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gatk-3.8/protected/java/test/org/broadinstitute/sting/gatk/walkers
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Eric Banks 2d518f3063 More RR-related updates and tests. 
- ReduceReads by default now sets up-front ReadWalker downsampling to 40x per start position.
   - This is the value I used in my tests with Picard to show that memory issues pretty much disappeared.
   - This should hopefully take care of the memory issues being reported on the forum.
- Added javadocs to SlidingWindow (the main RR class) to follow GATK conventions.
- Added more unit tests to increase coverage of BaseCounts class.
- Added more unit tests to test I/D operators in the SlidingWindow class.
 		2013-02-04 12:57:43 -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-related updates and tests. 2013-02-04 12:57:43 -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 Move BaseUtils back to the GATK by request, along with associated utility methods 2013-01-30 13:09:44 -05:00
haplotypecaller Adding unit tests for KBestPaths class and fixing edge case bugs. 2013-02-01 13:51:31 -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