jmaguire 1fa71aa31d Now outputs stats. Doesn't do the downsampling thing because I think I'll have enough counts. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1184 348d0f76-0448-11de-a6fe-93d51630548a		2009-07-07 15:29:31 +00:00
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gatk	Temporary fix for Eric's problems with SOLiD reads: make sure the command-line argument system takes the --validation-strictness command-line argument into account when creating SAMFileReaders.	2009-07-07 15:18:05 +00:00
playground	Now outputs stats. Doesn't do the downsampling thing because I think I'll have enough counts.	2009-07-07 15:29:31 +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	Temporary fix for Eric's problems with SOLiD reads: make sure the command-line argument system takes the --validation-strictness command-line argument into account when creating SAMFileReaders.	2009-07-07 15:18:05 +00:00