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gatk-3.8/scala/src/org/broadinstitute/sting/queue/extensions
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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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gatk Bam gathering passes on the compression_level and the create_index flag to MergeSamFiles. 2011-03-25 03:58:38 +00:00
picard Bam gathering passes on the compression_level and the create_index flag to MergeSamFiles. 2011-03-25 03:58:38 +00:00
samtools More updates to the CleanBamFile pipeline. 2010-08-17 14:59:42 +00:00