rpoplin 70df30fc1b Added method to AlignmentUtils which takes a read's cigar and the refBases char array given to a ReadWalker and returns the aligned reference char array. Bug fix in solid_recal_modes to use this aligned reference array. Recalibrator version number is no longer separate for each of the two walkers. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2589 348d0f76-0448-11de-a6fe-93d51630548a		2010-01-15 15:36:59 +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	Added method to AlignmentUtils which takes a read's cigar and the refBases char array given to a ReadWalker and returns the aligned reference char array. Bug fix in solid_recal_modes to use this aligned reference array. Recalibrator version number is no longer separate for each of the two walkers.	2010-01-15 15:36:59 +00:00
test/org/broadinstitute/sting	First successful test of new sharding system prototype. Can traverse over reads from a single	2010-01-15 03:35:55 +00:00