Mauricio Carneiro 3dbb86b052 Outputting missing intervals in DiagnoseTargets ... Problem ------ Diagnose Targets identifies holes in the coverage of a targetted experiment, but it only reports them doesn't list the actual missing loci Solution ------ This commit implements an optional intervals file output listing the exact loci that did not pass filters Itemized changes -------------- * Cache callable statuses (to avoid recalculation) * Add functionality to output missing intervals * Implement new tool to qualify the missing intervals (QualifyMissingIntervals) by gc content, size, type of missing coverage and origin (coding sequence, intron, ...)		2013-05-13 11:51:56 -04:00
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src/org/broadinstitute/sting	Outputting missing intervals in DiagnoseTargets	2013-05-13 11:51:56 -04:00
test/org/broadinstitute/sting	New faster Smith-Waterman implementation that is edge greedy and assumes that ref and haplotype have same global start/end points.	2013-05-13 09:36:39 -04:00