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gatk-3.8/public/java/test/org/broadinstitute/sting/utils
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Mauricio Carneiro 5af373a3a1 BQSR with indels integrated! 
* added support to base before deletion in the pileup
   * refactored covariates to operate on mismatches, insertions and deletions at the same time
   * all code is in private so original BQSR is still working as usual in public
   * outputs a molten CSV with mismatches, insertions and deletions, time to play!
   * barely tested, passes my very simple tests... haven't tested edge cases.
 		2012-02-09 18:46:45 -05:00
..
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
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 UnitTest for reverseAlleleClipping 2012-01-18 07:35:11 -05:00
collections Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
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 make the size of a GenomeLoc int instead of long 2012-02-03 17:12:42 -05:00
io Device files like /dev/null are now tracked as special by Queue and are not used to generate .out file paths, scattered into a temporary directory, gathered, deleted, etc. 2012-01-23 16:17:04 -05:00
pileup GATKSAMRecord refactor 2011-11-03 15:43:26 -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 BQSR with indels integrated! 2012-02-09 18:46:45 -05:00
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 Bug fix for incorrect logic in subsetSamples 2011-12-14 16:14:26 -05:00
BaseUtilsUnitTest.java Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -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
MWUnitTest.java Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
MathUtilsUnitTest.java Added knuth-shuffle (KS) and randomSubset using KS to MathUtils 2012-01-03 09:29:46 -05:00
PathUtilsUnitTest.java Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -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