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gatk-3.8/public/java/test/org/broadinstitute/sting/gatk
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Eric Banks a7578e85e8 Rewriting a few of the indel integration tests for multi-allelics. The old tests were running b37 calls against a b36 reference, so the calls were all ref. The new tests are run against the pilot1 data and then those calls are fed back into the the same bam to test genotype given alleles, with a sprinkling of bi- and tri-allelics. 2012-03-16 14:21:27 -04:00
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datasources Avoid buffer underflow in GATKBAMIndex by detecting premature EOF in BAM indices 2012-03-08 15:30:44 -05:00
executive Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
filters Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
iterators a) Bug fix in calling new functions that give indel bases and length from regular pileup in LocusIteratorByState, b) Added unit test to cover these. 2012-02-25 13:57:28 -05:00
refdata Merge with master 2011-11-19 09:56:06 -05:00
report Revert "First implementation of GATKReportGatherer" 2012-02-08 23:28:55 -05:00
samples Added UnitTests for getFamilies() and getChildrenWithParents() 2011-12-09 15:57:07 +01:00
traversals First pass of the asynchronous block loader. 2011-11-18 15:02:59 -05:00
walkers Rewriting a few of the indel integration tests for multi-allelics. The old tests were running b37 calls against a b36 reference, so the calls were all ref. The new tests are run against the pilot1 data and then those calls are fed back into the the same bam to test genotype given alleles, with a sprinkling of bi- and tri-allelics. 2012-03-16 14:21:27 -04:00
EngineFeaturesIntegrationTest.java Bugfix for incorrect error messages for missing BAMs and VCFs 2012-01-23 09:52:07 -05:00
GenomeAnalysisEngineUnitTest.java Allow processing of empty intervals, but warn user when this case is encountered. 2011-10-28 12:12:14 -04:00
WalkerManagerUnitTest.java Moving more tools over to use the standard VC arg collection. Also, while I'm in there, I removed all of the empty references to @Requires given that it's no longer relevant. 2011-08-10 12:20:18 -04:00