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gatk-3.8/public/java/test/org/broadinstitute/sting/utils
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Ryan Poplin dda2173c66 Moved the Smith-Watermaning of haplotypes to earlier in the process so that alleles sent to genotyping would have the exact genomic sequence of the active region they represent. As a side effect cleaned up some edge case problems with variants, both real and false, which show up on the edges of active regions. Removed code that was replicated between the Haplotype class and ReadUtils. Finally figured out how to ensure that the indel calls coming out of the HC were left aligned. 2012-04-04 16:04:29 -04:00
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R No more hunting down R "resources". As a tradeoff Rscript cannot be specified on the commandline and will be found in the environment path. 2011-10-27 14:17:07 -04:00
activeregion BQSR Gatherer implementation and integration tests 2012-03-27 13:50:22 -05:00
baq Putative fix for BAQ array out of bounds 2011-09-21 11:25:08 -04:00
clipping Add support for reads starting with insertion 2012-01-03 09:29:45 -05:00
codecs Adding test for reading samtools VCF file 2012-02-27 17:05:50 -05:00
collections Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
crypt Do not fail tests that require the GATK private key if the user does not have permission to read it 2012-03-06 15:57:02 -05:00
fasta Reduced the number of combinations being tested here, which was overkill 2011-09-01 10:42:43 -04:00
fragments GATKSAMRecord refactor 2011-11-03 15:43:26 -04:00
genotype/vcf Change interface to getNegLog10PError to getLog10PError 2011-11-18 21:07:30 -05:00
interval When constructing VariantContexts from symbolic alleles, check for the END tag in the INFO field; if present, set the stop position of the VC accordingly. Added integration test to ensure that this is working properly for use with -L intervals. 2012-04-04 10:57:05 -04:00
io Public-key authorization scheme to restrict use of NO_ET 2012-03-06 00:09:43 -05:00
pileup GATKSAMRecord refactor 2011-11-03 15:43:26 -04:00
recalibration BQSR with GATKReport implementation 2012-03-23 15:42:32 -04:00
report Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
runtime No more hunting down R "resources". As a tradeoff Rscript cannot be specified on the commandline and will be found in the environment path. 2011-10-27 14:17:07 -04:00
sam BitSet implementation of the on-the-fly recalibration using the CSV format file. 2012-03-16 13:02:15 -04:00
text GATKReport v0.2: 2011-08-03 00:24:47 -04:00
threading Removed GATK use of distributed parallelism framework. 2011-07-20 16:26:09 -04:00
variantcontext Fix up broken non-pool UG tests: GenotypeLikelihoods.calcNumLikelihoods now expects total # of alleles, not # of alt ones. Add doc to new function implementation. Add unit test for function. Add unit test for PoolGenotypeLikelihoods (not fully done yet) 2012-04-03 20:51:24 -04:00
BaseUtilsUnitTest.java Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
BitSetUtilsUnitTest.java BitSets keys to lower BQSR's memory footprint 2012-03-16 13:01:48 -04:00
GenomeLocParserUnitTest.java During flanking interval creation merging overlapping flanks so that on scatter the list doesn't accidentally genotype the same site twice. 2011-11-17 13:56:42 -05:00
GenomeLocSortedSetUnitTest.java Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
GenomeLocUnitTest.java Support for list of known CNVs in VariantEval 2011-11-30 17:05:16 -05:00
HaplotypeUnitTest.java Moved the Smith-Watermaning of haplotypes to earlier in the process so that alleles sent to genotyping would have the exact genomic sequence of the active region they represent. As a side effect cleaned up some edge case problems with variants, both real and false, which show up on the edges of active regions. Removed code that was replicated between the Haplotype class and ReadUtils. Finally figured out how to ensure that the indel calls coming out of the HC were left aligned. 2012-04-04 16:04:29 -04:00
MWUnitTest.java Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
MathUtilsUnitTest.java Forgot to add tolerance to new MathUtils unit tests 2012-03-28 08:18:36 -04:00
PathUtilsUnitTest.java Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
QualityUtilsUnitTest.java Caching log calculations cut the non-Map runtime of HaplotypeCaller in half. Moved the qual log cache used in HC and PairHMM into a common place and added unit tests. 2012-03-21 08:45:42 -04:00
ReservoirDownsamplerUnitTest.java Moving reduced read functionality into GATKSAMRecord 2011-10-21 13:28:05 -04:00
SimpleTimerUnitTest.java The right fix for this test is just to delete it. 2011-11-15 14:53:27 -05:00
UtilsUnitTest.java Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00