Mark DePristo e1bba91836 Ready for full-scale evaluation adaptive BQSR contexts ... -- VisualizeContextTree now can write out an equivalent BQSR table determined after adaptive context merging of all RG x QUAL x CONTEXT trees -- Docs, algorithm descriptions, etc so that it makes sense what's going on -- VisualizeContextTree should really be simplified when into a single tool that just visualize the trees when / if we decide to make adaptive contexts standard part of BQSR -- Misc. cleaning, organization of the code (recalibation tests were in private but corresponding actual files were public)		2012-08-03 16:02:53 -04:00
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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	Merged bug fix from Stable into Unstable	2012-08-03 10:45:01 -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	Ready for full-scale evaluation adaptive BQSR contexts	2012-08-03 16:02:53 -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