search

sanger-pathogens / Bio-Tradis

A set of tools to analyse the output from TraDIS analyses
https://sanger-pathogens.github.io/Bio-Tradis/
Other
22 stars 29 forks source link

Added support for samtools 1.x, -n multi-core option and fixed -m default #64

Closed RoyChaudhuri closed 8 years ago

RoyChaudhuri commented 8 years ago

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.

andrewjpage commented 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).

andrewjpage commented 8 years ago

Manually merged with PR https://github.com/sanger-pathogens/Bio-Tradis/issues/65