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biomedicalinformaticsgroup / Sargasso

Sargasso disambiguates mixed-species high-throughput sequencing data.
http://biomedicalinformaticsgroup.github.io/Sargasso/
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Add a "permissive" startup option which only compares read mappings #47

Closed lweasel closed 7 years ago

lweasel commented 7 years ago

i.e. only assign reads to genomes based on which is the better match, and don't reject any reads due to their intrinsic mapping qualities. This corresponds to the option values:

--mismatch-threshold 100 --minmatch-threshold 100 --multimap-threshold --overhang-threshold 0

lweasel commented 7 years ago

nb. actual option values implemented:

--mismatch-threshold 25 --minmatch-threshold 25 --multimap-threshold 999999 --overhang-threshold 0