ebanks 08f2214f14 Stage 1 of massive Variation/Genotype refactoring. ... This stage consists only of the code originating in the Genotyper and flowing through to the genotype writers. I haven't finished refactoring the writers and haven't even touched the readers at all. The major changes here are that 1. Variations which are BackedByGenotypes are now correctly associated with those Genotypes 2. Genotypes which have an associated Variation can actually be associated with it (and then return it when toVariation() is called). The only integration tests which need to be updated are MSG-related (because the refactoring now made it easy for me to prevent MSG from emitting tri-allelic sites). git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2269 348d0f76-0448-11de-a6fe-93d51630548a		2009-12-06 03:12:41 +00:00
..
annotator	- All annotations are now required to return their VCF INFO keys and descriptions	2009-12-02 17:24:06 +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	Stage 1 of massive Variation/Genotype refactoring.	2009-12-06 03:12:41 +00:00
indels	Another case of reordering of read groups blowing up checksums.	2009-11-13 00:07:35 +00:00
recalibration	Eliminated unnecessary boxing of longs in RecalDatum. Changes to RecalDatum in preparation for new AnalyzeCovariates script. Updated TableRecalibrationWalker to make use of these changes.	2009-12-01 16:49:05 +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