Menachem Fromer a8c7edca05 Fixed fragment handling in DepthOfCoverage		2012-11-21 16:01:10 -05:00
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qscript/org/broadinstitute/sting/queue/qscripts	Fixed fragment handling in DepthOfCoverage	2012-11-21 16:01:10 -05:00
src/org/broadinstitute/sting/queue	Keep SNPs and indels separately for batch merging; Add options to DepthOfCoverage to count fragments (to not double-count overlapping reads of same fragment); DepthOfCoverage should now support ReducedReads; Replace recusrion with loop in DoC/package.scala (for lists longer than 5000 elements)	2012-11-21 15:56:53 -05:00
test/org/broadinstitute/sting/queue	Allow each pipeline test the max of 10 hours to run	2012-11-02 12:40:56 -04:00