh3lh3 | 2009-04-12 20:08:02 +0100 (Sun, 12 Apr 2009) | 3 lines
Changed paths:
   M /trunk/samtools/bam_import.c
   M /trunk/samtools/bamtk.c
   M /trunk/samtools/kseq.h

 * samtools-0.1.2-22
 * the field separater is TAB only, now

------------------------------------------------------------------------
r207 | lh3lh3 | 2009-04-08 15:18:03 +0100 (Wed, 08 Apr 2009) | 2 lines
Changed paths:
   M /trunk/samtools/examples/ex1.sam.gz

 * fixed the problem in the example alignment due to the bug in fixmate

------------------------------------------------------------------------
r206 | lh3lh3 | 2009-04-08 15:15:05 +0100 (Wed, 08 Apr 2009) | 3 lines
Changed paths:
   M /trunk/samtools/bam_mate.c
   M /trunk/samtools/bamtk.c
   M /trunk/samtools/misc/soap2sam.pl

 * samtools-0.1.2-21
 * fixed a nasty bug in `fixmate'

------------------------------------------------------------------------
r205 | lh3lh3 | 2009-04-08 10:57:08 +0100 (Wed, 08 Apr 2009) | 2 lines
Changed paths:
   M /trunk/samtools/misc/bowtie2sam.pl
   M /trunk/samtools/misc/soap2sam.pl
   M /trunk/samtools/misc/wgsim_eval.pl

make the script robust to the bugs in SOAP-2.1.7

------------------------------------------------------------------------
r200 | lh3lh3 | 2009-04-02 15:14:56 +0100 (Thu, 02 Apr 2009) | 3 lines
Changed paths:
   M /trunk/samtools/bam_stat.c
   M /trunk/samtools/bamtk.c

 * samtools-0.1.2-20
 * check if file is truncated in flagstat

------------------------------------------------------------------------
r199 | lh3lh3 | 2009-04-02 15:09:10 +0100 (Thu, 02 Apr 2009) | 3 lines
Changed paths:
   M /trunk/samtools/bamtk.c

 * samtools-0.1.2-19
 * print the header if requested

------------------------------------------------------------------------
r193 | lh3lh3 | 2009-03-27 15:09:50 +0000 (Fri, 27 Mar 2009) | 3 lines
Changed paths:
   M /trunk/samtools/bam_plcmd.c
   M /trunk/samtools/bamtk.c

 * samtools-0.1.2-18
 * fixed a minor bug reported by Nils Homer

------------------------------------------------------------------------
r185 | lh3lh3 | 2009-03-24 11:50:32 +0000 (Tue, 24 Mar 2009) | 2 lines
Changed paths:
   A /trunk/samtools/Makefile (from /trunk/samtools/Makefile.std:184)
   D /trunk/samtools/Makefile.std
   A /trunk/samtools/misc/Makefile (from /trunk/samtools/misc/Makefile.std:184)
   D /trunk/samtools/misc/Makefile.std

rename Makefile.std as Makefile. GNU building systerm is not ready and may take some time...

------------------------------------------------------------------------
r184 | lh3lh3 | 2009-03-24 10:36:38 +0000 (Tue, 24 Mar 2009) | 4 lines
Changed paths:
   D /trunk/samtools/Makefile
   A /trunk/samtools/Makefile.std (from /trunk/samtools/Makefile:183)
   M /trunk/samtools/bam_sort.c
   M /trunk/samtools/bam_tview.c
   M /trunk/samtools/bamtk.c
   D /trunk/samtools/misc/Makefile
   A /trunk/samtools/misc/Makefile.std (from /trunk/samtools/misc/Makefile:182)
   M /trunk/samtools/samtools.1

 * samtools-0.1.2-17
 * incorporating Nils' changes
 * rename Makefile to Makefile.std and prepare to add the GNU building systerms (also by Nils)

