Mark DePristo b5b63eaac7 New GATKSAMRecord concept of a strandless read, update to FS ... -- Strandless GATK reads are ones where they don't really have a meaningful strand value, such as Reduced Reads or fragment merged reads. Added GATKSAMRecord support for such reads, along with unit tests -- The merge overlapping fragments code in FragmentUtils now produces strandless merged fragments -- FisherStrand annotation generalized to treat strandless as providing 1/2 the representative count for both strands. This means that that merged fragments are properly handled from the HC, so we don't hallucinate fake strand-bias just because we managed to merge a lot of reads together. -- The previous getReducedCount() wouldn't work if a read was made into a reduced read after getReducedCount() had been called. Added new GATKSAMRecord method setReducedCounts() that does the right thing. Updated SlidingWindow and SyntheticRead to explicitly call this function, and so the readTag parameter is now gone. -- Update MD5s for change to FS calculation. Differences are just minor updates to the FS		2013-03-13 11:16:36 -04:00
..
commandline	Updated all JAVA file licenses accordingly	2013-01-10 17:06:41 -05:00
gatk	Increase timeout for a test in the EngineFeaturesIntegrationTest	2013-03-12 23:53:26 -04:00
jna	Fix more tests that fail when run in parallel on the farm	2013-03-12 16:53:30 -04:00
utils	New GATKSAMRecord concept of a strandless read, update to FS	2013-03-13 11:16:36 -04:00
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	Fix tests that were consistently or intermittently failing when run in parallel on the farm	2013-03-06 13:56:54 -05:00
WalkerTest.java	Replace org.broadinstitute.variant with jar built from the Picard repo	2013-02-05 17:24:25 -05:00