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

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author ryanmorin
date Wed, 12 Oct 2011 19:50:38 -0400
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/SNV/SNVMix2_source/SNVMix2-v0.12.1-rc1/samtools-0.1.6/ChangeLog	Wed Oct 12 19:50:38 2011 -0400
@@ -0,0 +1,2657 @@
+------------------------------------------------------------------------
+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
+
+------------------------------------------------------------------------
+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)
+
+------------------------------------------------------------------------
+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.
+
+------------------------------------------------------------------------
+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
+
+------------------------------------------------------------------------
+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
+
+------------------------------------------------------------------------
+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
+
+ * 
+
+------------------------------------------------------------------------
+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"
+
+------------------------------------------------------------------------
+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"
+
+------------------------------------------------------------------------
+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
+
+------------------------------------------------------------------------
+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.
+
+------------------------------------------------------------------------
+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
+
+------------------------------------------------------------------------
+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
+
+------------------------------------------------------------------------
+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)
+
+------------------------------------------------------------------------
+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
+
+------------------------------------------------------------------------
+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
+
+------------------------------------------------------------------------
+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".
+
+------------------------------------------------------------------------
+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
+
+------------------------------------------------------------------------
+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.
+
+------------------------------------------------------------------------
+r430 | lh3lh3 | 2009-08-01 23:21:07 +0100 (Sat, 01 Aug 2009) | 2 lines
+Changed paths:
+   M /trunk/samtools/knetfile.c
+
+add comments
+
+------------------------------------------------------------------------
+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
+
+------------------------------------------------------------------------
+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
+
+------------------------------------------------------------------------
+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/
+
+------------------------------------------------------------------------
+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.
+
+------------------------------------------------------------------------
+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
+
+------------------------------------------------------------------------
+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
+
+------------------------------------------------------------------------
+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.
+
+------------------------------------------------------------------------
+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
+
+------------------------------------------------------------------------
+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.
+
+------------------------------------------------------------------------
+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
+
+------------------------------------------------------------------------
+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
+
+------------------------------------------------------------------------
+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
+
+------------------------------------------------------------------------
+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.
+
+------------------------------------------------------------------------
+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
+
+------------------------------------------------------------------------
+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
+
+------------------------------------------------------------------------
+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)
+
+------------------------------------------------------------------------
+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.
+
+------------------------------------------------------------------------
+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
+
+------------------------------------------------------------------------
+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
+
+------------------------------------------------------------------------
+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
+
+------------------------------------------------------------------------
+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...
+
+------------------------------------------------------------------------
+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
+
+------------------------------------------------------------------------
+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
+
+------------------------------------------------------------------------
+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)
+
+------------------------------------------------------------------------
+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
+
+------------------------------------------------------------------------
+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
+
+------------------------------------------------------------------------
+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()
+
+------------------------------------------------------------------------
+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)
+
+------------------------------------------------------------------------
+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.
+
+------------------------------------------------------------------------
+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
+
+------------------------------------------------------------------------
+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
+
+------------------------------------------------------------------------
+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
+
+------------------------------------------------------------------------
+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)
+
+------------------------------------------------------------------------
+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!)
+
+------------------------------------------------------------------------
+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)
+
+------------------------------------------------------------------------
+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
+
+------------------------------------------------------------------------
+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)
+
+------------------------------------------------------------------------
+r371 | lh3lh3 | 2009-07-07 01:13:32 +0100 (Tue, 07 Jul 2009) | 2 lines
+Changed paths:
+   M /trunk/samtools/samtools.1
+
+update documentation
+
+------------------------------------------------------------------------
+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.
+
+------------------------------------------------------------------------
+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!)
+
+------------------------------------------------------------------------
+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
+
+------------------------------------------------------------------------
+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
+
+------------------------------------------------------------------------
+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
+
+------------------------------------------------------------------------
+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.
+
+------------------------------------------------------------------------
+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
+
+------------------------------------------------------------------------
+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)
+
+------------------------------------------------------------------------