hanna 88d0677379 Misc correctness enhancements: develop the bin selector into a recursive algorithm and return a shard when reads are missing. Also improve the performance of the read filter that clips reads not actually present in the shard. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2870 348d0f76-0448-11de-a6fe-93d51630548a		2010-02-22 22:19:06 +00:00
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alignment	Misc bug fixes.	2010-01-05 14:48:19 +00:00
analyzecovariates	Added an option to AnalyzeCovariates to set the max value of the histograms to make them easier to directly compare.	2010-01-31 23:13:57 +00:00
gatk	Misc correctness enhancements: develop the bin selector into a recursive algorithm and return a shard when reads are missing. Also improve the performance of the read filter that clips reads not actually present in the shard.	2010-02-22 22:19:06 +00:00
oneoffprojects	Adding depth of coverage features to firehose summary tools	2010-02-19 19:47:16 +00:00
playground	Added a playground concordance analyzer for summarizing VariantEval across a group.	2010-02-22 20:28:52 +00:00
utils	Optimization - Added method to Covariates: void getValues( SAMRecord read, Comparable[] comparable ) which takes an array of size (at least) read.getReadLength() and fills it with covariate values for all positions in the given read. Made CovariateCounterWalker and TableRecalibrationWalker use this method instead of calling getValue(..) for each covariate and each offset.	2010-02-22 17:35:25 +00:00