Illumina / hap.py

Haplotype VCF comparison tools
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--version option not working on pre.py and hap.py #156

Open nvnieuwk opened 2 years ago

nvnieuwk commented 2 years ago

I can't get the versions of pre.py and hap.py:

$ hap.py --version
Hap.py

and

$ pre.py --version
usage: VCF preprocessor [-h] [--location LOCATIONS] [--pass-only]
                        [--filters-only FILTERS_ONLY] [-R REGIONS_BEDFILE]
                        [-T TARGETS_BEDFILE] [-L] [--no-leftshift]
                        [--decompose] [-D] [--bcftools-norm] [--fixchr]
                        [--no-fixchr] [--bcf] [--somatic]
                        [--set-gt {half,hemi,het,hom,first}] [--filter-nonref]
                        [--convert-gvcf-to-vcf]
                        [--gender {male,female,auto,none}] [-v] [-r REF]
                        [-w WINDOW] [--threads THREADS] [--logfile LOGFILE]
                        [--verbose | --quiet]
                        input output
VCF preprocessor: error: too few arguments

I've tried this using the bioconda::hap.py=0.3.14 conda package and the quay.io/biocontainers/hap.py:0.3.14--py27h5c5a3ab_0 Docker image.

Is anyone else having this problem? And is there any way I can fix this? Thanks!