Mauricio Carneiro 1466396a31 Diagnose target is outputting intervals out of order ... Problem ------- When the interval had no reads, it was being sent to the VCF before the intervals that just got processed, therefore violating the sort order of the VCF. Solution -------- Use a linked hash map, and make the insertion and removal all happen in one place regardless of having reads or not. Since the input is ordered, the output has to be ordered as well. Itemized changes -------------- * Clean up code duplication in LocusStratification and SampleStratification * Add number of uncovered sites and number of low covered sites to the VCF output. * Add new VCF format fields * Fix outputting multiple status when threshold is 0 (ratio must be GREATER THAN not equal to the threshold to get reported) [fixes #48780333] [fixes #48787311]		2013-05-13 11:50:22 -04:00
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java	Diagnose target is outputting intervals out of order	2013-05-13 11:50:22 -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