sjia 98076db6b4 Modified CreatePedFileWalker to output PED file given HLA allele names ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1763 348d0f76-0448-11de-a6fe-93d51630548a		2009-10-05 03:06:42 +00:00
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alignment	Fixed bug where not all alignments were returned if read aligned to multiple locations. Enhanced test suite to validate all alignments.	2009-10-04 18:20:20 +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	Modified CreatePedFileWalker to output PED file given HLA allele names	2009-10-05 03:06:42 +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