modkit Request/Bug: Allow compressed reference

Dear modkit team, we have been using modkit for a while and every time we need to select a different reference during the workflow as modkit does not allow for compressed reference (genome.fasta.gz). I have tried gzip and bgzip and got the same results with version 0.4.3 and the latest 0.5.0

The output shows the following message

> fetching sequence failed, FASTA file is truncated.

endlessly and does not terminate the process. If the output is being saved in memory (i.e subprocess.run) it fills the memory of the pyhton process and crashes the computer, if its being directed to a log file it fills the disk if the pipeline is being run unattended (as it usually is the case)

Cheers Luis

Jun 03 '25 20:06 lfpaulin

Hello @lfpaulin,

I'll get a release candidate that allows this ASAP. Sorry that it didn't make it into the latest release.

Jun 03 '25 22:06 ArtRand

Thanks a lot

Jun 04 '25 03:06 lfpaulin

Hello @lfpaulin,

Here's a build that allows .gz references. If you want to build it yourself, I've also pushed the branch. These changes will make it into the next release after I do some testing/benchmarking, but I thought I'd give you a chance to try it first.

modkit_deva3b3405_u16_x86_64.tar.gz

Jun 06 '25 16:06 ArtRand