ebanks 438d21842a 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. ... The major effects of this commit are as follows: 1. We no longer skip any good bases (of course, this change alone breaks every single integration test). 2. The dinuc covariate returns a "no dinuc" value for the first base of a read (but not for the last base anymore, since there is a valid dinuc) or if the previous base is a bad base (e.g. 'N'). I've done a bunch of testing on real data and everything looks right; however, let's wait until the recalibrator guru gets back from vacation next week and can double-check everything before shipping this out in another early access release. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2443 348d0f76-0448-11de-a6fe-93d51630548a		2009-12-24 20:41:29 +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	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
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