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git.donarmstrong.com Git - samtools.git/log
Heng Li [Sat, 25 Apr 2009 10:49:40 +0000 (10:49 +0000)]
* samtools-0.1.3-6 (r244)
* fixed segfault for unmapped reads
Heng Li [Fri, 24 Apr 2009 20:27:26 +0000 (20:27 +0000)]
* samtools-0.1.3-5 (r243)
* fixed a long existing bug which may cause memory leak
* check MD
* consensus calling now works with "=", but indel calling not
Heng Li [Fri, 24 Apr 2009 19:44:46 +0000 (19:44 +0000)]
* samtools-0.1.3-4 (r242)
* fixed a memory leak
Heng Li [Fri, 24 Apr 2009 15:40:18 +0000 (15:40 +0000)]
* samtools-0.1.3-3 (r240)
* generate MD tag
* generate "=" bases
* the plain pileup now support "=" bases, but consensus calling and glfgen may fail
Heng Li [Fri, 24 Apr 2009 11:08:20 +0000 (11:08 +0000)]
* samtools-0.1.3-2 (r239)
* fixed bugs in bam_aux.c (these functions nevered used by samtools)
* removed bam_aux_init()/bam_aux_destroy()
* added tagview for testing bam_aux
Heng Li [Tue, 21 Apr 2009 22:17:39 +0000 (22:17 +0000)]
* samtools-0.1.3-1
* fixed a bug in pileup: the first read in a chromosome may not be printed
Heng Li [Thu, 16 Apr 2009 14:25:43 +0000 (14:25 +0000)]
a missing file in Makefile.lite
Heng Li [Wed, 15 Apr 2009 21:02:53 +0000 (21:02 +0000)]
Release samtools-0.1.3
Heng Li [Wed, 15 Apr 2009 13:31:32 +0000 (13:31 +0000)]
* samtools-0.1.2-28
* make samtools more robust to weird input such as empty file
Heng Li [Wed, 15 Apr 2009 13:05:33 +0000 (13:05 +0000)]
prepare for release 0.1.3
Heng Li [Wed, 15 Apr 2009 12:32:14 +0000 (12:32 +0000)]
convert NCBI-BLASTN to SAM
Heng Li [Wed, 15 Apr 2009 12:18:19 +0000 (12:18 +0000)]
* samtools-0.1.2-27
* fixed a small memory leak in tview
Heng Li [Wed, 15 Apr 2009 12:00:08 +0000 (12:00 +0000)]
* samtools-0.1.2-26
* fixed a bug in rmdup when there are unmapped reads
Heng Li [Tue, 14 Apr 2009 21:28:58 +0000 (21:28 +0000)]
proposed NEWS for the new release (have not yet)
Heng Li [Tue, 14 Apr 2009 21:10:46 +0000 (21:10 +0000)]
* samtools.pl-0.1.1
* improve indelFilter to avoid filtering true indels. The new filter relies
on the new pileup indel line implemented in samtools-0.1.2-25
Heng Li [Tue, 14 Apr 2009 21:04:19 +0000 (21:04 +0000)]
* samtools-0.1.2-25
* change the pileup indel line to shows the number of alignments actually
containing indels
Heng Li [Mon, 13 Apr 2009 11:07:13 +0000 (11:07 +0000)]
update ChangeLog from "svn log"
Heng Li [Sun, 12 Apr 2009 19:57:05 +0000 (19:57 +0000)]
* samtools-0.1.2-24
* in merge, gives a warning rather than error if the target sequence length is different
* allow empty header
Heng Li [Sun, 12 Apr 2009 19:32:44 +0000 (19:32 +0000)]
* samtools-0.1.2-23
* recognize '*' at the QUAL field
Heng Li [Sun, 12 Apr 2009 19:08:02 +0000 (19:08 +0000)]
* samtools-0.1.2-22
* the field separater is TAB only, now
Heng Li [Wed, 8 Apr 2009 14:18:03 +0000 (14:18 +0000)]
* fixed the problem in the example alignment due to the bug in fixmate
Heng Li [Wed, 8 Apr 2009 14:15:05 +0000 (14:15 +0000)]
* samtools-0.1.2-21
* fixed a nasty bug in `fixmate'
Heng Li [Wed, 8 Apr 2009 09:57:08 +0000 (09:57 +0000)]
make the script robust to the bugs in SOAP-2.1.7
Heng Li [Thu, 2 Apr 2009 14:14:56 +0000 (14:14 +0000)]
* samtools-0.1.2-20
* check if file is truncated in flagstat
Heng Li [Thu, 2 Apr 2009 14:09:10 +0000 (14:09 +0000)]
* samtools-0.1.2-19
* print the header if requested
Heng Li [Fri, 27 Mar 2009 15:09:50 +0000 (15:09 +0000)]
* samtools-0.1.2-18
* fixed a minor bug reported by Nils Homer
Heng Li [Tue, 24 Mar 2009 11:50:32 +0000 (11:50 +0000)]
rename Makefile.std as Makefile. GNU building systerm is not ready and may take some time...
