ebanks 2fa2ae43ec Enough people have found this useful, so... ... Moving Callset Concordance tool to core and adding integration test. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2003 348d0f76-0448-11de-a6fe-93d51630548a		2009-11-09 20:59:18 +00:00
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concordance	Enough people have found this useful, so...	2009-11-09 20:59:18 +00:00
fasta	a fix for a bug Andrey discovered: in read-based interval traversals we're dupplicating reads in rare cases. The problem was that to accomidate a bug in SAM JDK indexing, we were forced to add one to the stop of our QueryOverlapping() calls to ensure we always got all of the overlapping reads.	2009-11-05 05:26:33 +00:00
filters	changes to VCF output, and updated MD5's in the integration tests	2009-10-14 18:42:48 +00:00
genotyper	Added optional field DP to VCF output for Mark.	2009-11-06 20:03:22 +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