------------------------------------------------------------------------
r183 | lh3lh3 | 2009-03-24 10:30:23 +0000 (Tue, 24 Mar 2009) | 4 lines
Changed paths:
   M /trunk/samtools/Makefile
   M /trunk/samtools/bam_import.c
   M /trunk/samtools/bam_maqcns.c
   M /trunk/samtools/bam_maqcns.h
   M /trunk/samtools/bam_plcmd.c
   M /trunk/samtools/bamtk.c
   M /trunk/samtools/kseq.h
   A /trunk/samtools/kstring.c
   A /trunk/samtools/kstring.h

 * samtools-0.1.2-16
 * made pileup take a list of proposed indels. An insertion is N at the moment.
 * added my kstring library for a bit complex parsing of the position list.

------------------------------------------------------------------------
r169 | lh3lh3 | 2009-03-12 13:40:14 +0000 (Thu, 12 Mar 2009) | 3 lines
Changed paths:
   M /trunk/samtools/misc/soap2sam.pl

 * soap2sam.pl-0.1.2
 * more robust to truncated soap output

------------------------------------------------------------------------
r168 | lh3lh3 | 2009-03-11 10:49:00 +0000 (Wed, 11 Mar 2009) | 2 lines
Changed paths:
   M /trunk/samtools/Makefile.lite

added bam_stat.o to Makefile.lite

------------------------------------------------------------------------
r167 | lh3lh3 | 2009-03-10 22:11:31 +0000 (Tue, 10 Mar 2009) | 3 lines
Changed paths:
   M /trunk/samtools/bam_maqcns.c
   M /trunk/samtools/bamtk.c

 * samtools-0.1.2-15
 * generate RMS of mapQ instead of max mapQ

------------------------------------------------------------------------
r166 | lh3lh3 | 2009-03-10 22:06:45 +0000 (Tue, 10 Mar 2009) | 3 lines
Changed paths:
   M /trunk/samtools/bam_plcmd.c
   M /trunk/samtools/bamtk.c
   M /trunk/samtools/glf.c
   M /trunk/samtools/glf.h
   M /trunk/samtools/misc/Makefile

 * samtools-0.1.2-14
 * implemented GLFv3

------------------------------------------------------------------------
r159 | lh3lh3 | 2009-03-03 11:26:08 +0000 (Tue, 03 Mar 2009) | 3 lines
Changed paths:
   M /trunk/samtools/bam_plcmd.c
   M /trunk/samtools/bamtk.c

 * samtools-0.1.2-13
 * fixed a minor bug in displaying pileup

------------------------------------------------------------------------
r158 | lh3lh3 | 2009-03-03 11:24:16 +0000 (Tue, 03 Mar 2009) | 3 lines
Changed paths:
   M /trunk/samtools/ChangeLog
   M /trunk/samtools/bamtk.c

 * samtools-0.1.2-12
 * optionally print SAM header

------------------------------------------------------------------------
r153 | lh3lh3 | 2009-03-02 10:45:28 +0000 (Mon, 02 Mar 2009) | 3 lines
Changed paths:
   M /trunk/samtools/bamtk.c
   M /trunk/samtools/glf.c

 * samtools-0.1.2-11
 * use "GLF\3" as the magic for GLFv3 files

------------------------------------------------------------------------
r152 | lh3lh3 | 2009-03-02 10:39:09 +0000 (Mon, 02 Mar 2009) | 5 lines
Changed paths:
   M /trunk/samtools/Makefile
   M /trunk/samtools/bam_import.c
   M /trunk/samtools/bam_index.c
   M /trunk/samtools/bam_plcmd.c
   M /trunk/samtools/bamtk.c
   M /trunk/samtools/glf.c
   M /trunk/samtools/glf.h

 * samtools-0.1.2-10
 * fixed a bug in import: core.bin is undefined for unmapped reads
 * this bug can be alleviated (not completely solved) in bam_index.c
 * update to GLFv3: pos is changed to offset for better compression

------------------------------------------------------------------------
r151 | lh3lh3 | 2009-03-01 15:18:43 +0000 (Sun, 01 Mar 2009) | 3 lines
Changed paths:
   M /trunk/samtools/misc/wgsim.c

 * wgsim-0.2.3
 * fixed a bug in simulating indels

------------------------------------------------------------------------
r145 | lh3lh3 | 2009-02-26 19:43:57 +0000 (Thu, 26 Feb 2009) | 4 lines
Changed paths:
   M /trunk/samtools/misc/wgsim.c

 * wgsim-0.2.2
 * allow to print mismatch information as fastq comment. MAQ does
   not like long read names.

