Bug: macs3 hmmratac --cutoff-analysis-only always exits with exitcode 1 #704
Description
macs3 hmmratac --cutoff-analysis-only always exits with exitcode 1
This is because of line 244 in Commands/hmmratac_cmd.py, which says to sys.exit(1) if --cutoff-analysis-only is specified.
This causes issues when trying to include hmmratac in pipelines.
To Reproduce
macs3 hmmratac -i sample.bam --cutoff-analysis-only
Expected behavior
Should exit with exitcode 0.
System:
- OS: Rocky Linux 8
- Python version 3.11.5
- Numpy version 2.2.2
- MACS Version 3.0.3