ebanks 19bfe43173 First pass at a unified caller, being checked in now so Mark can give feedback if he chooses and so Matt can debug issues with the ArgumentCollection class. ... Some notes: 1. This design should be flexible enough to include pooled calling (for now) after discussions with Chris. 2. Using the unified caller with the SingleSampleCalculationModel emits the exact same output as SSG over all of chr20 for NA12878. Additionally, when we include the "max deletions allowed at a locus" argument (so we don't try to call SNPs at deletion sites), it removed 233 SNP calls in chr20 that were clearly indel artficts. 3. The MultiSampleEMCalculationModel is still a work in progress and will be checked in later this week. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1740 348d0f76-0448-11de-a6fe-93d51630548a		2009-09-29 16:48:15 +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	First pass at a unified caller, being checked in now so Mark can give feedback if he chooses and so Matt can debug issues with the ArgumentCollection class.	2009-09-29 16:48:15 +00:00
test/org/broadinstitute/sting	Cosmetic change to list sampling functions: the typical usage of n and k were reversed. No change in functionality of the classes has been made and unit tests still pass.	2009-09-28 18:12:32 +00:00