hanna 85bc9d3e91 (Hopefully) temporary hack: load contig information by contig name rather than contig id to avoid ... off-by-one errors. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2078 348d0f76-0448-11de-a6fe-93d51630548a		2009-11-18 23:33:27 +00:00
..
alignment	Finally reinstate the iterator-style interface. Get rid of some scaffolding code.	2009-11-16 02:34:19 +00:00
gatk	(Hopefully) temporary hack: load contig information by contig name rather than contig id to avoid	2009-11-18 23:33:27 +00:00
playground	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
secondarybase	Rev'ing Picard, which includes the update to get all the reads in the query region (GSA-173). With it come a bunch of fixes, including retiring the FourBaseRecaller code, and updated md5 for some walker tests.	2009-09-30 20:37:59 +00:00
utils	A bunch of changes needed to make outputting pooled calls possible	2009-11-18 18:42:57 +00:00