Mauricio Carneiro cf7afc1ad4 Fixed "skipped intervals" bug on DiagnoseTargets ... Problem ------- Diagnose targets was skipping intervals when they were not covered by any reads. Solution -------- Rework the interval iteration logic to output all intervals as they're skipped over by the traversal, as well as adding a loop on traversal done to finish outputting intervals past the coverage of teh BAM file. Summarized Changes ------------------ * Outputs all intervals it iterates over, even if uncovered * Outputs leftover intervals in the end of the traversal * Updated integration tests [fixes #47813825]		2013-04-22 23:53:09 -04:00
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java	Fixed "skipped intervals" bug on DiagnoseTargets	2013-04-22 23:53:09 -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