softmask improvements - Githubissues

artic-network / fieldbioinformatics

The ARTIC field bioinformatics pipeline

MIT License

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softmask improvements #18

Closed will-rowe closed 4 years ago

will-rowe commented 4 years ago

This PR covers a few improvements to the softmasking code in align_trim:

updates CIGAR processing to include additional operators
in the event that softmasking created a leading D operator, the read is no longer dropped and the alignment is instead shuffled to remove the D
added more error handling
removed a few unnecessary assignments and closed some filehandles
documented the code and updated some variable names to be more descriptive
added unit tests for the softmasking and the primer finding functions

A couple of minor things outside align_trim:

updated envs to only provide dependencies, not install the pipeline itself, and updated travis to install the pipeline instead
updated the doc templates (which are now being served at readthedocs)
merge CHANGELOG and HISTORY into a single CHANGELOG
move the lab-on-an-ssd markdown file to now be included as a section in the docs FAQ