sanger-pathogens/Bio-VertRes-Config — pull request #48 by CraigPorter (2013-09-17 11:08:12+00:00)
Title: bacteria mapping and snp-calling with smalt defaults to -r -1

Bacteria SNP-Calling and bacteria mapping with smalt default to smalt mapping parameter -r -1. Reads with multiple best matches are set to unmatched.

Do not merge this request until researchers informed.