gatk-3.8/java
ebanks ec174dc0ba As per Menachem's last commit, there's a minimally more efficient way of doing the MQ cap.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4782 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-03 16:37:08 +00:00
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config Provide a default logger, some config settings, and some doc updates. 2009-04-29 02:06:05 +00:00
src As per Menachem's last commit, there's a minimally more efficient way of doing the MQ cap. 2010-12-03 16:37:08 +00:00
test Set minMQ = max(minMQ, minBQ) for phasing since anyway we cap BQ by MQ; also, lowered MIN_BASE_QUALITY_SCORE for phasing to 17 (was previously 20) 2010-12-03 16:31:13 +00:00