gatk-3.8/protected/java/test/org/broadinstitute/sting/gatk/walkers
Chris Hartl 91030e9afa Bugfix: records that get paired up during the resolution of multiple-records-per-site were not going into genotype-level filtering. Caught via testing.
Testing for moltenized output, and for genotype-level filtering. This tool is now fully functional. There are three todo items:

1) Docs
2) An additional output table that gives concordance proportions normalized by records in both eval and comp (not just total in eval or total in comp)
3) Code cleanup for table creation (putting a table together the way I do takes -way- too many lines of code)
2013-01-18 09:49:48 -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 Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
compression/reducereads Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -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 Updating MD5s in HC and UG that changed due to new LIBS 2013-01-11 15:17:19 -05:00
haplotypecaller calculating the md5s for the new tests. 2013-01-11 15:43:52 -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 Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
variantrecalibration Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
variantutils Bugfix: records that get paired up during the resolution of multiple-records-per-site were not going into genotype-level filtering. Caught via testing. 2013-01-18 09:49:48 -05:00