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COMBINE-lab / pufferfish

An efficient index for the colored, compacted, de Bruijn graph
GNU General Public License v3.0
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Align command fails or shows help when options aren't in a specific order #41

Closed hermidalc closed 1 year ago

hermidalc commented 1 year ago

In align if index, mate1, mate2, output aren't in a specific order then the command shows the help and exits or fails with strange messages about the index missing. The is counterintuitive since all options are options with flags not positional parameters.

hermidalc commented 1 year ago

Actually sorry nevermind, it was giving index loading errors if there's an option you've specified that's not in the spec, which was throwing me off