chunk_snps.py works for autosomes only

[rkwalters]

Need to generalize chunk_snps.py to handle non-autosomal chromosomes. Current restriction is based on wanting the info file to handle centromeres for imputation chunking.

By extension this issue impacts gwas_rel.py (crashes if non-autosomal chromosomes present), but additional work will be needed there for testing non-autosomal chromosomes anyway.