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mhoban / rainbow_bridge

GNU General Public License v3.0
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Make some --skip-* options into things that are off by default #94

Closed mhoban closed 2 months ago

mhoban commented 2 months ago

The options for blast and lulu should probably be off by default, rather than on. Thus, instead of skipping blast on --skip-blast, we blast on the existence of a --blast-db option and instead of skipping on --skip-lulu, we'll do lulu on --lulu.

I think that --skip-primer-match is still probably appropriate since it's an edge case, but maybe we'll change the name to --no-pcr or something.

mhoban commented 2 months ago

Done and merged.

--blast and --lulu now enable those options (they're off by default) and --skip-primer-match is no --no-pcr.