[IO] BAM index support

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#2,985 6 comments 0 reactions 0 assignees View on GitHub

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Assessment

Difficulty
5/5
Estimated time
Over a week
Newbie friendliness
25/100
Issue type
Feature
Clarity
Needs clarification
Activity status
Stale
Tech stack
cpp
Domain
bioinformatics

Research direction

Start with the documented arbitrary-index support and the sam_file_input entry point mentioned in the issue. Determine whether companion *.bam.bai files are currently supported and what API or documentation changes would be needed for automatic loading. Done means the support behavior is implemented or clearly documented, with coverage for loading a BAM file alongside its index.

Written by the indexing model from the issue text.

Description

feature/proposal

Platform

  • SeqAn version: 3.0
  • Operating system: Linux kaya 5.17.9-arch1-1 #1 SMP PREEMPT Wed, 18 May 2022 17:30:11 +0000 x86_64 GNU/Linux
  • Compiler: gcc (GCC) 12.1.0

Question

Is there a way to use *.bam.bai files to use as an index? The documentation on your site covers generating arbitrary indexes, but can it also be used to (auto-)load the companion index file when loading the BAM file? I currently use seqan3::sam_file_input in{file}; to load the input file.

Thank you!

Dominant language
C++
Stars
463
Forks
90
Avg merge
1h 11m
Merged PRs (30d)
3

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