Mauricio Carneiro 8c07614321 QualifyMissingIntervals: support different formats ... Problem ------- Qualify Missing Intervals only accepted GATK formatted interval files for it's coding sequence and bait parameters. Solution ------- There is no reason for such limitation, I erased all the code that did the parsing and used IntervalUtils to parse it (therefore, now it handles any type of interval file that the GATK can handle). ps: Also added an average depth column to the output		2013-07-12 17:32:53 -04:00
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java	QualifyMissingIntervals: support different formats	2013-07-12 17:32:53 -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