aaron 85f2968104 add convenience methods for RODs-for-reads: the ability to get all the RODs covering the read, regardless of their type or position on the read. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4912 348d0f76-0448-11de-a6fe-93d51630548a		2010-12-29 20:46:03 +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	add convenience methods for RODs-for-reads: the ability to get all the RODs covering the read, regardless of their type or position on the read.	2010-12-29 20:46:03 +00:00
test	Support for indels in hapmap. This was non-trivial because not only does hapmap not tell you whether the allele is an insertion or deletion, but it also has a completely different positioning strategy (rightmost base). I'll send out an email tomorrow when the new HapMap3.3 VCF is ready.	2010-12-27 07:37:46 +00:00