kiran 1085bbf303 Fixed issue where all comp tracks were being treated as known tracks. Fixed issue where multiple JEXL expressions were causing an exception because the underlying object did not implement the Comparable interface. Fixed issue where variants being compared to the known track were not being checked for equality of variation type. Fixed issue where functional annotations were not being iterated over properly. Refactored a lot of helper methods into a separate VariantEvalUtils utility class. Significantly expanded the test suite using a small VCF with SNPs, indels, and non-variant loci which makes it much easier to see what the proper answer should be, and included the appropriate grep and awk commands in the comments to confirm the values. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5204 348d0f76-0448-11de-a6fe-93d51630548a		2011-02-06 19:19:20 +00:00
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annotator	Reverting back to the old definition of QD because it works better with large numbers of samples. The new QD is relegated to a new annotation: sumGLbyD. Tweaks to the new HaplotypeScore based on evaluation with better QD calculation. The default qual threshold in GenerateVariantClusters is updated to be in line with the variant quality scores coming from the exact model.	2011-01-13 14:12:30 +00:00
beagle	There's no reason to special case no-calls if they already have PLs associated with them. Just use the PLs!	2011-01-31 15:05:45 +00:00
coverage	More testng fallout: fixing another seemingly 'random' issue arising from an	2011-02-01 15:25:50 +00:00
fasta	Changing testing framework from junit -> testng, for its enhanced configurability.	2010-11-01 21:31:44 +00:00
filters	Remove the extra trailing tab at the end of the VCF ## header line. Unfortunately, this meant updating every freaking integration test.	2010-12-08 17:22:29 +00:00
genotyper	added integration test for --sites_only option	2011-01-26 14:58:15 +00:00
indels	Changing testing framework from junit -> testng, for its enhanced configurability.	2010-11-01 21:31:44 +00:00
phasing	Remove the extra trailing tab at the end of the VCF ## header line. Unfortunately, this meant updating every freaking integration test.	2010-12-08 17:22:29 +00:00
qc	Changing testing framework from junit -> testng, for its enhanced configurability.	2010-11-01 21:31:44 +00:00
recalibration	Bug fix in CountCovariates, skip over indel records as well as SNPs in the dbsnp file. CountCovariates is now called CountCovariatesWalker. I've always hated that the name was swapped.	2010-12-02 18:43:24 +00:00
sequenom	Updated integration test's MD5s reflect the fact that assay sequences were previously designed incorrectly for indels, the bug is now fixed.	2011-01-28 23:00:22 +00:00
varianteval	Fixed issue where all comp tracks were being treated as known tracks. Fixed issue where multiple JEXL expressions were causing an exception because the underlying object did not implement the Comparable interface. Fixed issue where variants being compared to the known track were not being checked for equality of variation type. Fixed issue where functional annotations were not being iterated over properly. Refactored a lot of helper methods into a separate VariantEvalUtils utility class. Significantly expanded the test suite using a small VCF with SNPs, indels, and non-variant loci which makes it much easier to see what the proper answer should be, and included the appropriate grep and awk commands in the comments to confirm the values.	2011-02-06 19:19:20 +00:00
variantrecalibration	Removed LibBat.SUB2_BSUB_BLOCK since the use of it exits the JVM.	2010-12-14 19:57:20 +00:00
variantutils	Pulled out CpG stratification in test results at Kiran's suggestion.	2011-02-01 18:36:09 +00:00
BAQIntegrationTest.java	Better query start / stop function that directly parses the cigar string, unlike the previous version. Now properly handles H (hard-clipped) reads. Added -baq OFF and -baq RECALCULATE integration tests on all three 1KG technologies. Please let me know if this new code somehow fails.	2011-01-28 15:08:21 +00:00
ClipReadsWalkersIntegrationTest.java	Changing testing framework from junit -> testng, for its enhanced configurability.	2010-11-01 21:31:44 +00:00
PileupWalkerIntegrationTest.java	Changing testing framework from junit -> testng, for its enhanced configurability.	2010-11-01 21:31:44 +00:00
PrintReadsWalkerUnitTest.java	Changing testing framework from junit -> testng, for its enhanced configurability.	2010-11-01 21:31:44 +00:00
VariantsToVCFIntegrationTest.java	Support for indels in hapmap. This was non-trivial because not only does hapmap not tell you whether the allele is an insertion or deletion, but it also has a completely different positioning strategy (rightmost base). I'll send out an email tomorrow when the new HapMap3.3 VCF is ready.	2010-12-27 07:37:46 +00:00