depristo 43fdd31e20 Significant performance optimization for reduced reads due to better algorithm for including reads in the variable regions. Fixed a critical bug that actually produced multiple copies of the same read in the variable regions with this optimization as well. Scala exploration script updated as well. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@6005 348d0f76-0448-11de-a6fe-93d51630548a		2011-06-16 12:54:59 +00:00
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qscript	Significant performance optimization for reduced reads due to better algorithm for including reads in the variable regions. Fixed a critical bug that actually produced multiple copies of the same read in the variable regions with this optimization as well. Scala exploration script updated as well.	2011-06-16 12:54:59 +00:00
src/org/broadinstitute/sting	samtools merge requires indexed files, so added them as implicit inputs.	2011-06-08 15:02:51 +00:00
test/org/broadinstitute/sting/queue	Minor update so the debug messages don't show temp files as chromosome 208799060637697164972	2011-05-26 22:56:33 +00:00