Closed RoyChaudhuri closed 8 years ago
Thanks a million for the Pull Request. We'll take a look and fix up the Travis samtools tests (they changed the sort syntax in 1.3).
Manually merged with PR https://github.com/sanger-pathogens/Bio-Tradis/issues/65
Added support for samtools 1.x (older versions will still work)
Added -n option to allow use of multiple cores for SMALT and samtools sort
Changed the default for -m from 30 to 0. Filtering on mapping quality can have unintended consequences for TraDIS analysis, as it effectively removes ambiguously-mapped reads from the analysis, meaning that repeat regions of the genome can be incorrectly identified as essential.