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gatk-3.8/public/java/test/org/broadinstitute/sting/gatk/walkers
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Mark DePristo 0892f2b8b2 Closing GSA-287:LocusReferenceView doesn't do very well in the case where contigs land off the end of the reference 
-- Confirmed that reads spanning off the end of the chromosome don't cause an exception by adding integration test for a single read that starts 7 bases from the end of chromosome 1 and spans 90 bases or so off.  Added pileup integration test to ensure this behavior continues to work
 		2012-09-03 20:18:56 -04:00
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CNV BCF2 with support symbolic alleles 2012-06-30 11:22:48 -04:00
annotator Update MD5s with new FS score 2012-08-28 08:06:47 -04:00
beagle Fixing remaining integration test errors. Adding missing ex2.bcf 2012-06-30 16:23:11 -04:00
bqsr Cleanup BQSR classes 2012-07-31 08:11:03 -04:00
coverage number of stashed changes are lurking in here. In order of importance: 2012-08-21 07:08:58 -04:00
diagnostics Fixing remaining integration test errors. Adding missing ex2.bcf 2012-06-30 16:23:11 -04:00
diffengine Cleanup of VCF header lines and constants, BCF2 bugfixes 2012-06-21 15:16:31 -04:00
fasta Several more walkers have been brought up to use the new Allele representation. 2012-07-27 02:14:25 -04:00
filters Integration test to ensure VariantFiltration makes . -> PASS/FAIL like VQSR 2012-07-25 08:56:39 -04:00
genotyper Update MD5s with new FS score 2012-08-28 08:06:47 -04:00
indels Cleanup of VCF header lines and constants, BCF2 bugfixes 2012-06-21 15:16:31 -04:00
phasing - Multi-allelic sites are now correctly ignored - Reporting of mendelian violations enhanced - Corrected TP overflow by caping it to Bye.MAX_VALUE 2012-07-17 15:21:10 -04:00
qc First version of VariantContextBuilder 2011-11-18 11:06:15 -05:00
validation Allele refactoring checkpoint #3: all integration tests except for PoolCaller are passing now. Fixed a couple of bugs from old code that popped up during md5 difference review. Added VariantContextUtils.requiresPaddingBase() method for tools that create alleles to use for determining whether or not to add the ref padding base. One of the HaplotypeCaller tests wasn't passing because of RankSumTest differences, so I added a TODO for Ryan to look into this. 2012-07-27 15:48:40 -04:00
varianteval In AlleleCount stratification, check to make sure the AC (or MLEAC) is valid (i.e. not higher than number of chromosomes) and throw a User Error if it isn't. Added a test for bad AC. 2012-08-14 15:02:30 -04:00
variantrecalibration Update md5s for VQSR, as VQSLOD is now a double and gets the standard double precision treatment in VCF 2012-08-30 19:41:49 -04:00
variantutils Fix for badIndelLength() throwing NPE at non-indel sites. Added integration test. 2012-08-25 12:38:23 -07:00
BAQIntegrationTest.java merge master 2011-10-25 16:08:39 -04:00
ClipReadsWalkersIntegrationTest.java Cleanup of VCF header lines and constants, BCF2 bugfixes 2012-06-21 15:16:31 -04:00
FlagStatIntegrationTest.java Adding integration test for Flag Stat 2012-04-10 22:40:38 -04:00
PileupWalkerIntegrationTest.java Closing GSA-287:LocusReferenceView doesn't do very well in the case where contigs land off the end of the reference 2012-09-03 20:18:56 -04:00
PrintReadsIntegrationTest.java ReadShard are no longer allowed to span multiple contigs 2012-08-30 10:15:11 -04:00
PrintReadsUnitTest.java Removed the "Walker" suffix from all walkers that had it. 2012-07-20 17:27:11 -04:00