kiran b6339967f8 Updated GenomicAnnotator integration tests to include the -NO_HEADER argument so that they tests op yelling about trtrivial differences ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5398 348d0f76-0448-11de-a6fe-93d51630548a		2011-03-07 23:07:01 +00:00
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annotator	Updated GenomicAnnotator integration tests to include the -NO_HEADER argument so that they tests op yelling about trtrivial differences	2011-03-07 23:07:01 +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	-ct x no longer includes coverage in the previous bin	2011-02-24 15:52:04 +00:00
fasta	Changing testing framework from junit -> testng, for its enhanced configurability.	2010-11-01 21:31:44 +00:00
filters	Adding integration test for indels in VF	2011-02-11 16:58:57 +00:00
genotyper	EMIT_ALL_SITES now does exactly that - even when there's no coverage or too many deletions	2011-03-01 05:05:00 +00:00
indels	Adding performance test for case with very high coverage (> 600,000x) over an interval	2011-02-28 19:48:56 +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 integration test to reflect changes regarding when comp tracks got subset to fewer samples and whether no-call sites would get pulled in for comp tracks.	2011-03-07 20:25:57 +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	Switched the CVUnitTest broken info from an Integer to a String since as of r5383 Integers are no longer broken when converted to Floats.	2011-03-07 16:33:14 +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