hanna 53db7b8faa Did some refactoring which broke some unit tests, and then failed to run ... the unit tests. Definitely not my best effort... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5599 348d0f76-0448-11de-a6fe-93d51630548a		2011-04-08 03:31:52 +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	Adding a ReadFilter to hard-clip out bases from adaptor sequences. This is actually slightly more correct than having it be part of LocusIteratorByState because it allows us to remove reads that are complete garbage (and there are definitely some) based on the insert sizes. However, although conceptually this is great, it doesn't actually work. 'Why?' you may ask. Because when we hard-clip reads it often changes their start positions... which means that reads are no longer passed to LocusIteratorByState in coordinate order... which makes it (understandably) barf all over the place (and makes for some really fascinating SNP calls). This took me forever to find. I'm going to bed.	2011-04-08 03:15:58 +00:00
test	Did some refactoring which broke some unit tests, and then failed to run	2011-04-08 03:31:52 +00:00