Fix #60: "strand sometimes no conserved when AvoidPattern is localized"

Zulko commented 2 years ago

This fixes #60 (@veghp @deto). Changes:

The fix: In overlap_region(self), the final location always gets the strand of self.
Cosmetic: I renamed variable names (to left_location and right_location) in overlap_region because 5-year-ago me wrote this method in a very confusing way.
Added a new test based on @deto's example in #60. The test fails before this MR, succeeds after.
Formatting: The commit is a bit polluted by a couple of auto-edits from running black to format the files (sorry for that), but didn't want to undo the changes as they go in the right direction.

I didn't version-bump because I'm not 100% sure what the workflow is there @veghp

Zulko commented 2 years ago

@veghp I belive this can be merged and released, closing #60 .

veghp commented 2 years ago

Thanks, I merged with dev -- Travis seems to be down, so I'll release it once it's okay. Also addressed https://github.com/Edinburgh-Genome-Foundry/DnaChisel/issues/53 to be released with it.

Edinburgh-Genome-Foundry / DnaChisel