depristo d77f4ebe31 CalibrateGenotypeLikelihoods now emits a molten data set with REF and ALT alleles, so that GL calibration can be evaluated as a function of the REF/ALT bases. DigestTable is a stand-alone Rscript that digests the multi-GB molten data table into a tiny table that shows reported vs. empirical GLs, as a function of a variety of features of the data, like REF/ALT, comp GT, eval GT, and GL itself. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5833 348d0f76-0448-11de-a6fe-93d51630548a		2011-05-21 14:02:30 +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	CalibrateGenotypeLikelihoods now emits a molten data set with REF and ALT alleles, so that GL calibration can be evaluated as a function of the REF/ALT bases. DigestTable is a stand-alone Rscript that digests the multi-GB molten data table into a tiny table that shows reported vs. empirical GLs, as a function of a variety of features of the data, like REF/ALT, comp GT, eval GT, and GL itself.	2011-05-21 14:02:30 +00:00
test	Significant change to the way subsetting by sample works with monomorphic sites. Now keeps the alt allele, even if a record is AC=0 after the subset. Previously, the system dropped the alt allele, which I don't think is the right behavior. If you really want a VCF without monomorphic sites, use the option to drop monomorphic sites after subsetting. See detailed information below.	2011-05-21 13:59:16 +00:00