kshakir 3e3ff4a9e7 Bam gathering passes on the compression_level and the create_index flag to MergeSamFiles. ... VCF gathering passes on the no_header and sites_only flags to CombineVariants. Fixed deletion of gathered log files. Although they are intermediate and do not need to be re-run if not present, they should not be deleted. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5508 348d0f76-0448-11de-a6fe-93d51630548a		2011-03-25 03:58:38 +00:00
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qscript	Minor updates to match the wiki documentation.	2011-03-24 20:22:23 +00:00
src/org/broadinstitute/sting	Bam gathering passes on the compression_level and the create_index flag to MergeSamFiles.	2011-03-25 03:58:38 +00:00
test/org/broadinstitute/sting/queue	Walkers can now specify a class extending from Gatherer to merge custom output formats. Add @Gather(MyGatherer.class) to the walker @Output.	2011-03-24 14:03:51 +00:00