[Bug]: sist hangs indefinitely on linux-aarch64 due to upstream irf bug

[harryswift01]

Bug Report

sist hangs indefinitely on linux-aarch64 (Ubuntu ARM) during regression testing. The hang is inside the third-party irf binary, not in sist's code.

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To Reproduce

YAML configuration

matrix:
  os: [ubuntu-26.04, ubuntu-26.04-arm, macos-26-intel, macos-26]

CLI command used

conda build conda-recipe --override-channels -c conda-forge -c bioconda --no-anaconda-upload

Actual output

On ubuntu-26.04-arm only, pytest hangs indefinitely in the cruciform/competition tests until the job times out. A bounded subprocess.run(..., timeout=...) around the irf call confirmed a subprocess.TimeoutExpired inside Popen._wait()/waitpid(), the hang is inside the irf child process itself.

Expected output

Completes in ~30s, all tests passing, same as linux-64/macOS.

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Environment and Versions

• Operating System: ubuntu-26.04-arm (linux-aarch64)
• Package Version: sist 1.0.0
• Python Version: 3.14.7
• Package list: irf 3.09-h661a7b0_0 (bioconda)

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Additional Context

Root cause: upstream IRF (Benson-Genomics-Lab/IRF, tag IRFv3.09), irfrun.h line 215, stores getc()'s result in a char instead of an int. On Linux aarch64, char defaults to unsigned, so the EOF check (-1) never matches and the read loop spins forever. linux-64 and osx-arm64 keep char signed, so they're unaffected.

[harryswift01]

Opened a fix for this: IRF PR root cause is irfrun.h's LoadSequenceFromFile storing getc()'s result in a char instead of an int, which breaks the EOF check specifically on platforms where char defaults to unsigned (Linux aarch64). Verified the fix builds and runs correctly on linux-64, linux-aarch64, macos-26-intel, and macos-26.