Possible 4x speed up of merge --gvcf ref.fa

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Assessment

Difficulty
4/5
Estimated time
3-5 days
Newbie friendliness
32/100
Issue type
Bug
Clarity
Needs clarification
Activity status
Stale
Tech stack
c
Domain
cli, performance

Research direction

Start by reproducing the reported timing difference between merge --gvcf ref.fa and merge --gvcf -. Inspect the merge --gvcf path and its use of faidx_fetch_seq, then determine whether reference pre-loading or caching affects the result. Done means a measured comparison and a confirmed explanation or documented outcome.

Written by the indexing model from the issue text.

Description

This needs to be tested, but it appears that merge --gvcf ref.fa is 4x slower than merge --gvcf -. This may be caused by inefficient use of faidx_fetch_seq; would pre-loading and caching the reference sequence help?

Dominant language
C
Stars
891
Forks
277
Avg merge
2d 23h
Merged PRs (30d)
2

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