X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=samtools.git;a=blobdiff_plain;f=ChangeLog;h=c0afc458da745949eaecc674e2adc4c264f54e6a;hp=3bf82a59c9f2f5d0249c9d457022a93f3758d751;hb=d363084f0412f3bcdeb0304aeb0974c9a10c7649;hpb=b27e00385f41769d03a8cca4dbd71275fc9fa906 diff --git a/ChangeLog b/ChangeLog index 3bf82a5..c0afc45 100644 --- a/ChangeLog +++ b/ChangeLog @@ -1,3 +1,561 @@ +------------------------------------------------------------------------ +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: