Eric Banks 8e2094d2af Updated AssessReducedQuals and applied it systematically to all ReduceReads integration tests. ... * Moved to protected for packaging purposes. * Cleaned up and removed debugging output. * Fixed logic for epsilons so that we really only test significant differences between BAMs. * Other small fixes (e.g. don't include low quality reduced reads in overall qual). * Most RR integration tests now automatically run the quals test on output. * A few are disabled because we expect them to fail in various locations (e.g. due to downsampling).		2013-03-31 00:27:14 -04:00
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java	Updated AssessReducedQuals and applied it systematically to all ReduceReads integration tests.	2013-03-31 00:27:14 -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