Mauricio Carneiro 371ea2f24c Fixed IndelRealigner reference length bug (GSA-774) ... -- modified ReadBin GenomeLoc to keep track of softStart() and softEnd() of the reads coming in, to make sure the reference will always be sufficient even if we want to use the soft-clipped bases -- changed the verification from readLength to aligned bases to allow reads with soft-clipped bases -- switched TreeSet -> PriorityQueue in the ConstrainedMateFixer as some different reads can be considered equal by picard's SAMRecordCoordinateComparator (the Set was replacing them) -- pulled out ReadBin class so it can be testable -- added unit tests for ReadBin with soft-clips -- added tests for getMismatchCount (AlignmentUtils) to make sure it works with soft-clipped reads GSA-774 #resolve		2013-02-19 16:00:36 -05:00
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commandline	Updated all JAVA file licenses accordingly	2013-01-10 17:06:41 -05:00
gatk	ActivityProfile and ActiveRegions respects engine interval boundaries	2013-02-18 10:40:25 -05:00
jna	Updated all JAVA file licenses accordingly	2013-01-10 17:06:41 -05:00
utils	Fixed IndelRealigner reference length bug (GSA-774)	2013-02-19 16:00:36 -05:00
BaseTest.java	Replace org.broadinstitute.variant with jar built from the Picard repo	2013-02-05 17:24:25 -05:00
ExampleToCopyUnitTest.java	Replace org.broadinstitute.variant with jar built from the Picard repo	2013-02-05 17:24:25 -05:00
MD5DB.java	Encrypt GATK AWS keys using the GATK private key, and decrypt as needed as a resource when uploading to AWS logs	2013-01-30 16:42:23 -05:00
MD5Mismatch.java	Updated all JAVA file licenses accordingly	2013-01-10 17:06:41 -05:00
StingTextReporter.java	Updated all JAVA file licenses accordingly	2013-01-10 17:06:41 -05:00
TestNGTestTransformer.java	Extend default timeout to 20 minutes	2013-02-13 17:43:40 -08:00
WalkerTest.java	Replace org.broadinstitute.variant with jar built from the Picard repo	2013-02-05 17:24:25 -05:00