fix: Check against HN tag instead of is_unmapped property
#69
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I think there needs to be a further change here, or at least a clear explanation/justification of why not. I think when the record is marked as unmapped, what that really means is that bwa believes the primary alignment to be erroneous - and as such I think to_hits() should ignore the primary alignment and only decode the secondary alignments.
WalkthroughThe changes in the pull request primarily focus on the Assessment against linked issues
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prymer/offtarget/bwa.py (1)
159-162: Remove unnecessary whitespace in docstring blank lineThe blank line at line 161 contains whitespace. Please remove the extra whitespace to adhere to PEP 8 style guidelines.
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161-161: Blank line contains whitespace
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prymer/offtarget/bwa.py (2)
363-373: Logic for adjusting hit counts is correctThe updated logic in lines 363-373 appropriately adjusts
num_hitsandhits, ensuring that theBwaResultaccurately reflects the total number of hits even when the number of hits exceedsmax_hits.
418-422: Correctly filter out hits that extend beyond contig boundariesThe added filtering in lines 418-422 effectively removes artifacts from
bwa aln's alignment process by excluding hits that extend beyond the end of a contig, enhancing the accuracy of the results.
Co-authored-by: Tim Fennell <[email protected]>
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prymer/offtarget/bwa.py (1)
161-161: Remove whitespace on blank lineThere's trailing whitespace on the blank line at line 161. This can lead to style inconsistencies.
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161-161: Blank line contains whitespace
Remove whitespace from blank line
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prymer/offtarget/bwa.py
161-161: Blank line contains whitespace
Remove whitespace from blank line
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prymer/offtarget/bwa.py (2)
363-376: Logic correctly utilizesHNtag for hit countThe updated logic appropriately uses the
HNtag to determine the number of hits, aligning with the PR objectives. It correctly handles cases where the number of hits is zero, between zero andself.max_hits, and greater than or equal toself.max_hits.
421-424: Properly filters out hits spanning contig boundariesThe addition ensures that hits extending beyond the end of a contig are removed, addressing artifacts from
bwa aln's alignment process. This enhances the accuracy of the returned hits.
Closes #68
bwa alnproduces inconsistent behavior when recording the mapped status of multiply mapping reads. In most cases, such reads are flagged as mapped with a mapq of 0. However, we have discovered some cases where these reads are flagged as unmapped.prymercurrently relies on the unmapped flag to identify reads with a hit count of zero. This has been yielding errors when attempting to parse reads in the latter category. This information can instead be obtained directly from theHNtag.