delangel 600617a63c Enabled code to deal with hard-clipping adaptor sequence when processing reads in pileup in indel caller. Proven now that changes are minimal (4 less calls in NA12878 chr20, quals slightly different), minor changes in vcf fields in integration tests. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5679 348d0f76-0448-11de-a6fe-93d51630548a		2011-04-22 14:10:33 +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	Enabled code to deal with hard-clipping adaptor sequence when processing reads in pileup in indel caller. Proven now that changes are minimal (4 less calls in NA12878 chr20, quals slightly different), minor changes in vcf fields in integration tests.	2011-04-22 14:10:33 +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	My fixes to Tribble yesterday revealed that some of the test VCFs for integration tests were actually malformed. Also, Guillermo updated the b37 dbSNP VCF and that broke some tests. Should be good for now.	2011-04-17 03:39:11 +00:00
variantrecalibration	Minor bug fix in empiricalMu prior calculation in VQSR.	2011-03-10 00:42:38 +00:00
variantutils	VariantsToTable now blows up by default if you ask for a field that isn't present in a record.	2011-04-14 14:42:43 +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