ebanks 0571d9dcb9 Point MAX_QUAL_SCORE to SAMUtils.MAX_PHRED_SCORE. ... Also, array size for caches should be max score + 1. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2444 348d0f76-0448-11de-a6fe-93d51630548a		2009-12-24 20:47:32 +00:00
..
config	Provide a default logger, some config settings, and some doc updates.	2009-04-29 02:06:05 +00:00
src	Point MAX_QUAL_SCORE to SAMUtils.MAX_PHRED_SCORE.	2009-12-24 20:47:32 +00:00
test/org/broadinstitute/sting	The new recalibrator had been mimicking the behavior of the old one in that if there was no dinuc available (following a no-call base or at either end of a read), it didn't try to recalibrate. Now that Ryan has modularized the system, we no longer need to skip the base completely (we just need to skip the dinuc value)... which is good because the Picard people complained after realizing that cycle #1 never got recalibrated.	2009-12-24 20:41:29 +00:00