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matsengrp / cft

Clonal family tree
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274 alignment #292

Closed eharkins closed 4 years ago

eharkins commented 4 years ago

Aligning only if necessary and when doing so, warning to check the alignment since the alignment step in CFT will be removed once aligning is default in partis (and therefore we're not spending the time testing CFT alignment code to be sure it doesn't suffer from ignoring partis indel information).

See https://github.com/matsengrp/cft/issues/274

metasoarous commented 4 years ago

Overall, LGTM :+1:. Only thing I'd give a bit more thought to is the option name. Will update if I have any clearer thoughts on that, but have to switch gears for now.

eharkins commented 4 years ago

@metasoarous could go with --align but wanted it to be clear that indel reversed sequences will be used unless you use the option (assuming indels exist). Could go with --preserve-indels?