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Same parameter abbreviation for --bed and --sample-b in duo mode #5

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Fu-Yilei opened this issue Nov 21, 2024 · 1 comment
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@Fu-Yilei
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Fu-Yilei commented Nov 21, 2024

-b, --bed BED file with repeat coordinates
-o, --out Output tsv path
--trid TRID of a specific repeat to analyze, should be in the BED file
-@ [default: 1]
-a, --sample-a Prefix of first sample VCF and spanning reads BAM files
-b, --sample-b Prefix of second sample VCF and spanning reads BAM files

they are both -b and using the abbreviation causes error: the argument '--bed <BED>' cannot be used multiple times

@tmokveld
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Thanks for the catch, I'll fix it in the next minor release. For now you can use --sample-b to circumvent this.

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