Mauricio Carneiro e991307eb5 Including SplitByRG in the FullProcessingPipeline ... Why wasn't it there before, you ask ---------------------------------- Before I was running it separately (by hand), but now it's integrated in the FullProcessingPipeline. Integration was a pain because of Queue's limitation of only allowing 1 @Output file. This forced me to write the ugliest piece of code of my life, but it's working and it's processing the YRI from scratch using that right now. So I'm happy... somewhat. Other changes to the pipeline ----------------------------- * Add --filter_bases_not_stored to the IndelRealigner step -- sometimes BAM files have reads with no bases stored in the unmapped section (no idea why) but this disrupts the pipeline. * Change adaptor marking parameter to "dual indexed" instead of "pair-ended" -- for PCR Free data.		2013-08-18 00:51:32 -04:00
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qscript/org/broadinstitute/sting/queue/qscripts	Now that we don't generate dict and fai files, the resource script needs to copy them to the bundle.	2013-05-02 15:18:13 -04:00
src/org/broadinstitute/sting/queue	Including SplitByRG in the FullProcessingPipeline	2013-08-18 00:51:32 -04:00
test/org/broadinstitute/sting/queue	Disable RetryMemoryLimit pipeline test	2013-07-03 13:38:28 -04:00