7 Commits (de3ca65232db2fec1ef4eacf3badd71463ac2cba)

Author	SHA1	Message	Date
Khalid Shakir	de3ca65232	Bumping HTSJDK version to pickup a bug fix for CRAM.	2015-01-26 14:47:39 -03:00
Phillip Dexheimer	b73e9d506a	Added GATKVCFConstants and GATKVCFHeaderLines to consolidate the GATK-specific VCF annotations ... * Removed unused annotations (CCC and HWP) * Renamed one of the two GC annotations to "IGC" (for Interval GC) * Revved picard & htsjdk (GATK constants are now removed from htsjdk) * PT 82046038	2015-01-13 21:32:09 -05:00
Phillip Dexheimer	fc67e50faa	Revved Picard/htsjdk ... Removed inefficient array->List conversion in AlleleCountBySample	2014-10-30 21:16:25 -04:00
Phillip Dexheimer	b3b569f43a	Picard made major changes post-v1.123. Update our tools to handle them	2014-10-30 21:16:24 -04:00
Phillip Dexheimer	1482a53aba	Added -writeFullFormat engine-level argument ... * This argument forces GATK to always write every record in the VCF format field, even if some records at the end are missing and could be removed * Revved htsjdk and picard * PT 70993484	2014-09-17 08:25:27 -04:00
Laura Gauthier	4373922ee6	Update GATK to work with latest htsjdk ... ValidationStringency was moved from htsjdk.samtools.SAMFileReader to htsjdk.samtools samtools find BAM index file method was also moved (and made public!)	2014-07-30 12:05:14 -04:00
Khalid Shakir	cc3f1f2b96	Revved picard libraries. ... Third of four commits for picard/htsjdk package rename.	2014-05-08 19:13:27 +08:00