Khalid Shakir c50274e02e During flanking interval creation merging overlapping flanks so that on scatter the list doesn't accidentally genotype the same site twice. ... Moved flanking interval utilies to IntervalUtils with UnitTests.		2011-11-17 13:56:42 -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
clipreads	Added more basic UnitTests for ReadClipper	2011-11-15 00:13:52 -05:00
codecs	Removing all instances of -BTI (in tests and in GATKdocs) and replacing them with the appropriate alternative.	2011-10-27 23:55:11 -04:00
collections	…
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	Make DiploidGenotype enum private to walkers.genotyper	2011-09-24 08:48:33 -04:00
interval	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
io	Embedding gsalib source and queueJobReport R scripts in the dist and package jars.	2011-10-24 15:58:34 -04:00
pileup	GATKSAMRecord refactor	2011-11-03 15:43:26 -04:00
report	…
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	…
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	Merge branch 'PhaseByTransmission'	2011-11-14 11:31:28 +01:00
BaseUtilsUnitTest.java	…
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	…
GenomeLocUnitTest.java	…
MWUnitTest.java	…
MathUtilsUnitTest.java	…
PathUtilsUnitTest.java	…
ReadUtilsUnitTest.java	compress Reduce Read counts bytes by offset	2011-11-14 18:30:24 -05:00
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	…