rohanmaddamsetti/parallyze — pull request #4 by camillescott (2014-04-02 17:50:46+00:00)
Title: debugging code for gd parsing problem

I added some debugging code which highlights the issue you're having; namely, that intergenic SNPs are never being parsed, because column 13 (line[12]) never contains the key "snp_type." That key is in a much later column. So, when it should be finding intergenic SNPs, it's now outputting "unaccounted for SNP type."

I left he debugging code in so you can get an idea of how I tackle these sorts of problems. Good luck!