kshakir 88a0d77433 Changed parsing engine to store the order the argument bindings based on their definition in the class, moving "-T" to the front of Queue command lines. ... Queue GATK generated .intervals is now a List(File) again removing special case handling in the generator. Instead of using @Scatter annotation, using ScatterFunction instance to determine if a job can be scattered. Implemented special VcfGatherFunction which only uses the header from the first file, even if the other files differ in their headers. Added a -deleteIntermediates to Queue to delete the outputs from intermediate commands after a successful run. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4536 348d0f76-0448-11de-a6fe-93d51630548a		2010-10-20 21:43:52 +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	Changed parsing engine to store the order the argument bindings based on their definition in the class, moving "-T" to the front of Queue command lines.	2010-10-20 21:43:52 +00:00
test	ReadBackedPhasing now uses a SortedVCFWriter to simplify, and has the ability to merge phased SNPs into MNPs on the fly [turned off by default]; MergeSegregatingPolymorphismsWalker can also do this as a post-processing step; Integration tests for MergeSegregatingPolymorphismsWalker were also added	2010-10-20 20:27:10 +00:00