Ryan Poplin 902ca7ea70 Merge branch 'master' of github.com:broadinstitute/gsa-unstable		2012-12-18 15:45:33 -05:00
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src/org/broadinstitute/sting	Merge branch 'master' of github.com:broadinstitute/gsa-unstable	2012-12-18 15:45:33 -05:00
test/org/broadinstitute/sting	Changing the HC over to using the non-contamination-downsampled read maps for the purposes of annotations. This behavior now matches the UG. There is a new command line option to go back to the older behavior to explore the differences.	2012-12-17 11:27:44 -05:00