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git.donarmstrong.com Git - samtools.git/log
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
Heng Li [Sat, 13 Jun 2009 12:58:48 +0000 (12:58 +0000)]
added an example of calculating read depth
Heng Li [Sat, 13 Jun 2009 12:00:08 +0000 (12:00 +0000)]
* 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
Heng Li [Sat, 13 Jun 2009 10:17:14 +0000 (10:17 +0000)]
* 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
Heng Li [Sat, 13 Jun 2009 09:35:19 +0000 (09:35 +0000)]
update INSTALL
Heng Li [Fri, 12 Jun 2009 23:15:24 +0000 (23:15 +0000)]
* samtools-0.1.4-8 (r338)
* parse the @RG header lines and allow to choose library at the "samtools view"
command line
Heng Li [Fri, 12 Jun 2009 20:25:50 +0000 (20:25 +0000)]
* samtools-0.1.4-7 (r337)
* bgzf.c: support mode string "wu": uncompressed output
* "samtools view" support "-u" command-line option
Heng Li [Fri, 12 Jun 2009 16:20:12 +0000 (16:20 +0000)]
* 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
Heng Li [Fri, 12 Jun 2009 15:47:33 +0000 (15:47 +0000)]
remove zlib for simplification...
Heng Li [Fri, 12 Jun 2009 14:43:36 +0000 (14:43 +0000)]
* 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 )
Heng Li [Fri, 12 Jun 2009 14:33:42 +0000 (14:33 +0000)]
update ChangeLog
Heng Li [Fri, 12 Jun 2009 14:21:21 +0000 (14:21 +0000)]
fixed minor things in Makefile
Heng Li [Fri, 12 Jun 2009 14:07:05 +0000 (14:07 +0000)]
* samtools-0.1.4-5 (r3310
* no change to samtools itself. Version number is increased to reflect the
changes in the Makefile building system.
Heng Li [Fri, 12 Jun 2009 14:03:38 +0000 (14:03 +0000)]
update information...
Heng Li [Fri, 12 Jun 2009 13:52:21 +0000 (13:52 +0000)]
* updated novoalign converter by Colin Hercus et al.
* this version works with indels
Heng Li [Fri, 12 Jun 2009 13:50:53 +0000 (13:50 +0000)]
* update Makefile
* update INSTALL instruction
Heng Li [Fri, 12 Jun 2009 13:18:29 +0000 (13:18 +0000)]
* added zlib-1.2.3 as razip requires that
* prepare to changed back to the Makefile building system
* unfinished! (will be soon)
Heng Li [Fri, 12 Jun 2009 13:12:03 +0000 (13:12 +0000)]
Unfinished
Heng Li [Wed, 10 Jun 2009 15:27:59 +0000 (15:27 +0000)]
* samtools-0.1.4-4 (r325)
* further avoid wrong consensus calls in repetitive regions.
Heng Li [Wed, 10 Jun 2009 14:56:17 +0000 (14:56 +0000)]
* samtools-0.1.4-3 (r324)
* make maqcns generate the correct call in repetitive regions.
* allow filtering on mapQ at the pileup command line
Heng Li [Wed, 10 Jun 2009 09:04:21 +0000 (09:04 +0000)]
* samtools.pl-0.3.2 (r322)
* indels and SNPs use different mapping quality threshold
Heng Li [Wed, 10 Jun 2009 09:03:22 +0000 (09:03 +0000)]
fixed a typo
Heng Li [Tue, 9 Jun 2009 08:21:48 +0000 (08:21 +0000)]
just typo. no real change
Heng Li [Mon, 8 Jun 2009 13:32:51 +0000 (13:32 +0000)]
a little bit code cleanup
Heng Li [Mon, 8 Jun 2009 13:22:33 +0000 (13:22 +0000)]
* samtools.pl-0.3.1
* change default parameters
* optionally print filtered variants
Heng Li [Mon, 8 Jun 2009 13:14:26 +0000 (13:14 +0000)]
* samtools.pl-0.3.0
* combine snpFilter and indelFilter
Heng Li [Mon, 8 Jun 2009 10:31:42 +0000 (10:31 +0000)]
* samtools.pl-0.2.3
* change a default parameter