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 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 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 [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, 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 [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 [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 [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 [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 [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 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 [Mon, 18 May 2009 20:01:23 +0000 (20:01 +0000)]
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.
Heng Li [Wed, 13 May 2009 09:07:55 +0000 (09:07 +0000)]
* 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