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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alignment	Add in weights. Massive performance improvements.	2009-09-24 23:19:15 +00:00
gatk	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
playground	Convert de novo SNP caller to run using parent1 and parent2 BAM files (by splitting contexts by reader using getMergedReadGroupsByReaders) instead of geli files providing a large speed-up and obviating the need for large whole-genome geli files.	2009-09-29 06:42:21 +00:00
secondarybase	Cleanup...deprecate FastaSequenceFile2 in favor of IndexedFastaSequenceFile or ReferenceSequenceFile from Picard, depending on the application.	2009-07-08 18:49:08 +00:00
utils	Generalized deletions in pileup	2009-09-29 15:58:43 +00:00