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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R	Merged bug fix from Stable into Unstable	2012-08-01 14:35:30 -04:00
c	At chartl's request, add the bwa aln -N and bwa aln -m parameters to the bindings.	2012-01-17 14:47:53 -05:00
chainFiles	…
doc	…
java	Ready for full-scale evaluation adaptive BQSR contexts	2012-08-03 16:02:53 -04:00
keys	Public-key authorization scheme to restrict use of NO_ET	2012-03-06 00:09:43 -05:00
packages	Removed 'Walker' suffix from packages/GATKEngine.xml that were breaking the packaged release.	2012-07-23 16:32:31 -04:00
perl	Update to the bindings for liftOverVCF.pl (to -V from -B)	2011-09-15 15:33:09 -04:00
scala	Hmm, I thought I used the right md5s last time. Let's try again.	2012-08-02 11:25:10 -04:00
testdata	Reverting move of BQSR tests to public, as per DR's email	2012-07-19 10:02:05 -04:00