Roger Zurawicki b8b139841d DiagnoseTargets with working Q1,Median,Q3 ... - Merged Roger's metrics with Mauricio's optimizations - Added Stats for DiagnoseTargets - now has functions to find the median depth, and upper/lower quartile - the REF_N callable status is implemented - The walker now runs efficiently - Diagnose Targets accepts overlapping intervals - Diagnose Targets now checks for bad mates - The read mates are checked in a memory efficient manner - The statistics thresholds have been consolidated and moved outside of the statistics classes and into the walker. - Fixed some bugs - Removed rod binding Added more Unit tests - Test callable statuses on the locus level - Test bad mates - Changed NO_COVERAGE -> COVERAGE_GAPS to avoid confusion Signed-off-by: Mauricio Carneiro <carneiro@broadinstitute.org>		2012-05-29 10:16:45 -04:00
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net/sf	GATK tests use public/testdata not /humgen/ as much as possible	2012-05-24 10:58:58 -04:00
org/broadinstitute/sting	DiagnoseTargets with working Q1,Median,Q3	2012-05-29 10:16:45 -04:00