ebanks 1cde4161b7 Fixed another test ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2399 348d0f76-0448-11de-a6fe-93d51630548a		2009-12-18 05:05:03 +00:00
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annotator	1. Fixed VCFGenotypeRecord bug (it needs to emit fields in the order specified by the GenotypeFormatString)	2009-12-18 04:14:14 +00:00
concordance	I want to move over to hpprojects tonight, so I'm checking in various changes all in one go:	2009-12-13 02:52:18 +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	Fixed another test	2009-12-18 05:05:03 +00:00
genotyper	1. Fixed VCFGenotypeRecord bug (it needs to emit fields in the order specified by the GenotypeFormatString)	2009-12-18 04:14:14 +00:00
indels	fixing md5 sum; new version of IndelIntervalWalker does the right thing...	2009-12-17 01:04:13 +00:00
recalibration	Updating the two solid_recal_mode options to also change the previous base since solid aligner prefers single color mismatch alignments over true SNP alignments. COUNT_AS_MISMATCH mode has been removed completely. The default mode is now SET_Q_ZERO.	2009-12-17 20:07:26 +00:00
DepthOfCoverageIntegrationTest.java	- Moved various header line printing into a single method	2009-12-04 02:15:43 +00:00
PileupWalkerIntegrationTest.java	fixes for VariantAnnotations and second bases. Misc. removal of failing (and unstable) integration tests that require rereview	2009-12-02 15:41:35 +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