kshakir 08c13f3944 Using embedded GATK. ... Hardcoded the reference and dbsnp since the training rods are also hardcoded, for now. Changed freeze/chr20 to wg/chr20/cent1 to also test the heaviest known shard. Other cleanup. TODO: Memory command line options or have the script figure it out using FLS or similar. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5799 348d0f76-0448-11de-a6fe-93d51630548a		2011-05-12 23:19:49 +00:00
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qscript	Using embedded GATK.	2011-05-12 23:19:49 +00:00
src/org/broadinstitute/sting	Corrected memory handling and jobName formatting issues	2011-05-12 17:47:56 +00:00
test/org/broadinstitute/sting/queue	Moved some of the java to scala conversions from production to test code as it's not needed in production and slows down the code.	2011-05-05 04:11:15 +00:00