ebanks ee348ac9d4 Add a hidden mode to the realigner to turn off SW but still use indels other than known ones (i.e. those already in the reads) ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4969 348d0f76-0448-11de-a6fe-93d51630548a		2011-01-10 20:27:04 +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 a hidden mode to the realigner to turn off SW but still use indels other than known ones (i.e. those already in the reads)	2011-01-10 20:27:04 +00:00
test	Implemented a new argument (-DQS --defaultQualityScore) that allows GATK to deal with BAM files missing quality scores. If a value is specified, all reads are filled with the default quality score. Appropriate exception is thrown if -DQS is not provided and BAM file doesn't have quality scores for every base.	2011-01-05 22:25:08 +00:00