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escape % in help text for --do-not-penalize-chimeras to fix TypeError…
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… when using 'bwameth.py --help' (#87)
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boegel authored Apr 7, 2023
1 parent af57384 commit 4330567
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4 changes: 3 additions & 1 deletion bwameth.py
Original file line number Diff line number Diff line change
Expand Up @@ -540,8 +540,10 @@ def main(args=sys.argv[1:]):
"multiple sets separated by commas, e.g. ... a_R1.fastq,b_R1.fastq"
" a_R2.fastq,b_R2.fastq note that the order must be maintained.")

# need to escape '%' in help text to avoid problems with --help,
# see https://github.com/brentp/bwa-meth/issues/85
p.add_argument('--do-not-penalize-chimeras', action='store_true', help="do not use the heuristic"
" that if the longest match is not 44% of the sequence length, we mark"
" that if the longest match is not 44%% of the sequence length, we mark"
" it as failed QC and un-pair it, and set all members of pair to unmapped")

args, pass_through_args = p.parse_known_args(args)
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