------------------------------------------------------------------------
r141 | lh3lh3 | 2009-02-26 14:53:03 +0000 (Thu, 26 Feb 2009) | 6 lines
Changed paths:
   M /trunk/samtools/ChangeLog
   M /trunk/samtools/misc/wgsim.c
   M /trunk/samtools/misc/wgsim_eval.pl

 * wgsim-0.2.1
 * fixed a bug about color read coordinates
 * fixed a bug in read names
 * wgsim_eval.pl-0.1.3
 * make the script work with color reads

------------------------------------------------------------------------
r140 | lh3lh3 | 2009-02-26 14:02:57 +0000 (Thu, 26 Feb 2009) | 2 lines
Changed paths:
   M /trunk/samtools/misc/Makefile
   M /trunk/samtools/misc/wgsim.c

 * wgsim: added a note

------------------------------------------------------------------------
r139 | lh3lh3 | 2009-02-26 11:39:08 +0000 (Thu, 26 Feb 2009) | 7 lines
Changed paths:
   M /trunk/samtools/misc/wgsim.c
   M /trunk/samtools/misc/wgsim_eval.pl

 * wgsim-0.2.0
 * considerable code clean up
 * print number of substitutions/indels/errors on each read
 * potentially support SOLiD simulation, though not tested at the moment
 * wgsim_eval.pl-0.1.2
 * change in accordant with wgsim

------------------------------------------------------------------------
r129 | lh3lh3 | 2009-02-18 22:23:27 +0000 (Wed, 18 Feb 2009) | 3 lines
Changed paths:
   M /trunk/samtools/bam_index.c
   M /trunk/samtools/bamtk.c

 * samtools-0.1.2-9
 * fixed a bug in bam_fetch, caused by completely contained adjacent chunks

------------------------------------------------------------------------
r128 | bhandsaker | 2009-02-18 19:06:57 +0000 (Wed, 18 Feb 2009) | 2 lines
Changed paths:
   M /trunk/samtools/bamtk.c

Fix annoying segv when invalid region specified.

------------------------------------------------------------------------
r127 | lh3lh3 | 2009-02-17 10:49:55 +0000 (Tue, 17 Feb 2009) | 2 lines
Changed paths:
   D /trunk/samtools/misc/indel_filter.pl
   A /trunk/samtools/misc/samtools.pl

 * move indel_filter.pl to samtools.pl

------------------------------------------------------------------------
r126 | lh3lh3 | 2009-02-14 21:22:30 +0000 (Sat, 14 Feb 2009) | 3 lines
Changed paths:
   M /trunk/samtools/bam_mate.c
   M /trunk/samtools/bamtk.c

 * samtools-0.1.2-7
 * fixed a bug in fixmate: SE reads are flagged as BAM_FMUNMAP

------------------------------------------------------------------------
r125 | lh3lh3 | 2009-02-13 09:54:45 +0000 (Fri, 13 Feb 2009) | 3 lines
Changed paths:
   M /trunk/samtools/bam_stat.c
   M /trunk/samtools/bamtk.c

 * samtools-0.1.2-7
 * fixed a minor bug in flagstat

------------------------------------------------------------------------
r124 | lh3lh3 | 2009-02-12 11:15:32 +0000 (Thu, 12 Feb 2009) | 3 lines
Changed paths:
   M /trunk/samtools/bam_maqcns.c
   M /trunk/samtools/bamtk.c
   M /trunk/samtools/misc/indel_filter.pl

