]>
git.donarmstrong.com Git - samtools.git/log
Heng Li [Wed, 14 Oct 2009 18:18:12 +0000 (18:18 +0000)]
* samtools-0.1.6-12 (r478)
* fixed a bug in the indel caller
Heng Li [Sat, 10 Oct 2009 10:12:26 +0000 (10:12 +0000)]
* samtools-0.1.6-11 (r477)
* fixed a bug due to recent change in bam_index.c (thank Nicole Washington for the patch)
Petr Danecek [Fri, 9 Oct 2009 15:45:36 +0000 (15:45 +0000)]
Added the sam2vcf.pl script.
Heng Li [Thu, 8 Oct 2009 14:19:16 +0000 (14:19 +0000)]
Unfinished modification. Please do not use this revision...
Petr Danecek [Thu, 8 Oct 2009 10:39:54 +0000 (10:39 +0000)]
Removed the offending knet_seek message.
Petr Danecek [Tue, 6 Oct 2009 13:26:35 +0000 (13:26 +0000)]
Bug fix - faidx on RAZF compressed files now working.
Heng Li [Fri, 2 Oct 2009 12:42:57 +0000 (12:42 +0000)]
Clarify the meaning of a region like "chr2:1,000,000".
Heng Li [Fri, 2 Oct 2009 09:42:19 +0000 (09:42 +0000)]
Fixed minor bugs in novo2sam.pl (on behalf of Ken Chen and Colin Hercus)
Heng Li [Tue, 29 Sep 2009 19:01:27 +0000 (19:01 +0000)]
* samtools-0.1.6-9 (r470)
* make knetfile.c compatible with MinGW (thank Martin Morgan for the patch)
Heng Li [Tue, 29 Sep 2009 12:07:44 +0000 (12:07 +0000)]
* samtools-0.1.6-9 (r469)
* refactor bam_fetch() for Python binding. On behalf of Leo Goodstadt.
Heng Li [Mon, 28 Sep 2009 09:18:29 +0000 (09:18 +0000)]
* samtools-0.1.6-7 (r468)
* make merge stable
Petr Danecek [Mon, 28 Sep 2009 08:51:29 +0000 (08:51 +0000)]
Changed the mode for newly created files to 0666. This allows less strict permissions with umask properly set (e.g. 0002 vs. 0022).
Heng Li [Thu, 24 Sep 2009 10:29:19 +0000 (10:29 +0000)]
* samtools-0.1.6-6 (r466)
* do not crash calmd when some sequences are absent from the reference.
On behalf of John Marshall [Wed, 23 Sep 2009 10:14:32 +0000 (10:14 +0000)]
Suppress bgzf_check_EOF() messages when reading from a pipe, as there is
no way to seek on a pipe and the messages always appear.
Petr Danecek [Wed, 16 Sep 2009 11:05:41 +0000 (11:05 +0000)]
A bug fix, "samtools view" is now working again.
Heng Li [Wed, 16 Sep 2009 08:51:07 +0000 (08:51 +0000)]
* samtools-0.1.6-5 (r462)
* Added knetfile support in razf and faidx (on behalf of Petr Danecek)
Heng Li [Wed, 9 Sep 2009 11:06:22 +0000 (11:06 +0000)]
fixed a formatting issue
Heng Li [Tue, 8 Sep 2009 22:14:08 +0000 (22:14 +0000)]
* samtools-0.1.6-4 (r459)
* make sort output the result to stdout when -o is in use
Heng Li [Mon, 7 Sep 2009 09:10:28 +0000 (09:10 +0000)]
* samtools-0.1.6-2 (r458)
* added more interface to faidx (by Nils)
* updated documentation
Heng Li [Sat, 5 Sep 2009 20:12:04 +0000 (20:12 +0000)]
* samtools-0.1.6-2 (r457)
* get rid of three assert() in bam_sort.c
On behalf of John Marshall [Fri, 4 Sep 2009 16:46:25 +0000 (16:46 +0000)]
Return NULL from _razf_open() (and hence razf_open()/razf_open2())
when opening the file fails.
Heng Li [Wed, 2 Sep 2009 12:56:33 +0000 (12:56 +0000)]
Release samtools-0.1.6
Heng Li [Wed, 2 Sep 2009 09:44:48 +0000 (09:44 +0000)]
* samtools-0.1.5-34 (r451)
* applied the patch by John
* improved the help message a little bit
Heng Li [Wed, 2 Sep 2009 08:55:55 +0000 (08:55 +0000)]
* samtools-0.1.5-33 (r450)
* fixed a bug in bam_color.c (on behalf of Nils Homer)
Heng Li [Sat, 29 Aug 2009 19:36:41 +0000 (19:36 +0000)]
* 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.
