kcibul 25c30b12bb added MAF-style output ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1163 348d0f76-0448-11de-a6fe-93d51630548a		2009-07-03 15:10:19 +00:00
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gatk	Cleanup pileup and depth of coverage in preparation for release. Add pileup, depth of coverage, and print reads to package for distribution.	2009-07-02 14:54:01 +00:00
playground	added MAF-style output	2009-07-03 15:10:19 +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	Lot of code for coverage evaluation tools including first version of python script to evaluate the downsampled SSG callls made and the java code to make all the calls at Hapmap chip sites at various downsampling levels; ListUtils contains functions for randomnly subsetting lists (with replacement) which are useful for subsetting the same elements in both the reads and the offsets lists of a LocusWalker	2009-07-03 08:07:02 +00:00