David Roazen 2a7af43164 Fix improper dependencies in QScripts used by pipeline tests, and attempt to fix the flawed MisencodedBaseQualityUnitTest ... -Some QScripts used by public pipeline tests unnecessarily used the (now protected) UnifiedGenotyper. Changed them to use PrintReads instead. -Moved ExampleUnifiedGenotyperPipelineTest to protected -Attempt to fix the flawed and sporadically failing MisencodedBaseQualityUnitTest: After looking at this class a bit, I think the problem was the use of global arrays for the quals shared across all reads in all tests (BAMRecord class definitely does not make a separate copy for each read!). One test (testFixBadQuals) modifies the bad quals array, and if this happens to run before the testBadQualsThrowsError test the bad quals array will have been "fixed" and no exception will be thrown.		2013-02-27 04:45:53 -05:00
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org/broadinstitute/sting/queue/qscripts	Fix improper dependencies in QScripts used by pipeline tests, and attempt to fix the flawed MisencodedBaseQualityUnitTest	2013-02-27 04:45:53 -05:00