kiran 3aa56037af If asked, filters out triple-het situations too (which cannot be simply phased by transmission). ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5829 348d0f76-0448-11de-a6fe-93d51630548a		2011-05-20 18:48:19 +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	If asked, filters out triple-het situations too (which cannot be simply phased by transmission).	2011-05-20 18:48:19 +00:00
test	Contracts for Java now write for GenomeLoc and GenomeLocParser. The semantics of GenomeLoc are now much clearer. It is no longer allowed to create invalid GenomeLocs -- you can only create them with well formed start, end, and contigs, with respect to the mater dictionary. Where one previously created an invalid GenomeLoc, and asked is this valid, you must now provide the raw arguments to helper functions to assess this. Providing bad arguments to GenomeLoc generates UserExceptions now. Added utilty functions contigIsInDictionary and indexIsInDictionary to help with this.	2011-05-20 15:43:27 +00:00