PureCN: restrict input coverage to standard chromosomes
PureCN: restrict input coverage to standard chromosomes

Avoid haplotype and other chromosomes as inputs by removing these additional
chromosomes from the CNVkit input cnr files.

a113n/bcbio-nextgen,a113n/bcbio-nextgen,vladsaveliev/bcbio-nextgen,vladsaveliev/bcbio-nextgen,chapmanb/bcbio-nextgen,lbeltrame/bcbio-nextgen,lbeltrame/bcbio-nextgen,a113n/bcbio-nextgen,vladsaveliev/bcbio-nextgen,chapmanb/bcbio-nextgen,chapmanb/bcbio-nextgen,lbeltrame/bcbio-nextgen