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gatk-3.8/public/java/test/org/broadinstitute/sting
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Christopher Hartl ba8622ff0d number of stashed changes are lurking in here. In order of importance: 
- Fix for M_Trieb's error report on the forum, and addition of integration tests to cover the walker.
 - Addition of StructuralIndel as a class of variation within the VariantContext. These are for variants with a full alt allele that's >150bp in length.
 - Adaptation of the MVLikelihoodRatio to work for a set of trios (takes the max over the trios of the MVLR)
 - InsertSizeDistribution changed to use the new gatk report output (it was previously broken)
 - RetrogeneDiscovery changed to be compatible with the new gatk report
 - A maxIndelSize argument added to SelectVariants
 - ByTranscriptEvaluator rewritten for cleanliness
 - VariantRecalibrator modified to not exclude structural indels from recalibration if the mode is INDEL
 - Documentation added to DepthOfCoverageIntegrationTest (no, don't yell at chartl ;_; )

Also sorry for the long commit history behind this that is the result of fixing merge conflicts. Because this *also* fixes a conflict (from git stash apply), for some reason I can't rebase all of them away. I'm pretty sure some of the commit notes say "this note isn't important because I'm going to rebase it anyway".
 		2012-08-21 07:08:58 -04:00
..
alignment Reinitialize random seed in the bwa bindings from the fixed seed stored in the 2011-07-22 13:41:53 -04:00
commandline Cleanup of VCF header lines and constants, BCF2 bugfixes 2012-06-21 15:16:31 -04:00
gatk number of stashed changes are lurking in here. In order of importance: 2012-08-21 07:08:58 -04:00
jna Updated hard limit MathUtils.MAXN number of samples from 11,000 to 50,000. 2012-05-29 11:18:22 -04:00
utils Updated and more thorough version of the BadCigar read filter 2012-08-17 17:05:27 -04:00
BaseTest.java Extensive unit tests, contacts, and documentation for RecalDatum 2012-07-31 08:11:03 -04:00
MD5DB.java Finalizing BCF2 mark III commit 2012-06-21 15:16:27 -04:00
MD5Mismatch.java Final updates to integration tests for BCF2 2012-05-24 10:58:59 -04:00
StingTextReporter.java Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
WalkerTest.java On the way to really sorting out HMS error handling 2012-07-25 22:11:10 -04:00