Join GitHub today
GitHub is home to over 28 million developers working together to host and review code, manage projects, and build software together.Sign up
Adding ADAMContig back to ADAMVariant. #245
All automated tests passed.
added a commit
this pull request
May 21, 2014
@hammer Good question; I'm not 100% sure why it was removed (paging @mlinderm) but I believe the reason it was removed is because the code that converts from VCF only has (easy) access to the contig name.* I've added it back, because it is useful to track this info if we are generating VCFs from data that is already in ADAM (and that already has all the contig data). Otherwise, the contig name is a subset of the full contig info, so there's no correctness issue.
* I believe that the full contig info can be recovered from the VCF input; due to the way that Picard is designed, you need to do some dirty dancing. I'll try to fix this in a follow-on pull request.