Support indexed GAF - Githubissues

vgteam / vg

tools for working with genome variation graphs

https://biostars.org/tag/vg/

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Support indexed GAF #4248

Closed adamnovak closed 2 months ago

adamnovak commented 3 months ago

Changelog Entry

To be copied to the draft changelog by merger:

vg now supports reading from indexed GAF files of reads in many places where an indexed GAM file can be used

Description

This pulls in @jmonlong's GAF indexing machinery.

We should wait for htslib to take https://github.com/samtools/htslib/pull/1759 first, unless we want to maintain a fork of htslib again.