kshakir 0a58d7aa1a Marked boolean SAMFileWriterATD arguments as flags so scala generator maps them to Boolean instead of Option[Boolean]. ... Using the VCFWriterATD isCompressed to check if the VCF index will be auto generated. Tracking BAM and Tribble indexes as @Inputs and @Outputs in generated QFunctions. Updates to the BamGatherFunction to disable the index during merge when disable_bam_indexing = true. Made a shortcut for live-running pipelinetest, pipelinetestrun. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5606 348d0f76-0448-11de-a6fe-93d51630548a		2011-04-08 18:44:32 +00:00
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qscript	Minor bug fixes	2011-04-08 17:30:40 +00:00
src/org/broadinstitute/sting	Marked boolean SAMFileWriterATD arguments as flags so scala generator maps them to Boolean instead of Option[Boolean].	2011-04-08 18:44:32 +00:00
test/org/broadinstitute/sting/queue	Instead of always merging Picard interval files they are optionally merged by Sting Utils.	2011-04-06 21:12:05 +00:00