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.
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all_flags = "".join([i for i in self.params_string.split(" ") if i.startswith("-")]) |
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if "a" in all_flags: |
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raise ValueError("Alignments must not be in SAM format (-a).") |
Adding additional mm2 params of
-xasm5throws an error because RagTag sees a "-a" flag indicating SAM output from minimap. The actual argument is equivalent in minimap2's eyes as-x asm5which 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