Added support for samtools 1.x, -n multi-core option and fixed -m default #64
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…g/sorting and changed default mapping quality to 0 (to prevent repeat regions from being incorrectly called as essential)
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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). |
Merged
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Manually merged with PR #65 |
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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.