chartl 88d0890cc3 Made PooledGenotypeConcordance a standard test in VariantEval ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1759 348d0f76-0448-11de-a6fe-93d51630548a		2009-10-02 20:03:31 +00:00
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alignment	Support negative strand alignments.	2009-09-30 18:10:26 +00:00
gatk	A big fix for MergingSamRecordIterator, where we weren't correctly handling the comparisons of SAMRecords correctly (we weren't applying the new reference index first, so sometimes the MT contig would be ID 23, sometimes 24 in different records).	2009-10-02 19:35:35 +00:00
playground	Made PooledGenotypeConcordance a standard test in VariantEval	2009-10-02 20:03:31 +00:00
secondarybase	Rev'ing Picard, which includes the update to get all the reads in the query region (GSA-173). With it come a bunch of fixes, including retiring the FourBaseRecaller code, and updated md5 for some walker tests.	2009-09-30 20:37:59 +00:00
utils	changes for corrected GLF likelihood output, along with better tests	2009-10-01 20:45:05 +00:00