gatk-3.8

Author	SHA1	Message	Date
depristo	50ae1763f7	Support for -continue_after_errors flag in the validating pileup walker in case you want to see errors as they arise, rather than aborting greedily git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@461 348d0f76-0448-11de-a6fe-93d51630548a	2009-04-17 03:13:11 +00:00
depristo	24722a442e	Slight code cleanup git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@421 348d0f76-0448-11de-a6fe-93d51630548a	2009-04-14 22:21:36 +00:00
depristo	72a3d84ed2	General purpose pileup code -- you can use these features to obtain detailed pileup data from reads and offsets. Useful for all pileup based walkers. Expanded support for rodSAMPileup to enable the new ValidatingPileupWalker, which takes a samtools pileup output and checks that GATK gives identical output as samtools on a per base and per qual pileup. It's going to be a very useful validation tool. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@418 348d0f76-0448-11de-a6fe-93d51630548a	2009-04-14 22:13:10 +00:00