rpoplin 30a19a00fe Fix for when running with EMIT_ALL_SITES but not GENOTYPE_GIVEN_ALLELES. Still want to emit a site even when over the deletion fraction for example. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5617 348d0f76-0448-11de-a6fe-93d51630548a		2011-04-12 20:07:06 +00:00
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annotator	Updating to reflect my recent Tribble fix	2011-04-08 11:48:00 +00:00
beagle	Checked for consistency with the previous integration tests, and updated the walker and test to use the new I/O system (always prints 4 digits on floats.	2011-03-13 15:24:22 +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	Fix for when running with EMIT_ALL_SITES but not GENOTYPE_GIVEN_ALLELES. Still want to emit a site even when over the deletion fraction for example.	2011-04-12 20:07:06 +00:00
indels	As I threatened yesterday, I've moved the various and disparate randomization code out of the walkers. Now they all (except VQSRv1, whose days are numbered anyways) use a static generator available in the engine itself. Please use this from now on. The seed is reset before every individual integration test is run. I think there may still be an issue with the IndelRealigner but I need to confirm with the commit to see what testNG does. Integration tests are already broken anyways, so no big deal.	2011-04-07 17:03:48 +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	As I threatened yesterday, I've moved the various and disparate randomization code out of the walkers. Now they all (except VQSRv1, whose days are numbered anyways) use a static generator available in the engine itself. Please use this from now on. The seed is reset before every individual integration test is run. I think there may still be an issue with the IndelRealigner but I need to confirm with the commit to see what testNG does. Integration tests are already broken anyways, so no big deal.	2011-04-07 17:03:48 +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	A better output for Genotype Concordance summary. Now does only % comp hom-ref called hom-ref, het called het, and hom-var called hom-var, which are the quantities we typically show in slides. Updated intergration tests to reflect this change.	2011-03-12 02:03:48 +00:00
variantrecalibration	Minor bug fix in empiricalMu prior calculation in VQSR.	2011-03-10 00:42:38 +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	Updated to now longer include 2nd-best base output	2011-04-03 20:13:10 +00:00
PrintReadsIntegrationTest.java	--simplifyBAM is now in the SAMFileWriterArgumentTypeDescriptor, as suggested by map. PrintReads has an integrationtest now that writes out a 1 MB bit of HiSeq normally, with compress 0, and with simplifyBAM on.	2011-03-26 14:57:18 +00:00
PrintReadsWalkerUnitTest.java	Changing testing framework from junit -> testng, for its enhanced configurability.	2010-11-01 21:31:44 +00:00