Feature request: extend mpileup API

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#1,453 3 comments 0 reactions 0 assignees View on GitHub

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Assessment

Difficulty
5/5
Estimated time
Over a week
Newbie friendliness
30/100
Issue type
Feature
Clarity
Needs clarification
Activity status
Stale
Tech stack
c
Domain
bioinformatics

Research direction

Start with the mpileup API entry point bam_mplp_auto() and inspect how its per-read structures are exposed. Determine an API design for retaining per-position data, including overlapping soft-clipped reads, and define completion around that data being available to mpileup callers for variant annotation.

Written by the indexing model from the issue text.

Description

The current mpileup API (bam_mplp_auto()) gives access to an array of per-read structures but does not give the possibility to store per-position data.

One possible use case would be to store the number of overlapping soft-clipped reads at each position, this would allow to annotate candidate variants in difficult regions as suspicious. Currently the removed soft-clipped reads are invisible to the mpileup caller.

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

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