rpoplin 0fbd81766b CountCovariates now uses any rod of type VariationRod with the name dbsnp as the source of known variant sites to skip over. It also grabs the platform string out of the read group when deciding which algorithm to use to calculate machine cycle. In this way it can now handle multi-platform bams. I added a new covariate: PositionCovariate. This is simply the offset regardless of which platform the read came from. This will be useful for comparing between the two covariates. Finally, this message serves as a warning that I will be killing the old recalibrator tomorrow after I've updated and verified new integration tests. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2077 348d0f76-0448-11de-a6fe-93d51630548a		2009-11-18 23:03:47 +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	CountCovariates now uses any rod of type VariationRod with the name dbsnp as the source of known variant sites to skip over. It also grabs the platform string out of the read group when deciding which algorithm to use to calculate machine cycle. In this way it can now handle multi-platform bams. I added a new covariate: PositionCovariate. This is simply the offset regardless of which platform the read came from. This will be useful for comparing between the two covariates. Finally, this message serves as a warning that I will be killing the old recalibrator tomorrow after I've updated and verified new integration tests.	2009-11-18 23:03:47 +00:00
test/org/broadinstitute/sting	more effective & efficient test for SecondBaseSkew	2009-11-18 20:53:32 +00:00