+------------------------------------------------------------------------
+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:
projects / samtools.git / blobdiff