feat: allow for left/right primer hits to overlap when building primer pair hits with OverlapDetector

[ameynert]

See discussion.

The code before this PR does not return primer pair hits where the hits to the left and right primers overlap, and does not specify a minimum acceptable amplicon size.

This change adds two new parameters to the OffTargetDetector to address this:

• allow_overlapping_hits - defaults to False to maintain current behaviour. If this is set to True, then primer pair hits where the left and right primer hits overlap are allowed, as long as they meet the acceptable amplicon size criteria.
• min_amplicon_size - defaults to 1 to maintain current behaviour, and is overridden by allow_overlapping_hits=False.

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 96.81%. Comparing base (c9075ac) to head (22fc66f).

Additional details and impacted files

@@                            Coverage Diff                            @@
##           am_overlap_detector_post_init_validation     #102   +/-   ##
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  Coverage                                     96.81%   96.81%           
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  Files                                            26       26           
  Lines                                          1787     1792    +5     
  Branches                                        215      216    +1     
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+ Hits                                           1730     1735    +5     
  Misses                                           31       31           
  Partials                                         26       26           

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[tfenne]

I took a quick look at this ... and I'm leaning towards thinking that we should:
a) not even parameterize, but always allow overlapping hits
b) default the "min amplicon size" to something slightly higher, e.g. 20bp

@nh13 and @ameynert what do you think of that?

[ameynert]

I took a quick look at this ... and I'm leaning towards thinking that we should: a) not even parameterize, but always allow overlapping hits b) default the "min amplicon size" to something slightly higher, e.g. 20bp

@nh13 and @ameynert what do you think of that?

I agree - I implemented it this way with the intention of not making a breaking change, but I think a user is more likely to not care too much if the primers overlap a bit so long as they get a long enough amplicon.