Heng Li [Tue, 24 Mar 2009 10:36:38 +0000 (10:36 +0000)]
* samtools-0.1.2-17
* incorporating Nils' changes
* rename Makefile to Makefile.std and prepare to add the GNU building systerms (also by Nils)
Heng Li [Tue, 24 Mar 2009 10:30:23 +0000 (10:30 +0000)]
* samtools-0.1.2-16
* made pileup take a list of proposed indels. An insertion is N at the moment.
* added my kstring library for a bit complex parsing of the position list.
Heng Li [Thu, 12 Mar 2009 13:40:14 +0000 (13:40 +0000)]
* soap2sam.pl-0.1.2
* more robust to truncated soap output
Heng Li [Wed, 11 Mar 2009 10:49:00 +0000 (10:49 +0000)]
added bam_stat.o to Makefile.lite
Heng Li [Tue, 10 Mar 2009 22:11:31 +0000 (22:11 +0000)]
* samtools-0.1.2-15
* generate RMS of mapQ instead of max mapQ
Heng Li [Tue, 10 Mar 2009 22:06:45 +0000 (22:06 +0000)]
* samtools-0.1.2-14
* implemented GLFv3
Heng Li [Tue, 3 Mar 2009 11:26:08 +0000 (11:26 +0000)]
* samtools-0.1.2-13
* fixed a minor bug in displaying pileup
Heng Li [Tue, 3 Mar 2009 11:24:16 +0000 (11:24 +0000)]
* samtools-0.1.2-12
* optionally print SAM header
Heng Li [Mon, 2 Mar 2009 10:45:28 +0000 (10:45 +0000)]
* samtools-0.1.2-11
* use "GLF\3" as the magic for GLFv3 files
Heng Li [Mon, 2 Mar 2009 10:39:09 +0000 (10:39 +0000)]
* samtools-0.1.2-10
* fixed a bug in import: core.bin is undefined for unmapped reads
* this bug can be alleviated (not completely solved) in bam_index.c
* update to GLFv3: pos is changed to offset for better compression
Heng Li [Sun, 1 Mar 2009 15:18:43 +0000 (15:18 +0000)]
* wgsim-0.2.3
* fixed a bug in simulating indels
Heng Li [Thu, 26 Feb 2009 19:43:57 +0000 (19:43 +0000)]
* wgsim-0.2.2
* allow to print mismatch information as fastq comment. MAQ does
not like long read names.
