todo: Improve `--regions-overlap variant`

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#1,746 opened on Feb 9, 2024 0 comments 0 reactions 0 assignees View on GitHub

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Assessment

Difficulty: 5/5
Estimated time: Over a week
Newbie friendliness: 35/100

Issue type: Feature
Clarity: Mostly clear
Activity status: Stale
Tech stack: c
Domain: bioinformatics

Research direction

Start in synced_bcf_reader.c at the current --regions-overlap variant|2 implementation around line 569. Examine how left trimming handles variants such as ACGA > A--A and where the API would need to represent left- versus right-trimming choices. Done means the mode recognizes the actual affected bases without spurious overlaps, or a documented opposite-overlap mode is added.

Written by the indexing model from the issue text.

Description

The mode --regions-overlap variant|2 is supposed to recognize the actual bases affected by the variant. This is trickier than currently implemented in https://github.com/samtools/htslib/blob/develop/synced_bcf_reader.c#L569.

The existing code trims variants from the left, but does not take into account cases like ACGA > A--A, which can be trimmed from both ends.

In addition, the API does not give the choice to trim from the left or right in ambiguous cases. For many use cases, the desired behavior is to trim in such a way to prevent spurious overlaps. Alternatively, a new mode 3 can be added which acts the opposite way and reports an overlap whenever possible.

Dominant language: C
Stars: 950
Forks: 475
Avg merge: 3d 13h
Merged PRs (30d): 11

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