Eric Banks 05e69b6294 Refactoring of SlidingWindow class in RR to reduce complexity and fix important bug. ... * Allow RR to write its BAM to stdout by setting required=true for @Output. * Fixed bug in sliding window where a break in coverage after a long stretch without a variant region was causing a doubling of all the reads before the break. * Refactored SlidingWindow.updateHeaderCounts() into 3 separate tested methods. * Refactored polyploid consensus code out of SlidingWindow.compressVariantRegion().		2013-03-12 09:06:55 -04:00
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java	Refactoring of SlidingWindow class in RR to reduce complexity and fix important bug.	2013-03-12 09:06:55 -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