feat: allow for left/right primer hits to overlap when building primer pair hits with OverlapDetector
#102
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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. |
…sing min amplicon size parameter
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| @@ -165,13 +165,13 @@ def build_primer_pairs( # noqa: C901 | |||
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| # If the right primer isn't "to the right" of the left primer, move on | |||
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WalkthroughThe pull request introduces modifications to the off-target detection functionality in the Prymer library. The changes primarily focus on enhancing the Finishing Touches
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Actionable comments posted: 3
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prymer/api/picking.py(1 hunks)prymer/offtarget/offtarget_detector.py(11 hunks)tests/offtarget/test_offtarget.py(7 hunks)
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tests/offtarget/test_offtarget.py (1)
288-294: Tests updated appropriately.The tests correctly incorporate the new parameters, ensuring proper coverage for
min_amplicon_sizeandallow_overlapping_hits.
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prymer/offtarget/offtarget_detector.py (1)
643-651: Consider extracting the amplicon validation logic.The amplicon length and overlap validation logic could be moved to a separate method for better readability.
def _to_amplicons(...): + def _is_valid_amplicon(pos_hit: BwaHit, neg_hit: BwaHit) -> bool: + amplicon_length = neg_hit.end - pos_hit.start + 1 + return (min_len <= amplicon_length <= max_len and + (allow_overlapping_hits or neg_hit.start > pos_hit.end)) + ... for positive_hit in positive_hits_sorted: for negative_hit_index, negative_hit in enumerate(...): - amplicon_length: int = negative_hit.end - positive_hit.start + 1 - if min_len <= amplicon_length <= max_len and ( - allow_overlapping_hits or negative_hit.start > positive_hit.end - ): + if _is_valid_amplicon(positive_hit, negative_hit): amplicons.append(...)
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prymer/offtarget/offtarget_detector.py(11 hunks)
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🔇 Additional comments (4)
prymer/offtarget/offtarget_detector.py (4)
174-176: LGTM! Parameter additions are well-structured.The new parameters
min_amplicon_sizeandallow_overlapping_hitsare added with appropriate default values.
231-237: LGTM! Clear and comprehensive docstring updates.The documentation for new parameters is thorough and explains the interaction between
min_amplicon_sizeandallow_overlapping_hits.
262-266: LGTM! Robust parameter validation.The validation logic for
min_amplicon_sizeensures it falls within valid bounds (1 to max_amplicon_size).
381-383: LGTM! Clear documentation of overlapping hits behavior.The docstring clearly explains how
allow_overlapping_hitsaffects amplicon detection.
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
OffTargetDetectorto address this:allow_overlapping_hits- defaults toFalseto maintain current behaviour. If this is set toTrue, 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 to1to maintain current behaviour, and is overridden byallow_overlapping_hits=False.