kiran d412c5dc2f Updated to use SecondaryBaseAnnotator class. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1126 348d0f76-0448-11de-a6fe-93d51630548a		2009-06-30 16:08:43 +00:00
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gatk	When you get the reference string for a read that is mapped partially off the end of a contig, the string is masked with X's for base positions without corresponding reference positions.	2009-06-29 20:51:55 +00:00
playground	Updated to use SecondaryBaseAnnotator class.	2009-06-30 16:08:43 +00:00
secondarybase	A single class that can be handed reads for training and basecalling. When in training mode, we accumulate no more than 10000 reads and always replace the lowest-quality reads with superior quality reads. Thus, the training set always contains 10000 of the best reads available. After training is complete, the class can be interrogated to return the SQ tag for a given RawRead object.	2009-06-30 16:03:15 +00:00
utils	Some files to support generic genotype outputing	2009-06-26 15:43:41 +00:00