asivache 1339f3f3e3 make refseq annotation file an optional argument; if specified, indels will be annotated as genomic/utr/intron/coding (accidentally appearing 'unknowns' probably mean that there's something wrong with refseq annotations?) ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1077 348d0f76-0448-11de-a6fe-93d51630548a		2009-06-23 18:17:03 +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/org/broadinstitute/sting	make refseq annotation file an optional argument; if specified, indels will be annotated as genomic/utr/intron/coding (accidentally appearing 'unknowns' probably mean that there's something wrong with refseq annotations?)	2009-06-23 18:17:03 +00:00
test/org/broadinstitute/sting	Aaron: 1, GenomeLoc: 0. I changed our GenomeLoc class, seperating the creation of a genome loc (with the reference setup) to a parser class. GenomeLoc now just represents the actual genomic postion. The constructors are now package-protected (to enforce using the parser), but we may want to expose some constructors in the future.	2009-06-22 14:39:41 +00:00