depristo 27c8fb1e4d Added support for a general GATK option --simplifyBAM to automatically remove and simplify kept reads in an output BAM file. Specifically, duplicate, non-PF, and unmapped reads are removed, and all extended tags in the retained SAM records are removed except the RG:Z tag. This option is very useful when creating temporary BAM files (merged per-population or multi-sample cleaned) for future calling (as in the 1000G processing pipeline). Results in a significant reduction in space of the resulting BAM, faster reading of the BAM, and surprisingly even faster UG performance: ... 1-10mb of chromosome one, from NA12878 HiSeq 64x data set on hg18: Full BAM Write time: 8.6 m Size: 866M CountReads time: 2.9 m UG time: 11.3 m Simplified BAM: Write time: 6.2 Size: 458M CountReads time: 85.7 s UG time: 10.1 m git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5517 348d0f76-0448-11de-a6fe-93d51630548a		2011-03-26 01:21:35 +00:00
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config	Provide a default logger, some config settings, and some doc updates.	2009-04-29 02:06:05 +00:00
src	Added support for a general GATK option --simplifyBAM to automatically remove and simplify kept reads in an output BAM file. Specifically, duplicate, non-PF, and unmapped reads are removed, and all extended tags in the retained SAM records are removed except the RG:Z tag. This option is very useful when creating temporary BAM files (merged per-population or multi-sample cleaned) for future calling (as in the 1000G processing pipeline). Results in a significant reduction in space of the resulting BAM, faster reading of the BAM, and surprisingly even faster UG performance:	2011-03-26 01:21:35 +00:00
test	Enabled the parameterize option for debugging PipelineTest MD5s.	2011-03-26 00:41:47 +00:00