Heng Li [Wed, 19 Aug 2009 08:44:28 +0000 (08:44 +0000)]
* samtools-0.1.5-31 (r448)
* fixed an issue when the last CIGAR is I or D
Heng Li [Mon, 17 Aug 2009 08:34:57 +0000 (08:34 +0000)]
* samtools-0.1.5-30 (r447)
* fixed a bug in bam_aux_get(): 'A' is not checked
Heng Li [Mon, 17 Aug 2009 08:33:17 +0000 (08:33 +0000)]
*
Heng Li [Tue, 11 Aug 2009 09:02:36 +0000 (09:02 +0000)]
* samtools-0.1.5-28 (r444)
* bug in "merge -n"
Heng Li [Tue, 11 Aug 2009 08:29:11 +0000 (08:29 +0000)]
* samtools-0.1.5-27 (r443)
* SEQ and QUAL can be "*"
* parse CIGAR "=" and "X" as "M"
Heng Li [Fri, 7 Aug 2009 20:56:38 +0000 (20:56 +0000)]
* samtools-0.1.5-26 (r442)
* replace RSA Inc md5.* with ones under permissive lincense
* fixed a bug in detecting unsorted bam in pileup
On behalf of Bob Handsaker [Wed, 5 Aug 2009 13:41:28 +0000 (13:41 +0000)]
Change copyright notices now that MIT has approved open source distribution.
Heng Li [Wed, 5 Aug 2009 09:44:24 +0000 (09:44 +0000)]
* samtools-0.1.5-25 (r436)
* in flagstats, do not report singletons if both ends are unmapped
Heng Li [Tue, 4 Aug 2009 21:16:51 +0000 (21:16 +0000)]
fixed a SERIOUS bug in setting 0x20 flag
Heng Li [Tue, 4 Aug 2009 20:50:43 +0000 (20:50 +0000)]
fixed two minor bugs (suggested by Tim M Storm)
Heng Li [Tue, 4 Aug 2009 08:13:24 +0000 (08:13 +0000)]
* samtools-0.1.5-24 (r435)
* fixed a typo
Heng Li [Mon, 3 Aug 2009 09:40:42 +0000 (09:40 +0000)]
* samtools-0.1.5-23 (r434)
* in tview, press 'r' to show read names rather than sequences
Heng Li [Sun, 2 Aug 2009 18:13:35 +0000 (18:13 +0000)]
* tried to fixed the buggy FTP random access in Windows. FAILED.
* anyway, MinGW seems to have problem with "%lld".
Heng Li [Sat, 1 Aug 2009 23:32:07 +0000 (23:32 +0000)]
* samtools-0.1.5-22 (r432)
* faidx: fixed compitability issue with _WIN32
* razf: fixed potential compitability issue with _WIN32
* PDCurses support in Windows
Heng Li [Sat, 1 Aug 2009 22:34:54 +0000 (22:34 +0000)]
replace the GnuWin32 version of libz.a with my own build with MinGW.
Heng Li [Sat, 1 Aug 2009 22:21:07 +0000 (22:21 +0000)]
add comments
Heng Li [Sat, 1 Aug 2009 21:41:19 +0000 (21:41 +0000)]
* samtools-0.1.5-21 (r428)
* knetfile.c is now compatible with mingw-winsock
Heng Li [Fri, 31 Jul 2009 23:39:07 +0000 (23:39 +0000)]
simplify MinGW Makefile
Heng Li [Fri, 31 Jul 2009 23:30:54 +0000 (23:30 +0000)]
* 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/
Heng Li [Fri, 31 Jul 2009 22:32:09 +0000 (22:32 +0000)]
* samtools-0.1.5-19 (r426)
* fixed a bug caused by recent modifications. Sorry.
Heng Li [Fri, 31 Jul 2009 22:23:51 +0000 (22:23 +0000)]
compatible with Windows binary files
Heng Li [Fri, 31 Jul 2009 09:19:59 +0000 (09:19 +0000)]
* 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
Heng Li [Thu, 30 Jul 2009 21:00:36 +0000 (21:00 +0000)]
convert BLAT psl to SAM.
