gatk-3.8

Author	SHA1	Message	Date
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
depristo	9d35f0ca67	The system now requires a dictionary file for a fasta file, or it throws an error. You can't just operate without a sequence dictionary any longer. We will transition to a GenomeLoc system that assumes a dictionary is available. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@320 348d0f76-0448-11de-a6fe-93d51630548a	2009-04-07 22:21:57 +00:00
hanna	2ee2623926	Move non-java code out of playground. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@154 348d0f76-0448-11de-a6fe-93d51630548a	2009-03-23 19:31:38 +00:00