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Eric Banks e7c35a907f Fixes to BQSR for the --maximum_cycle_value argument. 
- It's now written into the recal report so that it can be used in the PrintReads step.
  - Note that we also now write the --deletions_default_quality value which accidentally wasn't being written before!
  - Added tests to make sure that the value of the --maximum_cycle_value is being used properly by PR with -BQSR.
(This is my last non-branch commit; all future pushes will follow new GATK practices)
 		2013-02-05 17:38:03 -05:00
..
src/org/broadinstitute/sting Fixes to BQSR for the --maximum_cycle_value argument. 2013-02-05 17:38:03 -05:00
test/org/broadinstitute/sting Fixes to BQSR for the --maximum_cycle_value argument. 2013-02-05 17:38:03 -05:00