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PacificBiosciences / trgt-denovo

De novo tandem repeat calling from PacBio HiFi data
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Same parameter abbreviation for --bed and --sample-b in duo mode #5

Open Fu-Yilei opened 5 days ago

Fu-Yilei commented 5 days ago

-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 commented 4 days ago

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