Guillermo del Angel a971e7ab6d Several improvements to ReadAdaptorTrimmer so that it can be incorporated into ancient DNA processing pipelines (for which it was developed): ... -- Add pair cleaning feature. Reads in query-name sorted order are required and pairs need to appear consecutively, but if -cleanPairs option is set, a malformed pair where second read is missing is just skipped instead of erroring out. -- Add integration tests -- Move walker to public		2013-04-13 13:41:36 -04:00
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CNV	Updated all JAVA file licenses accordingly	2013-01-10 17:06:41 -05:00
coverage	Refactored the het (polyploid) consensus creation in ReduceReads.	2013-03-25 09:34:54 -04:00
qc	Fix runtime public -> protected dependencies in the test suite	2013-02-26 21:19:12 -05:00
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