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sambamba (0.4.7) unstable, urgency=low
* use random subdirectories for temporary files in both sort and markdup utilities
(allows to run multiple processes in parallel)
* fixed bug in slice tool: when slicing last reference, unmapped reads were written too
* fixed a bug in uncompressed BAM output
* fixed a bug in intersecting with BED
-- Artem Tarasov <lomereiter@gmail.com> Fri, 20 Jun 2014 16:27:19 +0400
sambamba (0.4.6) unstable, urgency=low
* fixed a bug in duplicate marking tool
* fixed handling empty BAM files in sort tool
-- Artem Tarasov <lomereiter@gmail.com> Mon, 28 Apr 2014 23:47:20 +0400
sambamba (0.4.5) unstable, urgency=low
* new -L option in the 'view' tool for intersecting a file with BED
* preventing incidental file overwrites by checking output filename
* slightly improved performance of converting to SAM/JSON
-- Artem Tarasov <lomereiter@gmail.com> Tue, 04 Feb 2014 10:57:21 +0400
sambamba (0.4.4) unstable, urgency=low
* fixed sorting by name which didn't work in recent releases
-- Artem Tarasov <lomereiter@gmail.com> Wed, 18 Dec 2013 20:38:39 +0400
sambamba (0.4.3) unstable, urgency=low
* improved sorting performance
* bug fixed in the 'sort' tool
* 'view' supports '*' region, '--unmapped' option removed
-- Artem Tarasov <lomereiter@gmail.com> Sun, 01 Dec 2013 17:11:42 +0400
sambamba (0.4.2) unstable; urgency=low
* new option '--unmapped' in view tool (for indexed BAMs)
* fixed an epic bug in region queries introduced in 0.4.1
-- Artem Tarasov <lomereiter@gmail.com> Thu, 14 Nov 2013 02:45:58 +0400
sambamba (0.4.1) unstable, urgency=low
* integrated new BAM reader (better scaling on multicore)
* `index` tool now collects optional statistics (for idxstats)
* fixed a bug with outputting SAM when requested JSON
-- Artem Tarasov <lomereiter@gmail.com> Wed, 30 Oct 2013 00:42:33 +0400
sambamba (0.4.0) unstable; urgency=low
* added tool for marking duplicates, which uses Picard criteria
-- Artem Tarasov <lomereiter@gmail.com> Wed, 02 Oct 2013 23:07:14 +0400
sambamba (0.3.3) unstable; urgency=low
* reduced buffer size for uncompressed BAM output
so that it is less than pipe buffer size
* added subsampling option to sambamba view
-- Artem Tarasov <lomereiter@gmail.com> Sat, 13 Jul 2013 16:27:25 +0400
sambamba (0.3.2) unstable; urgency=low
* fixed bug in flagstat parameter parsing
* consistent naming for number of threads in CLI
-- Artem Tarasov <lomereiter@gmail.com> Tue, 16 Apr 2013 09:23:35 +0400
sambamba (0.3.1) unstable; urgency=low
* numerous bugfixes
* now requires at least v2.061 of D compiler
-- Artem Tarasov <lomereiter@gmail.com> Sun, 11 Mar 2013 01:03:17 +0400
sambamba (0.3.0) unstable; urgency=low
* new command line tool -- sambamba-slice
* several minor bugfixes
* compiles with LDC2
-- Artem Tarasov <lomereiter@gmail.com> Wed, 12 Dec 2012 22:57:12 +0400
sambamba (0.2.9) unstable; urgency=low
* random access speedup
-- Artem Tarasov <lomereiter@gmail.com> Sun, 08 Oct 2012 01:39:26 +0400
sambamba (0.2.8) unstable; urgency=low
* fix segfault on opening unexistent file
* fix random-access for files >2GB
-- Artem Tarasov <lomereiter@gmail.com> Wed, 26 Sep 2012 17:17:03 +0400
sambamba (0.2.7) unstable; urgency=low
* fix a stupid bug related to determining end of file
* add support for BAM files of size > 2GB (workaround for Phobos bug)
-- Artem Tarasov <lomereiter@gmail.com> Sun, 16 Sep 2012 14:45:09 +0400
sambamba (0.2.6) unstable; urgency=low
* add output in MessagePack format to sambamba-view
-- Artem Tarasov <lomereiter@gmail.com> Sun, 19 Aug 2012 19:42:48 +0400
sambamba (0.2.5) unstable; urgency=low
* fix bug in indexing (worked correctly for < 73Mbp long references)
-- Artem Tarasov <lomereiter@gmail.com> Sat, 18 Aug 2012 20:02:12 +0400
sambamba (0.2.4) unstable; urgency=low
* fix bug about outputting header to a file in SAM/JSON output
* consistent use of stderr for error messages and usage information
-- Artem Tarasov <lomereiter@gmail.com> Tue, 14 Aug 2012 21:31:52 +0400
sambamba (0.2.3) unstable; urgency=low
* fix bug in BAM output
* support for non-seekable streams (pipes, stdin/stdout)
-- Artem Tarasov <lomereiter@gmail.com> Sat, 11 Aug 2012 16:20:44 +0400
sambamba (0.2.1) unstable; urgency=low
* Initial release
-- Artem Tarasov <lomereiter@gmail.com> Tue, 7 Aug 2012 17:51:11 +0400
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