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gatk-3.8/protected/java/test/org/broadinstitute/sting/gatk/walkers
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Eric Banks 70f3997a38 More RR tests and fixes. 
* Fixed implementation of polyploid (het) compression in RR.
  * The test for a usable site was all wrong.  Worked out details with Mauricio to get it right.
  * Added comprehensive unit tests in HeaderElement class to make sure this is done right.
  * Still need to add tests for the actual polyploid compression.
  * No longer allow non-diploid het compression; I don't want to test/handle it, do you?
* Added nearly full coverage of tests for the BaseCounts class.
 		2013-02-04 15:55:15 -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 Update MD5s to reflect version number change in the BAM header 2013-02-01 13:51:31 -05:00
compression/reducereads More RR tests and fixes. 2013-02-04 15:55:15 -05:00
diagnostics Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -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 Apparently I'm a failure at rebasing...there should have been only one commit message to write. But whatever, here it is again: 2013-02-04 14:16:28 -05:00
haplotypecaller Added some docs, unit test, and contracts to SimpleDeBruijnAssembler. 2013-02-04 15:17:22 -05:00
indels Update MD5s to reflect version number change in the BAM header 2013-02-01 13:51:31 -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 Move BaseUtils back to the GATK by request, along with associated utility methods 2013-01-30 13:09:44 -05:00