Feature: Fuzzy motif search

[Adamtaranto]

Motif runs in clipped regions of raw ONT reads may contain homopolymer errors where the number of sequential repeated bases is incorrect. Currently teloclip has an option --noPoly which compresses homopolymer runs in both the motif and the read befor looking for matches. However, this is likely to reduce specificity and increase false positive matches.

Proposal: Replace homopolymer compression with a regex based fuzzy search method.

Steps:

• Convert input motif to regex where all runs of > 1 base allow for a +/- 1 range.
• Search given sequence with pattern
• Return count of non-overlapping matches
• Add noisy reporting of motif counts per readname in L/R end of contigname
• Add Warning for depreciated --noPoly to be removed in future major release.

Should default behaviour be exact match or fuzzy search?