Ryan Poplin b5b9d745a7 New implementation of the GGA mode in the HaplotypeCaller ... -- We now inject the given alleles into the reference haplotype and add them to the graph. -- Those paths are read off of the graph and then evaluated with the appropriate marginalization for GGA mode. -- This unifies how Smith-Waterman is performed between discovery and GGA modes. -- Misc minor cleanup in several places.		2013-05-31 10:35:36 -04:00
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java	New implementation of the GGA mode in the HaplotypeCaller	2013-05-31 10:35:36 -04:00
scala/test/org/broadinstitute/sting/queue/pipeline/examples	Fix improper dependencies in QScripts used by pipeline tests, and attempt to fix the flawed MisencodedBaseQualityUnitTest	2013-02-27 04:45:53 -05:00