Mark DePristo 315d25409f Improvement to RecalDatum and VisualizeContextTree ... -- Reorganize functions in RecalDatum so that error rate can be computed indepentently. Added unit tests. Removed equals() method, which is a buggy without it's associated implementation for hashcode -- New class RecalDatumTree based on QualIntervals that inherits from RecalDatum but includes the concept of sub data -- VisualizeContextTree now uses RecalDatumTree and can trivially compute the penalty function for merging nodes, which it displays in the graph		2012-07-31 08:11:04 -04:00
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R	Removed 'Walker' suffix from packages/GATKEngine.xml that were breaking the packaged release.	2012-07-23 16:32:31 -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	Improvement to RecalDatum and VisualizeContextTree	2012-07-31 08:11:04 -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	…
scala	Renaming BQSR to BaseRecalibrator	2012-07-23 10:17:17 -04:00
testdata	Reverting move of BQSR tests to public, as per DR's email	2012-07-19 10:02:05 -04:00