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aineniamh / snipit

snipit: summarise snps relative to your reference sequence
GNU General Public License v3.0
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change '--ignore-positions' to include/exclude ranges #4

Closed tomkinsc closed 3 years ago

tomkinsc commented 3 years ago

This replaces the argument --ignore-positions, which was confusingly named and only accepted specific integer positions, with --exclude-positions which accepts numeric ranges or specific positions (ex. '100-200' or '100 105'). A related argument, --include-positions, is provided to allow the user to pass a restricted range or list of positions to be included (only), as suggested by @aineniamh in #2. Position exclusion is considered after position inclusion. This also moves the x-axis scale labels to be adjacent to the genome map if --flip-vertical is specified.

tomkinsc commented 3 years ago

@aineniamh, thoughts on merging this if it looks ok? (or if it doesn't, I can revise/close this PR.)

aineniamh commented 3 years ago

Ah sorry, I'd missed this! Thanks for pinging me about it- I'll merge it in now!