Mark DePristo 80b94a4f9a AdaptiveContexts implement pruning to a given chi2 p value ... -- Added bonferroni corrected p-value pruning, so you tell it how significant of a different you are willing to collapse in the tree, and it prunes the tree down to this maximum threshold -- Penalty is now a phred-scaled p-value not the raw chi2 value -- Split command line arguments in VisualizeContextTree into separate arguments for each type of pruning		2012-08-07 17:22:39 -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	AdaptiveContexts implement pruning to a given chi2 p value	2012-08-07 17:22:39 -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