asivache 8d389e149f Now can deal with input files that contain multiple copies of the same event. Only one assay sequence will be designed for each distinct variant, redundant variants will be discarded. Redundancy is defined as same start, same variant type, same ref and alt alleles (it does not matter, e.g., what the sample was as we do not record sample information anywhere). ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5115 348d0f76-0448-11de-a6fe-93d51630548a		2011-01-28 21:42:29 +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	Now can deal with input files that contain multiple copies of the same event. Only one assay sequence will be designed for each distinct variant, redundant variants will be discarded. Redundancy is defined as same start, same variant type, same ref and alt alleles (it does not matter, e.g., what the sample was as we do not record sample information anywhere).	2011-01-28 21:42:29 +00:00
test	Better query start / stop function that directly parses the cigar string, unlike the previous version. Now properly handles H (hard-clipped) reads. Added -baq OFF and -baq RECALCULATE integration tests on all three 1KG technologies. Please let me know if this new code somehow fails.	2011-01-28 15:08:21 +00:00