Heng Li [Thu, 30 Jul 2009 10:24:39 +0000 (10:24 +0000)]
* 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
Heng Li [Thu, 30 Jul 2009 09:03:39 +0000 (09:03 +0000)]
* samtools-0.1.5-16 (r421)
* in view and pileup, load header from FASTA index if the input is SAM.
Heng Li [Wed, 29 Jul 2009 08:18:55 +0000 (08:18 +0000)]
do not set "read 1" if reads are not mapped in the PE mode of maq
Heng Li [Tue, 28 Jul 2009 08:52:33 +0000 (08:52 +0000)]
* 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
Heng Li [Fri, 24 Jul 2009 13:04:19 +0000 (13:04 +0000)]
skip @header lines in SAM
Heng Li [Fri, 24 Jul 2009 11:42:38 +0000 (11:42 +0000)]
* samtools-0.1.5-14 (r417)
* more help in "samtools view" due to the recent changes.
Heng Li [Fri, 24 Jul 2009 11:34:30 +0000 (11:34 +0000)]
* samtools-0.1.5-17 (r416)
* support import/export SAM with string tags
Heng Li [Fri, 24 Jul 2009 10:39:26 +0000 (10:39 +0000)]
* samtools-0.1.5-12 (r415)
* FLAG now can be in HEX
Heng Li [Wed, 22 Jul 2009 21:03:49 +0000 (21:03 +0000)]
fixed a compiling error (thank Ken for fixing it)
Heng Li [Tue, 21 Jul 2009 21:19:40 +0000 (21:19 +0000)]
Implemented Boyer-Moore search in the kstring library.
Heng Li [Fri, 17 Jul 2009 16:10:20 +0000 (16:10 +0000)]
do not include knetfile.h when _USE_KNETFILE is not defined
Heng Li [Fri, 17 Jul 2009 14:29:21 +0000 (14:29 +0000)]
* 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
Heng Li [Fri, 17 Jul 2009 13:46:56 +0000 (13:46 +0000)]
* samtools-0.1.5-10 (r407)
* implemented bam_aux_del() to remove a tag
* fillmd: generate the NM tag
* fillmd: cmd interface improvement
Heng Li [Thu, 16 Jul 2009 22:30:40 +0000 (22:30 +0000)]
Sorry. The old Makefile is for PDCurses...
Heng Li [Thu, 16 Jul 2009 22:30:11 +0000 (22:30 +0000)]
* samtools-0.1.5-9 (r405)
* improved the compatibility with PDCurses a little bit
Heng Li [Thu, 16 Jul 2009 22:23:52 +0000 (22:23 +0000)]
* samtools-0.1.5-8 (r404)
* compatible with PDCurses
Heng Li [Thu, 16 Jul 2009 21:39:39 +0000 (21:39 +0000)]
* samtools-0.1.5-7 (r403)
* fixed a bug in kseq.h for binary files (text files are fine)
Heng Li [Thu, 16 Jul 2009 10:49:53 +0000 (10:49 +0000)]
* samtools-0.1.5-6 (r402)
* fixed compiling error when "-D_USE_NETFILE" is not applied
* improve portability to MinGW
Heng Li [Mon, 13 Jul 2009 09:21:36 +0000 (09:21 +0000)]
* move bam_lite.c to bam-lite
* copy bam.h to bam-lite
Heng Li [Mon, 13 Jul 2009 09:12:57 +0000 (09:12 +0000)]
* samtools-0.1.5-5 (r395)
* added bam_pileup_file() and removed bam_lpileup_file()
Heng Li [Sun, 12 Jul 2009 23:35:10 +0000 (23:35 +0000)]
* samtools-0.1.5-4 (r394)
* http_proxy support in knetfile library (check http_proxy ENV)
Heng Li [Sun, 12 Jul 2009 22:57:07 +0000 (22:57 +0000)]
* 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.
Heng Li [Sun, 12 Jul 2009 17:50:55 +0000 (17:50 +0000)]
Remove the warning in tview
Heng Li [Sun, 12 Jul 2009 17:42:43 +0000 (17:42 +0000)]
* samtools-0.1.5-2 (r391)
* do not show a blank screen when no reads mapped
Heng Li [Thu, 9 Jul 2009 13:01:42 +0000 (13:01 +0000)]
* 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
Heng Li [Tue, 7 Jul 2009 15:53:29 +0000 (15:53 +0000)]
Release samtools-0.1.5c (fixed a bug in piping)
Heng Li [Tue, 7 Jul 2009 10:39:55 +0000 (10:39 +0000)]
Release samtools-0.1.5b (BUG! so embarrassing!)
