chartl d57a86ad41 Not nearly as badass as it looks. The problem I mentioned yesterday with "bleeding in" of samples comes from VCFUtils and SampleUtils looking for all VCF-class RODs in the tracker, and stealing the name from them. I have introduced a new HapmapVCF - type rod for use ... when you want to protect your VCF header from being infected by the samples in a bound hapmap VCF. Changes are as follows: VCFRecord - minor change to adapt isNovel() to the case where the dbsnp ID field is empty, but the info field has DB=1 HapmapVCFRod - introduced for the reason at the top RODRecordIterator - was: catch ( Exception e ) { throw new StingException("long ass message") } is now: catch ( Exception e ) { throw new StingException("long ass message",e) } to permit full stack ejaculation. RodVCF - Now with more brackets! ReferenceOrderedData - registering HapmapVCF as a bindable string VariantAnnotator - There's an extra space on a line. And some new brackets. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2733 348d0f76-0448-11de-a6fe-93d51630548a		2010-01-29 15:19:50 +00:00
..
config	Provide a default logger, some config settings, and some doc updates.	2009-04-29 02:06:05 +00:00
src	Not nearly as badass as it looks. The problem I mentioned yesterday with "bleeding in" of samples comes from VCFUtils and SampleUtils looking for all VCF-class RODs in the tracker, and stealing the name from them. I have introduced a new HapmapVCF - type rod for use	2010-01-29 15:19:50 +00:00
test/org/broadinstitute/sting	VariantFiltration now accepts any number of --name --filter expressions, and annotates the VCF file with each name that matches. Very useful	2010-01-29 12:13:08 +00:00