Fixed a bug in remove_insertions - it was sometimes removing insertions smaller than the minimum size the user sets - I've fixed it now
Made it so that you need a minimum of three sequences for remove_insertions, crop_ends and remove_divergent but a minimum of two for everything else - I think it's ok to remove gap only or short (or make mini alignments or a consensus) with two sequences.
Made it only run remove gap only multiple times if you actually run multiple cleaning functions - before it ran four times always
It was logging "removed sites: " with no numbers if it removed none - now it just logs nothing
Made everything consistent with the pep8 python style guide - https://www.python.org/dev/peps/pep-0008/ - the vast majority of the changes are for this and are either splitting lines so they are not too long and removing or adding whitespace.
I have:
Fixed a bug in remove_insertions - it was sometimes removing insertions smaller than the minimum size the user sets - I've fixed it now
Made it so that you need a minimum of three sequences for remove_insertions, crop_ends and remove_divergent but a minimum of two for everything else - I think it's ok to remove gap only or short (or make mini alignments or a consensus) with two sequences.
Made it only run remove gap only multiple times if you actually run multiple cleaning functions - before it ran four times always
It was logging "removed sites: " with no numbers if it removed none - now it just logs nothing
Made everything consistent with the pep8 python style guide - https://www.python.org/dev/peps/pep-0008/ - the vast majority of the changes are for this and are either splitting lines so they are not too long and removing or adding whitespace.