Eric Banks c2e27729c7 Renaming PileupElement.isBeforeDeletion() to PileupElement.isBeforeDeletedBase() so that it's more clear that it can still be true while inside a deletion. Added PileupElement.isBeforeDeletionStart() to cover the case that I want where we only trigger before the actual deletion event. Similarly for after a deletion. Updated counting code in ConsensusAlleleCounter accordingly.		2012-03-29 17:08:25 -04:00
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R	Further cleanup of R	2012-03-22 21:24:37 -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	Renaming PileupElement.isBeforeDeletion() to PileupElement.isBeforeDeletedBase() so that it's more clear that it can still be true while inside a deletion. Added PileupElement.isBeforeDeletionStart() to cover the case that I want where we only trigger before the actual deletion event. Similarly for after a deletion. Updated counting code in ConsensusAlleleCounter accordingly.	2012-03-29 17:08:25 -04:00
keys	Public-key authorization scheme to restrict use of NO_ET	2012-03-06 00:09:43 -05:00
packages	Public-key authorization scheme to restrict use of NO_ET	2012-03-06 00:09:43 -05:00
perl	Update to the bindings for liftOverVCF.pl (to -V from -B)	2011-09-15 15:33:09 -04:00
scala	Added more primitives to GATK Report Column Type	2012-03-28 09:07:54 -04:00
testdata	BQSR Gatherer implementation and integration tests	2012-03-27 13:50:22 -05:00