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gatk-3.8/public/java/test/org/broadinstitute/sting/gatk/walkers
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Mark DePristo ce3d1f89ea ReadShard are no longer allowed to span multiple contigs 
-- Previous behavior was unnecessary and causes all sorts of problems with RODs for reads.  The old implementation simply failed in this case.  The new code handles this correctly by forcing shards to have all of their data on a single contig.
-- Added a PrintReads integration test to ensure this behavior is correct
-- Adding test BAMs that have < 200 reads and span across contig boundaries
 		2012-08-30 10:15:11 -04:00
..
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 md5 in VariantRecalibrationWalkers test for BCF2 -- only encoding differences 2012-08-16 13:03:13 -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 Had some free time, so I unplugged extended events from the walkers. Now they exist only in LocusIteratorByState, but ReadProperties.generateExtendedEvents() always returns false so that block is never actually executed anymore. I don't want to touch LIBS because I think David is in there right now. 2012-04-02 14:27:36 -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