rpoplin ec1a870905 Working with byte arrays is faster than working with Strings so the Covariates now take in byte arrays. None of the Covariates themselves used the reference base so I removed it. DinucCovariate now returns a Dinuc object which implements Comparable instead of returning a String because it was too slow. CountCovariates now uses a read filter to filter out unmapped reads and allows the user to specify -cov all which will use all of the available covariates, of which there are 7 now. If no covariates are specified it defaults to ReadGroup and QualityScore, the two required covariates. Initial code in place to leave SOLID bases alone if they have bad color space quality. TableRecalibration uses @Requires to tell the GATK to not give the reference bases since they weren't being used for anything. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2062 348d0f76-0448-11de-a6fe-93d51630548a		2009-11-17 21:50:52 +00:00
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config	Provide a default logger, some config settings, and some doc updates.	2009-04-29 02:06:05 +00:00
src/org/broadinstitute/sting	Working with byte arrays is faster than working with Strings so the Covariates now take in byte arrays. None of the Covariates themselves used the reference base so I removed it. DinucCovariate now returns a Dinuc object which implements Comparable instead of returning a String because it was too slow. CountCovariates now uses a read filter to filter out unmapped reads and allows the user to specify -cov all which will use all of the available covariates, of which there are 7 now. If no covariates are specified it defaults to ReadGroup and QualityScore, the two required covariates. Initial code in place to leave SOLID bases alone if they have bad color space quality. TableRecalibration uses @Requires to tell the GATK to not give the reference bases since they weren't being used for anything.	2009-11-17 21:50:52 +00:00
test/org/broadinstitute/sting	Integration tests actually run on real data now.	2009-11-17 21:04:14 +00:00