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gatk-3.8/protected/java/test/org/broadinstitute/sting/gatk/walkers
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Eric Banks e4ec899a87 First pass at adding unit tests for the RR framework: I have added 3 tests and all 3 uncovered RR bugs! 
One of the fixes was critical: SlidingWindow was not converting between global and relative positions correctly.
Besides not being correct, it was resulting in a massive slow down of the RR traversal.
That fix definitely breaks at least one of the integration tests, but it's not worth changing md5s now because I'll be
changing things all over RR for the next few days, so I am going to let that test fail indefinitely until I can confirm
general correctness of the tool.
 		2013-01-29 15:51:07 -05:00
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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 updating BQSR integration test values for the PR half of BQSR. 2013-01-29 09:47:57 -05:00
compression/reducereads First pass at adding unit tests for the RR framework: I have added 3 tests and all 3 uncovered RR bugs! 2013-01-29 15:51:07 -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 org.broadinstitute.variant refactor, part 2 2013-01-28 09:03:46 -05:00
haplotypecaller Updating HC md5s for new cutting algorithm and default band pass filter parameters 2013-01-25 11:07:29 -05:00
indels Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -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 org.broadinstitute.variant refactor, part 2 2013-01-28 09:03:46 -05:00
variantrecalibration Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
variantutils org.broadinstitute.variant refactor, part 2 2013-01-28 09:03:46 -05:00