gatk-3.8/protected/java/test/org/broadinstitute/sting/gatk/walkers
Yossi Farjoun 9234a0efcd Merge pull request #223 from broadinstitute/mc_dt_gaddy_outputs
Bug fixes and missing interval functionality for Diagnose Targets

While the code seems fine, the complex parts of it are untested. This is probably fine for now, but private code can have a tendency to creep into the codebase once accepted. I would have preferred that unit test OR a big comment stating that the code is untested (and thus broken by Mark's rule).

It is with these cavets that I accept the pull request.
2013-05-16 09:25:54 -07:00
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annotator Update expected test output for Java 7 2013-05-01 16:18:01 -04:00
beagle Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
bqsr Trivial BQSR bug fixes and improvement 2013-04-11 17:08:35 -04:00
compression/reducereads Fix bug in Reduce Reads that arises in multi-sample mode. 2013-05-08 23:23:51 -04:00
diagnostics Update MD5s and the Diagnose Target scala script 2013-05-13 12:06:17 -04:00
diffengine Fixed issues raised by Appistry QA (mostly small fixes, corrections & clarifications to GATKDocs) 2013-03-12 10:57:14 -04:00
fasta Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
filters Don't allow users to specify keys and IDs that contain angle brackets or equals signs (not allowed in VCF spec). 2013-04-05 00:52:32 -04:00
genotyper Re-fix md5's that changed due to conflicting pushes 2013-05-03 14:59:16 -04:00
haplotypecaller NanoScheduled ActiveRegionTraversal and HaplotypeCaller 2013-05-13 11:09:02 -04:00
indels Secondary alignments were not handled correctly in IndelRealigner 2013-05-06 19:09:10 -04:00
phasing Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
validation MathUtils.randomSubset() now uses Collections.shuffle() (indirectly, through the other methods 2013-03-29 14:52:10 -04:00
varianteval Move some VCF/VariantContext methods back to the GATK based on feedback 2013-01-29 16:56:55 -05:00
variantrecalibration Update MD5s for VQSR header change 2013-04-16 11:45:45 -04:00
variantutils Update GCIT md5s to account for trivial changes to description strings 2013-05-14 19:45:30 -04:00