kshakir 8619f49d20 Added a utility method to retrieve the contig lengths for WG chunking. ... Added a rudimentary GATKReportParser for parsing VE3 results. Re-enabled the FCPTest using VE3, the GATKRP, and the PicardAggregationUtils. The tag type for .rod files is DBSNP, not ROD. More explicit return types on implicit methods. Added null checks for implicit string to/from file conversions. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5668 348d0f76-0448-11de-a6fe-93d51630548a		2011-04-20 19:22:21 +00:00
..
BatchMerge.q	BatchMerge - AlleleVCF --> AllelesVCF, this (combined with Eric's fix) will solve James P.'s forum issue.	2011-04-15 22:03:16 +00:00
FullCallingPipeline.q	Added a utility method to retrieve the contig lengths for WG chunking.	2011-04-20 19:22:21 +00:00
MultiFullCallingPipeline.scala	Walkers can now specify a class extending from Gatherer to merge custom output formats. Add @Gather(MyGatherer.class) to the walker @Output.	2011-03-24 14:03:51 +00:00
recalibrate.scala	Walkers can now specify a class extending from Gatherer to merge custom output formats. Add @Gather(MyGatherer.class) to the walker @Output.	2011-03-24 14:03:51 +00:00
wgs.q	Whole genome pipeline script. currently chunks, cleans, calls, merges, selects and filters indels, recalibrates, and evals.	2011-04-13 16:59:48 +00:00