 * samtools-0.1.2-6
 * improve indel caller by setting maximum window size

------------------------------------------------------------------------
r123 | lh3lh3 | 2009-02-12 10:30:29 +0000 (Thu, 12 Feb 2009) | 2 lines
Changed paths:
   M /trunk/samtools/bam_plcmd.c
   M /trunk/samtools/bamtk.c

 * output max mapping quality in indel line

------------------------------------------------------------------------
r122 | lh3lh3 | 2009-02-11 10:59:10 +0000 (Wed, 11 Feb 2009) | 2 lines
Changed paths:
   M /trunk/samtools/misc/maq2sam.c

fixed a bug in generating tag AM

------------------------------------------------------------------------
r121 | lh3lh3 | 2009-02-03 10:43:11 +0000 (Tue, 03 Feb 2009) | 2 lines
Changed paths:
   M /trunk/samtools/bam_index.c
   M /trunk/samtools/bamtk.c

fixed a potential memory problem in indexing

------------------------------------------------------------------------
r120 | bhandsaker | 2009-02-02 15:52:52 +0000 (Mon, 02 Feb 2009) | 2 lines
Changed paths:
   M /trunk/samtools/Makefile

Pass LIBS to recursive targets to facilitate building at Broad.

------------------------------------------------------------------------
r119 | lh3lh3 | 2009-02-02 10:12:15 +0000 (Mon, 02 Feb 2009) | 4 lines
Changed paths:
   M /trunk/samtools/ChangeLog
   M /trunk/samtools/bam_plcmd.c
   M /trunk/samtools/bam_stat.c
   M /trunk/samtools/bamtk.c

 * samtools-0.1.2-3
 * fixed a bug in generating GLFv2 for indels
 * improve flagstat report a little bit

------------------------------------------------------------------------
r118 | lh3lh3 | 2009-01-29 12:33:23 +0000 (Thu, 29 Jan 2009) | 3 lines
Changed paths:
   M /trunk/samtools/Makefile
   A /trunk/samtools/bam_stat.c
   M /trunk/samtools/bamtk.c

 * samtools-0.1.2-1
 * added flagstat command

------------------------------------------------------------------------
r116 | lh3lh3 | 2009-01-28 13:31:12 +0000 (Wed, 28 Jan 2009) | 2 lines
Changed paths:
   M /trunk/samtools/ChangeLog
   M /trunk/samtools/NEWS
   M /trunk/samtools/bamtk.c
   M /trunk/samtools/samtools.1

Release SAMtools-0.1.2

------------------------------------------------------------------------
r115 | lh3lh3 | 2009-01-28 12:54:08 +0000 (Wed, 28 Jan 2009) | 2 lines
Changed paths:
   A /trunk/samtools/misc/indel_filter.pl

Script for filtering indel results

------------------------------------------------------------------------
r114 | lh3lh3 | 2009-01-25 11:45:37 +0000 (Sun, 25 Jan 2009) | 2 lines
Changed paths:
   A /trunk/samtools/misc/zoom2sam.pl

convert ZOOM to SAM

------------------------------------------------------------------------
r113 | lh3lh3 | 2009-01-24 14:25:07 +0000 (Sat, 24 Jan 2009) | 2 lines
Changed paths:
   A /trunk/samtools/misc/novo2sam.pl

add a script to convert novo alignment to SAM

------------------------------------------------------------------------
r112 | lh3lh3 | 2009-01-23 20:57:39 +0000 (Fri, 23 Jan 2009) | 2 lines
Changed paths:
   M /trunk/samtools/ChangeLog
   M /trunk/samtools/ChangeLog.old
   M /trunk/samtools/samtools.1

update documentation and ChangeLog

------------------------------------------------------------------------
r111 | lh3lh3 | 2009-01-23 19:22:59 +0000 (Fri, 23 Jan 2009) | 3 lines
Changed paths:
   M /trunk/samtools/bam_sort.c
   M /trunk/samtools/bamtk.c