Heng Li [Thu, 26 Feb 2009 14:53:03 +0000 (14:53 +0000)]
* wgsim-0.2.1
* fixed a bug about color read coordinates
* fixed a bug in read names
* wgsim_eval.pl-0.1.3
* make the script work with color reads
Heng Li [Thu, 26 Feb 2009 14:02:57 +0000 (14:02 +0000)]
* wgsim: added a note
Heng Li [Thu, 26 Feb 2009 11:39:08 +0000 (11:39 +0000)]
* wgsim-0.2.0
* considerable code clean up
* print number of substitutions/indels/errors on each read
* potentially support SOLiD simulation, though not tested at the moment
* wgsim_eval.pl-0.1.2
* change in accordant with wgsim
Heng Li [Wed, 18 Feb 2009 22:23:27 +0000 (22:23 +0000)]
* samtools-0.1.2-9
* fixed a bug in bam_fetch, caused by completely contained adjacent chunks
On behalf of Bob Handsaker [Wed, 18 Feb 2009 19:06:57 +0000 (19:06 +0000)]
Fix annoying segv when invalid region specified.
Heng Li [Tue, 17 Feb 2009 10:49:55 +0000 (10:49 +0000)]
* move indel_filter.pl to samtools.pl
Heng Li [Sat, 14 Feb 2009 21:22:30 +0000 (21:22 +0000)]
* samtools-0.1.2-7
* fixed a bug in fixmate: SE reads are flagged as BAM_FMUNMAP
Heng Li [Fri, 13 Feb 2009 09:54:45 +0000 (09:54 +0000)]
* samtools-0.1.2-7
* fixed a minor bug in flagstat
Heng Li [Thu, 12 Feb 2009 11:15:32 +0000 (11:15 +0000)]
* samtools-0.1.2-6
* improve indel caller by setting maximum window size
Heng Li [Thu, 12 Feb 2009 10:30:29 +0000 (10:30 +0000)]
* output max mapping quality in indel line
Heng Li [Wed, 11 Feb 2009 10:59:10 +0000 (10:59 +0000)]
fixed a bug in generating tag AM
Heng Li [Tue, 3 Feb 2009 10:43:11 +0000 (10:43 +0000)]
fixed a potential memory problem in indexing
On behalf of Bob Handsaker [Mon, 2 Feb 2009 15:52:52 +0000 (15:52 +0000)]
Pass LIBS to recursive targets to facilitate building at Broad.
Heng Li [Mon, 2 Feb 2009 10:12:15 +0000 (10:12 +0000)]
* samtools-0.1.2-3
* fixed a bug in generating GLFv2 for indels
* improve flagstat report a little bit
Heng Li [Thu, 29 Jan 2009 12:33:23 +0000 (12:33 +0000)]
* samtools-0.1.2-1
* added flagstat command
Heng Li [Wed, 28 Jan 2009 13:31:12 +0000 (13:31 +0000)]
Release SAMtools-0.1.2
Heng Li [Wed, 28 Jan 2009 12:54:08 +0000 (12:54 +0000)]
Script for filtering indel results
Heng Li [Sun, 25 Jan 2009 11:45:37 +0000 (11:45 +0000)]
convert ZOOM to SAM
Heng Li [Sat, 24 Jan 2009 14:25:07 +0000 (14:25 +0000)]
add a script to convert novo alignment to SAM
Heng Li [Fri, 23 Jan 2009 20:57:39 +0000 (20:57 +0000)]
update documentation and ChangeLog
Heng Li [Fri, 23 Jan 2009 19:22:59 +0000 (19:22 +0000)]
* samtools-0.1.1-19
* fixed a bug in "merge" command line
Heng Li [Thu, 22 Jan 2009 15:36:48 +0000 (15:36 +0000)]
* merge from branches/dev/
* all future development will happen here
Heng Li [Thu, 22 Jan 2009 15:14:27 +0000 (15:14 +0000)]
* Merge from branches/dev/
* all future development will happen here at trunk/
On behalf of Bob Handsaker [Wed, 7 Jan 2009 21:42:15 +0000 (21:42 +0000)]
Fix problem with compiling without curses.
Heng Li [Mon, 22 Dec 2008 15:58:02 +0000 (15:58 +0000)]
Create trunk copy