Eric Banks 994a4ff387 Track all outputs from BQSR (.table, .csv., and .pdf) as @Output arguments. Updated integration tests because we no longer have command-line options not to generate plots (now just don't provide a pdf) or to keep the intermediate csv (now, just provide a filename on the command-line). This is currently busted because we can't access the original filenames from the Engine's storage/stub system and therefore cannot call out to the Rscript with the executor (which requires filename strings).		2012-09-12 11:24:53 -04:00
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config	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
src	Track all outputs from BQSR (.table, .csv., and .pdf) as @Output arguments. Updated integration tests because we no longer have command-line options not to generate plots (now just don't provide a pdf) or to keep the intermediate csv (now, just provide a filename on the command-line). This is currently busted because we can't access the original filenames from the Engine's storage/stub system and therefore cannot call out to the Rscript with the executor (which requires filename strings).	2012-09-12 11:24:53 -04:00
test	VCF/BCF writers once again automatically write out no-call genotypes for samples in the VCFHeader but not in the VC itself	2012-09-12 06:46:26 -04:00