samtools: fix ambiguous REF and ALT columns
samtools: fix ambiguous REF and ALT columns

Avoids non-N ambiguous bases in both samtools REF and ALT columns.
Thanks to Moiz Bootwalla
https://groups.google.com/forum/#!topic/biovalidation/ZsJyq4ao14s

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