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using Comonicon
"""# IntroBenchmark a set of bins agains a reference# Args- `ref`: Path to reference JSON file (see the `makeref subcommand`)- `bins`: Paths to TSV files of bins.# Options- `-r, --rank`: Taxonomic rank to benchmark- `-s, --sep`: Binsplit separator; delimiter to split bins- `--minsize`: Remove bins with shorter breadth- `--minseqs`: Remove bins fewer sequences- `--keep-flags`: Only keep genomes with all these flags set. Takes a comma-separated list of flags, e.g. "virus,plasmid"- `--remove-flags`: Remove genomes with any of these flags set. See above.- `--recalls`: Comma-separated list of recall thresholds to use- `--precisions`: Comma-separated list of precision thresholds to use# Flags- `--assembly`: Count number of recovered assemblies, not genomes- `--intersect`: Allow the same sequence to be in multiple bins"""
Comonicon.@mainfunctionbench(
ref::String,
bins...; #TODO: Explicit type here, but Comonicon issue #261 prevents this
rank::Int=0,
sep::Union{String, Nothing}=nothing,
minsize::Int=1,
minseqs::Int=1,
keep_flags::String,
remove_flags::String,
recalls::Vector{Float64}=[0.6, 0.7, 0.8, 0.9, 0.95, 0.99],
precisions::Vector{Float64}=[0.6, 0.7, 0.8, 0.9, 0.95, 0.99],
assembly::Bool=false,
intersect::Bool=false,
)
nothingend
And invoked like this: julia --startup=no --project=. foo.jl -h.
You can see in the screenshot below that the description for e.g. keep-flags wraps around, presumably because the display size is incorrectly computed.
Version of the package:
This is on Comonicon 1.0.6.
Expected behavior
I would expect the text to not wrap all the way to the left of the screen, but wrap on the right side, where the descriptions are.
Screenshots
The text was updated successfully, but these errors were encountered:
hmm, this is not expected, I guess something went wrong in detecting the displaysize, we just use this to detect the size, if your width is smaller than 80 however, we currently will use 80 instead. It might be better to see if we can provide a more compact printing instead of doing everything two column.
A script with the following content:
And invoked like this:
julia --startup=no --project=. foo.jl -h
.You can see in the screenshot below that the description for e.g.
keep-flags
wraps around, presumably because the display size is incorrectly computed.Version of the package:
This is on Comonicon 1.0.6.
Expected behavior
I would expect the text to not wrap all the way to the left of the screen, but wrap on the right side, where the descriptions are.
Screenshots
The text was updated successfully, but these errors were encountered: