gatk-3.8/protected/java/test/org/broadinstitute/sting/gatk/walkers
David Roazen c5c99c8339 Split long-running integration test classes into multiple classes
This is to facilitate the current experiment with class-level test
suite parallelism. It's our hope that with these changes, we can get
the runtime of the integration test suite down to 20 minutes or so.

-UnifiedGenotyper tests: these divided nicely into logical categories
 that also happened to distribute the runtime fairly evenly

-UnifiedGenotyperPloidy: these had to be divided arbitrarily into two
 classes in order to halve the runtime

-HaplotypeCaller: turns out that the tests for complex and symbolic
 variants make up half the runtime here, so merely moving these into
 a separate class was sufficient

-BiasedDownsampling: most of these tests use excessively large intervals
 that likely can't be reduced without defeating the goals of the tests. I'm
 disabling these tests for now until they can either be redesigned to use smaller
 intervals around the variants of interest, or refactored into unit tests
 (creating a JIRA for Yossi for this task)
2013-03-01 13:55:23 -05:00
..
annotator Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
beagle Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
bqsr Replace uses of NestedHashMap with NestedIntegerArray. 2013-02-27 14:03:39 -05:00
compression/reducereads Brought all of ReduceReads to fastutils 2013-02-23 22:53:23 -05:00
diagnostics walker to calculate per base coverage distribution 2013-02-07 16:33:05 -05:00
diffengine Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
fasta Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
filters Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
genotyper Split long-running integration test classes into multiple classes 2013-03-01 13:55:23 -05:00
haplotypecaller Split long-running integration test classes into multiple classes 2013-03-01 13:55:23 -05:00
indels Fixed IndelRealigner reference length bug (GSA-774) 2013-02-19 16:00:36 -05:00
phasing Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
validation Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
varianteval Move some VCF/VariantContext methods back to the GATK based on feedback 2013-01-29 16:56:55 -05:00
variantrecalibration Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
variantutils Replace org.broadinstitute.variant with jar built from the Picard repo 2013-02-05 17:24:25 -05:00