alimanfoo/vcfnp — pull request #11 by podpearson (2013-06-20 08:40:03+00:00)
Title: Allow variants, info and calldata to take a list of filenames in addition to a single filename string

Hi Alistair

I've modified variants, info and calldata so that in addition to running on a single vcf, they can now be run on a supplied list of filenames. These files will all need to have the same fields. If supplied with a list, each function will only use the first file in the list to ascertain fields. There is no checking that all other files in the list have these same fields.

I wrote this because my pipeline creates separate vcf files for different genomic regions, but I wanted to be able to read the information from all regions into a single numpy array, without having to first concatenate all the separate vcf files. I think this could also be useful to people working on other projects, for example the 1000 genomes project releases separate vcfs for each chromosome, and this would allow whole genome data to be read in from these.

Let me know what you think. No worries if you are not comfortable pulling this in, I'm happy to keep working with my own fork.

Cheers

Richard