5 Commits (d7f3102c3f31a2550b5a74a18a902af158c7fec2)

Author	SHA1	Message	Date
aaron	871cf0f4f6	Call out ROD types by there record type, instead of the codec type (which was clumsy). So instead of: ... @Requires(value={},referenceMetaData=@RMD(name="eval",type= VCFCodec.class)) you'd say: @Requires(value={},referenceMetaData=@RMD(name="eval",type= VCFRecord.class)) Which is more in-line with what was done before. All instances in the existing codebase should be switched over. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3457 348d0f76-0448-11de-a6fe-93d51630548a	2010-05-28 14:52:44 +00:00
ebanks	e2674671e7	The liftover code needs to *hard filter* records whose reference changes (since they no longer adhere to the VCF spec as they don't match the new reference - and can't be converted to VariantContext). ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3448 348d0f76-0448-11de-a6fe-93d51630548a	2010-05-27 19:22:47 +00:00
depristo	8a725b6c93	Restructuring of ReferenceContext and ReadWalkers to accept a ReferenceContext. Now ReferenceContext is byte[] backed not char[]. Please no more chars for the reference. All of the tests pass now. Coming check-ins are going to clean up the char / byte problems in the GATK ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3397 348d0f76-0448-11de-a6fe-93d51630548a	2010-05-19 23:27:55 +00:00
ebanks	44de92e09d	Checking in the liftover script. I am including a post-processing walker to filter out bad records written in under 10 minutes as per my agreement with Mark. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3321 348d0f76-0448-11de-a6fe-93d51630548a	2010-05-07 12:31:56 +00:00
ebanks	18f1d31a22	Moving to and organizing in core. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3320 348d0f76-0448-11de-a6fe-93d51630548a	2010-05-07 04:05:36 +00:00