aaron 63ada20da5 allow RefSeq files to optionally contain the header line, which is the default output from the UCSC table browser ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4065 348d0f76-0448-11de-a6fe-93d51630548a		2010-08-19 20:25:37 +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	allow RefSeq files to optionally contain the header line, which is the default output from the UCSC table browser	2010-08-19 20:25:37 +00:00
test	Fix for running the cleaner at the lane-level for known indels only: instead of relying on the reads to get the reference sequence, we now use an IndexedFastaSequenceFile in all cases and pad the reference with bases on either end. This allows us to deal with cases in which we are trying to clean just a single deletion-containing read with tiny LOD (so the read needs to be pushed off the seen reference; @Reference doesn't yet work for Read Walkers) and has the added benefit of allowing us now to get much larger known indels that aren't completely covered with reads.	2010-08-19 11:31:13 +00:00