gatk-3.8/scala
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
..
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