bam1_t build function

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#789 13 comments 0 reactions 0 assignees View on GitHub

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Assessment

Difficulty
4/5
Estimated time
3-5 days
Newbie friendliness
35/100
Issue type
Feature
Clarity
Mostly clear
Activity status
Stale
Tech stack
c
Domain
bioinformatics

Research direction

Start by reading the CRAM internal function bam_construct_seq and the surrounding functions, then inspect how BAM records are represented and assembled from component pieces. Define the construction path needed to avoid manual bit/byte shuffling, including sequence creation, and verify that it produces a valid BAM record.

Written by the indexing model from the issue text.

Description

See Will Stokes' request at https://sourceforge.net/p/samtools/mailman/message/36454348/

We desire a way to construct a BAM record from the component pieces that isn't just a manual mess of bit/byte shuffling. Most of it is easy, but some things such as creation of the sequence is complex.

CRAM has an internal function for this (bam_construct_seq), so looking at that and surrounding functions may be a suitable starting point.

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

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