ebanks 3484f652e7 1. Variation is now passed to VariantAnnotator along with the List of Genotypes so non-genotype calls has access to all relevant info. ... 2. Killed OnOffGenoype 3. SpanningDeletions is now SpanningDeletionFraction git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2151 348d0f76-0448-11de-a6fe-93d51630548a		2009-11-24 21:47:20 +00:00
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annotator	1. Variation is now passed to VariantAnnotator along with the List of Genotypes so non-genotype calls has access to all relevant info.	2009-11-24 21:47:20 +00:00
concordance	Fixed the sample mix-up bug Kiran discovered, and added a unit test in the VCF reader class (Thanks for the good example files Kiran). Also renamed the toStringRepresentation function to toStringEncoding, and added a matching method in VCFGenotypeRecord.	2009-11-19 18:17:47 +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	-Added VariantFiltration integration tests	2009-11-24 02:36:27 +00:00
genotyper	1. Variation is now passed to VariantAnnotator along with the List of Genotypes so non-genotype calls has access to all relevant info.	2009-11-24 21:47:20 +00:00
indels	Another case of reordering of read groups blowing up checksums.	2009-11-13 00:07:35 +00:00
recalibration	BAM files created by TableRecalibration now have the version number and list of covariates used appended to their header with a new 'PG' tag. Eventually the entire list of command line args will be put in there as well. Big thanks to Matt and Aaron. The integration test uses the --no_pg_tag so that the md5 doesn't change every time the version number changes.	2009-11-24 20:53:57 +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