Yossi Farjoun 3e2a0b15ed - Added a @Hidden option ( -outputInsertLength ) to PileupWalker that causes it to emit insert sizes together with the pileup (to assist Mark Daly's investigation of the contamination dependance on insert length) ... - Converted my old GATKBAMIndexText (within PileupWalkerIntegrationTest) to use a dataProvider - Added two integration tests to test -outputInsertLength option		2013-05-16 12:47:16 -04:00
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CNV	Updated all JAVA file licenses accordingly	2013-01-10 17:06:41 -05:00
coverage	e# This is a combination of 2 commits.	2013-05-03 11:19:14 -04:00
qc	- Added a @Hidden option ( -outputInsertLength ) to PileupWalker that causes it to emit insert sizes together with the pileup (to assist Mark Daly's investigation of the contamination dependance on insert length)	2013-05-16 12:47:16 -04:00
readutils	Several improvements to ReadAdaptorTrimmer so that it can be incorporated into ancient DNA processing pipelines (for which it was developed):	2013-04-13 13:41:36 -04:00
variantutils	Fixed bug in SelectVariants where maxIndelSize argument wasn't getting applied to deletions.	2013-03-13 15:11:34 -04:00
BAQIntegrationTest.java	Update MD5s to reflect version number change in the BAM header	2013-02-01 13:51:31 -05:00