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eblerjana / pangenie

Pangenome-based genome inference
MIT License
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command `PanGenie-index` has wrong cli-usage info #42

Open wjwei-handsome opened 1 year ago

wjwei-handsome commented 1 year ago

As the title says, the command PanGenie-index in newest master branch is :

program: PanGenie - genotyping based on kmer-counting and known haplotype sequences.
author: Jana Ebler

version: v3.0.0
usage:
PanGenie-index [options] -i <reads.fa/fq> -r <reference.fa> -v <variants.vcf> -o <index-prefix>

options:
    -e VAL  size of hash used by jellyfish (default: 3000000000).
    -k VAL  kmer size (default: 31).
    -o VAL  prefix of the output files. NOTE: the given path must not include non-existent folders.
    -r VAL  reference genome in FASTA format. NOTE: INPUT FASTA FILE MUST NOT BE COMPRESSED.
    -t VAL  number of threads to use for kmer-counting (default: 1).
    -v VAL  variants in VCF format. NOTE: INPUT VCF FILE MUST NOT BE COMPRESSED.

Error: option -v is mandatory.

The usage info showed -i <reads.fa/fq>, actually, it's not necessary . It could be trivial mistake:)

Best, Wei

eblerjana commented 1 year ago

Thanks for catching this! You are right, the -i option does not exist for the preprocessing step, I forgot to remove it the usage info. I pushed a corrected version to the master.