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gatk-3.8/java/test/org/broadinstitute/sting/gatk/walkers
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hanna aea121a9d5 <key>=<value> tagging support for command-line arguments. Unfortunately, still 
very hard to validate and still very hard to use (requires core hacking to 
support additional tags).


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5038 348d0f76-0448-11de-a6fe-93d51630548a
 		2011-01-21 00:22:42 +00:00
..
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 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
coverage Changing testing framework from junit -> testng, for its enhanced configurability. 2010-11-01 21:31:44 +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 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
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 Changing testing framework from junit -> testng, for its enhanced configurability. 2010-11-01 21:31:44 +00:00
varianteval 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
variantrecalibration Removed LibBat.SUB2_BSUB_BLOCK since the use of it exits the JVM. 2010-12-14 19:57:20 +00:00
variantutils <key>=<value> tagging support for command-line arguments. Unfortunately, still 2011-01-21 00:22:42 +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