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gatk-3.8/public/java/test/org/broadinstitute/sting/utils
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Khalid Shakir fac9932938 Embedding gsalib source and queueJobReport R scripts in the dist and package jars. 
Moved gsalib and queueJobReport.R to embeddable namespaced locations.
Updated packager dependencies/dir to add an @includes which filters the embedded fileset.
RScriptExecutor can now JIT compiles the gsalib.
RScriptExecutor uses ProcessController and sends the Rscript output to java's stdout when run under -l DEBUG.
Refactored ProcessController and IOUtils from Queue to Sting Utils.
Added more unit tests to ProcessController along with a utility class to hard stop OutputStreams at a specified byte count.
Replaced uses of some IOUtils with Apache Commons IO.
ShellJobRunner refactored to use direct ProcessController and now kills jobs on shutdown.
Better QGraph responsiveness on shutdown by using Object.wait() instead of Thread.sleep().
 		2011-10-24 15:58:34 -04:00
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R Embedding gsalib source and queueJobReport R scripts in the dist and package jars. 2011-10-24 15:58:34 -04:00
baq Putative fix for BAQ array out of bounds 2011-09-21 11:25:08 -04:00
bed Fixing broken paths to the testdata directory throughout the codebase. 2011-06-29 17:36:47 -04:00
clipreads Fixing conflicts 2011-10-03 19:07:59 -07:00
codecs Fixed long-standing bug in tribble index creation 2011-09-20 10:53:18 -04:00
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
genotype/vcf Make DiploidGenotype enum private to walkers.genotyper 2011-09-24 08:48:33 -04:00
interval Merged bug fix from Stable into Unstable 2011-10-04 21:00:34 -07:00
io Embedding gsalib source and queueJobReport R scripts in the dist and package jars. 2011-10-24 15:58:34 -04:00
pileup Renamed ReadBackedPileup getXSampleName() functions to getXSample 2011-09-30 10:02:57 -04:00
report Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
runtime Embedding gsalib source and queueJobReport R scripts in the dist and package jars. 2011-10-24 15:58:34 -04:00
sam Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -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 Treat ./X genotypes as MIXED so that isHet, isHom, etc. still return the expected and correct values. Added docs to these accessors with contracts explicitly mentioned. Fixed case where NPE could be thrown. 2011-10-19 15:11:13 -04:00
BaseUtilsUnitTest.java Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
GenomeLocParserUnitTest.java Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
GenomeLocSortedSetUnitTest.java Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
GenomeLocUnitTest.java Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
MWUnitTest.java Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
MathUtilsUnitTest.java Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
PathUtilsUnitTest.java Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
ReadUtilsUnitTest.java Fixing conflicts 2011-10-03 19:07:59 -07:00
ReservoirDownsamplerUnitTest.java Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
SimpleTimerUnitTest.java Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
UtilsUnitTest.java Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00