RagTag overly sensitive when identifying minimap2 SAM format flag

[ASLeonard]

Adding additional mm2 params of -xasm5 throws an error because RagTag sees a "-a" flag indicating SAM output from minimap. The actual argument is equivalent in minimap2's eyes as -x asm5 which is valid, because there is no "-" and "a" in the same string. Pretty annoying to catch all these cases, but raising in case anyone else hits this.

RagTag/ragtag_utilities/Aligner.py

Lines 197 to 199 in df751bf

	all_flags = "".join([i for i in self.params_string.split(" ") if i.startswith("-")])
	if "a" in all_flags:
	raise ValueError("Alignments must not be in SAM format (-a).")

[yjx1217]

Same issue here! -_-!
I ended up commenting out these two lines to make my code run ....

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

Best,
Jia-Xing