ebanks 3091443dc7 Sweeping changes to the genotype output system, as per several discussions with Matt & Aaron. ... Some things still need to be changed, but it will entail some more design decisions first (which means I get to bug M&A again tomorrow!). git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1930 348d0f76-0448-11de-a6fe-93d51630548a		2009-10-29 03:46:41 +00:00
..
fasta	This class no longer outputs in sequenom format	2009-10-14 17:16:36 +00:00
filters	changes to VCF output, and updated MD5's in the integration tests	2009-10-14 18:42:48 +00:00
genotyper	Sweeping changes to the genotype output system, as per several discussions with Matt & Aaron.	2009-10-29 03:46:41 +00:00
indels	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
recalibration	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
DepthOfCoverageIntegrationTest.java	bug fixes to LIBS and LIBH following ultra-aggressive regression testing across 454, solid, and solexa	2009-09-09 15:36:12 +00:00
PrintReadsWalkerTest.java	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