andrewk 4cbf069de1 First version of coverage evaluation tool ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1148 348d0f76-0448-11de-a6fe-93d51630548a		2009-07-01 20:52:25 +00:00
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gatk	Prep for documenting command-line arguments: delete some arguments that don't make sense any more given	2009-07-01 18:23:35 +00:00
playground	First version of coverage evaluation tool	2009-07-01 20:52:25 +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	Bug in setContig() fixed: sequence dictionary's .getSequences().contains() and .getSequences().indexOf() do NOT work when applied to contig names (Strings), since getSequences() returns a list of SAMSequenceRecord's; changed to querying the dictionary directly for specified contig name	2009-07-01 20:50:09 +00:00