hanna 7008a469dc Update MalformedReadFilter to pass reads that have cigar strings like 40S36I ... that have 0 aligned bases in the genome. We'll have to fix walkers as faults appear. Also added JIRA GSA-406: finer-grained control of MalformedReadFilter: want to exception out by default in these cases but pass them with a warning with a corresponding -U flag. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4476 348d0f76-0448-11de-a6fe-93d51630548a		2010-10-11 03:01:04 +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	Update MalformedReadFilter to pass reads that have cigar strings like 40S36I	2010-10-11 03:01:04 +00:00
test	More test cases for UG integration test. We currently fail doing multi-threaded gzip output, FYI	2010-10-08 20:22:12 +00:00