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gatk-3.8/java/test/org/broadinstitute/sting/gatk/walkers
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chartl 21a9a717e4 Some minor changes and test: 
- DepthOfCoverage is now by reference (so locus-by-locus output correctly reports zero-coverage bases)
  - VariantsToVCF now lets you bind variants with any string except intervals and dbsnp (not just NA######)
  - A PileupWalker integration test on a particularly nasty FHS site
  - Two second-base annotation related integration tests on that same site
       + outputs were all hand-validated in matlab; within a certain tolerance for the annotations




git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2197 348d0f76-0448-11de-a6fe-93d51630548a
 		2009-12-01 15:15:54 +00:00
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annotator Some minor changes and test: 2009-12-01 15:15:54 +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 Use Math.abs so we don't get (inconsistent) -0's 2009-11-25 19:08:34 +00:00
indels Another case of reordering of read groups blowing up checksums. 2009-11-13 00:07:35 +00:00
recalibration Changed the format of the recalibration csv file slightly so that it is easier to load the file into something like R and look at the values of the covariates. 2009-11-30 17:55:23 +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
PileupWalkerIntegrationTest.java Some minor changes and test: 2009-12-01 15:15:54 +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