 * samtools-0.1.1-19
 * fixed a bug in "merge" command line

------------------------------------------------------------------------
r110 | lh3lh3 | 2009-01-22 15:36:48 +0000 (Thu, 22 Jan 2009) | 3 lines
Changed paths:
   M /trunk/samtools/misc/Makefile
   A /trunk/samtools/misc/bowtie2sam.pl (from /branches/dev/samtools/misc/bowtie2sam.pl:108)
   M /trunk/samtools/misc/export2sam.pl
   A /trunk/samtools/misc/soap2sam.pl (from /branches/dev/samtools/misc/soap2sam.pl:108)
   A /trunk/samtools/misc/wgsim.c (from /branches/dev/samtools/misc/wgsim.c:108)
   A /trunk/samtools/misc/wgsim_eval.pl (from /branches/dev/samtools/misc/wgsim_eval.pl:108)

 * merge from branches/dev/
 * all future development will happen here

------------------------------------------------------------------------
r109 | lh3lh3 | 2009-01-22 15:14:27 +0000 (Thu, 22 Jan 2009) | 3 lines
Changed paths:
   M /trunk/samtools/COPYING
   M /trunk/samtools/ChangeLog
   A /trunk/samtools/INSTALL (from /branches/dev/samtools/INSTALL:108)
   M /trunk/samtools/Makefile
   A /trunk/samtools/Makefile.lite (from /branches/dev/samtools/Makefile.lite:108)
   M /trunk/samtools/bam.c
   M /trunk/samtools/bam.h
   M /trunk/samtools/bam_import.c
   M /trunk/samtools/bam_index.c
   M /trunk/samtools/bam_lpileup.c
   M /trunk/samtools/bam_maqcns.c
   M /trunk/samtools/bam_maqcns.h
   A /trunk/samtools/bam_mate.c (from /branches/dev/samtools/bam_mate.c:108)
   M /trunk/samtools/bam_pileup.c
   M /trunk/samtools/bam_plcmd.c
   A /trunk/samtools/bam_rmdup.c (from /branches/dev/samtools/bam_rmdup.c:108)
   M /trunk/samtools/bam_sort.c
   M /trunk/samtools/bamtk.c
   M /trunk/samtools/bgzf.h
   M /trunk/samtools/examples/00README.txt
   A /trunk/samtools/examples/Makefile (from /branches/dev/samtools/examples/Makefile:108)
   D /trunk/samtools/examples/ex1.fa.fai
   M /trunk/samtools/examples/ex1.sam.gz
   M /trunk/samtools/faidx.c
   A /trunk/samtools/glf.c (from /branches/dev/samtools/glf.c:108)
   M /trunk/samtools/glf.h
   M /trunk/samtools/misc/Makefile
   M /trunk/samtools/misc/maq2sam.c
   M /trunk/samtools/razf.c
   M /trunk/samtools/source.dot

 * Merge from branches/dev/
 * all future development will happen here at trunk/

------------------------------------------------------------------------
r79 | bhandsaker | 2009-01-07 21:42:15 +0000 (Wed, 07 Jan 2009) | 2 lines
Changed paths:
   M /trunk/samtools/bam_maqcns.c
   M /trunk/samtools/bam_tview.c

Fix problem with compiling without curses.

------------------------------------------------------------------------
r63 | lh3lh3 | 2008-12-22 15:58:02 +0000 (Mon, 22 Dec 2008) | 2 lines
Changed paths:
   A /trunk/samtools (from /branches/dev/samtools:62)

Create trunk copy

------------------------------------------------------------------------
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

------------------------------------------------------------------------
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

------------------------------------------------------------------------
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

------------------------------------------------------------------------
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

------------------------------------------------------------------------
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

------------------------------------------------------------------------
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

------------------------------------------------------------------------
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.

------------------------------------------------------------------------
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.

------------------------------------------------------------------------
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.

------------------------------------------------------------------------
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

------------------------------------------------------------------------
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

------------------------------------------------------------------------
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

------------------------------------------------------------------------
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

------------------------------------------------------------------------
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

------------------------------------------------------------------------
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

------------------------------------------------------------------------
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)

------------------------------------------------------------------------