gatk-3.8/public/java/test/org/broadinstitute/sting/gatk
Mark DePristo 6df96644d9 Unified, standard IndelSummary metrics for VariantEval
-- Now you always get SNP and indel metrics with VariantEval!
--   Includes Number of SNPs, Number of singleton SNPs, Number of Indels, Number of singleton Indels, Percent of indel sites that are multi-allelic, SNP to indel ratio, Singleton SNP to indel ratio, Indel novelty rate, 1 to 2 bp indel ratio, 1 to 3 bp indel ratio, 2 to 3 bp indel ratio, 1 and 2 to 3 bp indel ratio, Frameshift percent, Insertion to deletion ratio, Insertion to deletion ratio for 1 bp events, Number of indels in protein-coding regions labeled as frameshift, Number of indels in protein-coding regions not labeled as frameshift, Het to hom ratio for SNPs, Het to hom ratio for indels, a Histogram of indel lengths, Number of large (>10 bp) deletions, Number of large (>10 bp) insertions, Ratio of large (>10 bp) insertions to deletions
-- Updated VE integration tests as appropriate
2012-03-22 21:24:37 -04:00
..
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 Taking care of bad cigars in the GATK 2012-03-20 14:32:57 -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 GATK Report code cleanup 2012-03-19 11:53:57 -04:00
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 Unified, standard IndelSummary metrics for VariantEval 2012-03-22 21:24:37 -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