False positive for -a detection in --mm2-params when using --cap-kalloc option

[JohGi]

Hi,

I'm running into a false positive when passing certain --mm2-params to ragtag.py scaffold. For instance:

ragtag.py scaffold --mm2-params '--cap-kalloc 100m -x asm5' reference.fasta query.fasta

triggers this error:

Traceback (most recent call last):
  File "/usr/local/bin/ragtag_scaffold.py", line 577, in <module>
    main()
  File "/usr/local/bin/ragtag_scaffold.py", line 420, in main
    al.run_aligner()
  File "/usr/local/lib/python3.9/site-packages/ragtag_utilities/Aligner.py", line 126, in run_aligner
    if all([self.params_are_valid(), self.exec_is_valid()]):
  File "/usr/local/lib/python3.9/site-packages/ragtag_utilities/Aligner.py", line 199, in params_are_valid
    raise ValueError("Alignments must not be in SAM format (-a).")
ValueError: Alignments must not be in SAM format (-a)."

even though I'm not using -a. Looking at the code, it seems that the check causes any option containing the letter "a" (like --cap-kalloc) to trigger the error.

I think something like:

all_flags = self.params_string.split()
if "-a" in all_flags:
    raise ValueError("Alignments must not be in SAM format (-a).")

could fix the issue.

Thanks a lot for your work on RagTag!
Best,
Johanna