SFI index?

[mufernando]

Hi,

First, thanks for this great piece of software!!

I am getting some warnings about missing SFI index for my d4 files. I tried running the command the warning suggests but that doesn't do anything. In the docs there is no mention of SFI index, just bgzip index, which are present for this file:

[2026-03-30T18:45:57Z WARN  clam::loci::d4_bgzf] SFI index not found for D4 file: output/261OWLS/alignments/mosdepth/120794845.per-base.d4.gz, this will result in slower performance. You can create the index by running d4tools index build output/261OWLS/alignments/mosdepth/120794845.per-base.d4.gz

ls output/261OWLS/alignments/mosdepth/120794845.per-base.d4.gz*
output/261OWLS/alignments/mosdepth/120794845.per-base.d4.gz  output/261OWLS/alignments/mosdepth/120794845.per-base.d4.gz.gzi

[cademirch]

Hi. Thanks for the issue!

I should update the docs! The SFI warning is related to the D4 file. Before gzipping the d4 file, you can index the d4 file via d4tools index build -s <d4 file>. This should speed up querying it. However, this is not necessary and can be safely ignored.