add position ignore - Githubissues

aineniamh / snipit

snipit: summarise snps relative to your reference sequence

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add position ignore #2

Closed tomkinsc closed 3 years ago

tomkinsc commented 3 years ago

Feedback is welcome on this one.

This adds two new command line arguments:

--exclude-ambig-pos: excludes from the figure any positions where an ambiguous call exists
--ignore-positions: excludes from the figure any positions explicitly specified (accepting one or more integer positions)

Also, mea culpa! This also restores an import, import snp_functions as sfunks, to command.py that was lost in my previous PR due to an override I have in my dev config.

aineniamh commented 3 years ago

Sounds great too! I guess if there's positions you know you're not interested in! Could also add in a "range of interest", like if you're only wanting to look at a particular part of the input sequence.