scalvo bda427f078 Change specification of AnnotationInputTable, and fix 2 bugs. ... Previous output spec contained 3 columns: haplotypeReference,haplotypeAlternate,haplotypeStrand where haplotypeReference was always on the + strand, and haplotypeAlternate was on the strand specified by haplotypeStrand. The new specification contains 3 columns: haplotypeReference,haplotypeAlternate,transcriptStrand where haplotypeRef and haplotypeAlt are required to be on the + strand. transcriptStrand now specifies the strand of the transcript, which is needed for interpreting the haplotypes. Bugfix #1: fix incorrect assignment of variantCodon and variantAA (Previously variantCodon was incorrectly set to referenceCodon) Bugfix #2: fix incorrect codingCoordStr values for - strands (bug reported by Giulio Genovese), and incorrect usage of "m." for mitochondrial transcripts (bug reported by Steve Hershman) git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4444 348d0f76-0448-11de-a6fe-93d51630548a		2010-10-06 20:46:09 +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	Change specification of AnnotationInputTable, and fix 2 bugs.	2010-10-06 20:46:09 +00:00
test	Added the ability to Queue to run scala functions inside the JVM. NOTE: Extend from InProcessFunction instead of CommandLineFunction to use this functionality.	2010-10-06 18:29:56 +00:00