rpoplin 98f921fe24 The refactored CountCovariates now hashes the read object into a HashMap which holds all the properties the covariates pull out of the read over and over again such as read group string, bases string and its complement string, quality scores, etc. This results in a big speed up. CountCovariatesRefactored is now just slightly slower than CountCovariates (perhaps 1.07x according to my latest time trial). Thanks to Alec for suggesting IdentityHashMap. CycleCovariate now warns the user that is is defaulting to the Solexa definition of cycle when the platform string pulled out of the read is unrecognized instead of halting with an Exception. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2108 348d0f76-0448-11de-a6fe-93d51630548a		2009-11-21 20:38:17 +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/org/broadinstitute/sting	The refactored CountCovariates now hashes the read object into a HashMap which holds all the properties the covariates pull out of the read over and over again such as read group string, bases string and its complement string, quality scores, etc. This results in a big speed up. CountCovariatesRefactored is now just slightly slower than CountCovariates (perhaps 1.07x according to my latest time trial). Thanks to Alec for suggesting IdentityHashMap. CycleCovariate now warns the user that is is defaulting to the Solexa definition of cycle when the platform string pulled out of the read is unrecognized instead of halting with an Exception.	2009-11-21 20:38:17 +00:00
test/org/broadinstitute/sting	The Unified Genotyper now sorts the sample names in the vcf that it outputs.	2009-11-20 16:13:18 +00:00