Heng Li [Tue, 7 Jul 2009 10:20:06 +0000 (10:20 +0000)]
Release samtools-0.1.5a (for compatibility with Bio::DB::Sam)
Heng Li [Tue, 7 Jul 2009 09:26:57 +0000 (09:26 +0000)]
Release samtools-0.1.5
Heng Li [Tue, 7 Jul 2009 08:49:27 +0000 (08:49 +0000)]
* samtools-0.1.4-23 (r372)
* keep header text if "view -t" is used (by Gerton)
Heng Li [Tue, 7 Jul 2009 00:13:32 +0000 (00:13 +0000)]
update documentation
On behalf of Bob Handsaker [Thu, 2 Jul 2009 21:24:34 +0000 (21:24 +0000)]
Introduced LIBPATH variable so this could be overridden to allow samtools to build correct at the Broad.
Heng Li [Thu, 2 Jul 2009 12:36:53 +0000 (12:36 +0000)]
* samtools-0.1.4-22 (r369)
* in pileup, optionally print E2 and U2
* remove the debugging code in bam_aux_get() (Drat!)
Heng Li [Thu, 2 Jul 2009 10:32:26 +0000 (10:32 +0000)]
* 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
Heng Li [Tue, 30 Jun 2009 15:18:42 +0000 (15:18 +0000)]
reduce the chance of blocking in FTP connection
Heng Li [Tue, 30 Jun 2009 14:35:21 +0000 (14:35 +0000)]
minor changes to knetfile: invalid fd equals -1 rather than 0
Heng Li [Tue, 30 Jun 2009 13:04:30 +0000 (13:04 +0000)]
* samtools-0.1.4-20 (r365)
* download the BAM index file if it is not found in the current working directory.
Heng Li [Tue, 30 Jun 2009 11:39:07 +0000 (11:39 +0000)]
* samtools-0.1.4-19 (r364)
* knetfile: report error when the file is not present on FTP
Heng Li [Mon, 29 Jun 2009 22:23:32 +0000 (22:23 +0000)]
* samtools-0.1.4-18 (r363)
* knetfile: do not trigger network communication in FTP seek (lazy seek)
* bgzf: cache recent blocks (disabled by default)
Heng Li [Thu, 25 Jun 2009 20:04:34 +0000 (20:04 +0000)]
write changelog
Heng Li [Thu, 25 Jun 2009 20:03:10 +0000 (20:03 +0000)]
* samtools-0.1.4-17 (r361)
* if a file is given on FTP, search locally for the BAM index
Heng Li [Thu, 25 Jun 2009 19:44:52 +0000 (19:44 +0000)]
* 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
Heng Li [Thu, 25 Jun 2009 16:10:55 +0000 (16:10 +0000)]
fixed bugs in knetfile.*
Heng Li [Thu, 25 Jun 2009 12:53:19 +0000 (12:53 +0000)]
this is the header file
Heng Li [Thu, 25 Jun 2009 12:52:03 +0000 (12:52 +0000)]
* open a file at FTP
* preliminary version
Heng Li [Wed, 24 Jun 2009 13:02:25 +0000 (13:02 +0000)]
* samtools-0.1.4-15 (r354)
* fixed a memory leak in bam_view1(), although samtools is not using this routine.
Heng Li [Wed, 17 Jun 2009 23:16:26 +0000 (23:16 +0000)]
* 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...
Heng Li [Tue, 16 Jun 2009 13:37:01 +0000 (13:37 +0000)]
* samtools-0.1.4-13 (r350)
* fixed a small memory leak in pileup, caused by recent modifications
Heng Li [Sat, 13 Jun 2009 20:20:49 +0000 (20:20 +0000)]
* samtools-0.1.4-12 (r347)
* added `-S' to pileup, similar to `view -S'
Heng Li [Sat, 13 Jun 2009 16:52:31 +0000 (16:52 +0000)]
* samtools-0.1.4-11 (r346)
* allow to select a read group at view command-line
Heng Li [Sat, 13 Jun 2009 13:06:24 +0000 (13:06 +0000)]
added more comments
Heng Li [Sat, 13 Jun 2009 13:01:22 +0000 (13:01 +0000)]
nothing really