Mauricio Carneiro 765f5450ac Updated Full Processing Pipeline ... * add interleaved fastq option to sam2fastq * add optional adapter trimming path * add "skip_revert" option to skip reverting the bams (sometimes useful -- hidden parameter) * add a walker that reads in one bam file and outputs N bam files, one for each read group in the original bam. This is a very important step in any BAM reprocessing pipeline. I am using this new pipeline to process the CEU and YRI PCR Free WGS trios.		2013-08-13 23:35:32 -04:00
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engine	Update licenses for new PbsEngine* classes	2013-07-01 15:50:20 -04:00
extensions	Updated Full Processing Pipeline	2013-08-13 23:35:32 -04:00
function	Added a QFunction.jobLocalDir for optionally tracking a node local directory that may have faster intermediate storage, with SGF ensuring that if the directory happens to be on the same machine that it get's a clone specific sub-directory to avoid collisions.	2013-01-25 14:28:04 -05:00
library	Updating licenses for all scala files	2013-01-10 17:46:10 -05:00
util	Re-committing the following changes from Dec 18:	2013-01-16 12:43:15 -05:00
QCommandLine.scala	Message "script failed" moved to the correct place in the code	2013-02-04 15:37:23 -05:00
QCommandPlugin.scala	Updating licenses for all scala files	2013-01-10 17:46:10 -05:00
QException.scala	Updating licenses for all scala files	2013-01-10 17:46:10 -05:00
QScript.scala	Update QScript.scala	2013-08-02 14:09:26 -04:00
QScriptManager.scala	Updating licenses for all scala files	2013-01-10 17:46:10 -05:00
QSettings.scala	Updating licenses for all scala files	2013-01-10 17:46:10 -05:00