seidr roc has an incoherent error message

[nicolasDelhomme]

When I ran the following command (which misses the -p for the number of points)

seidr roc -n /mnt/picea/projects/spruce/vhurry/drought-stress-needles/preprosessed/se idr/backbone/aggregated.sf -g /mnt/picea/storage/reference/goldStandard/Picea-abies_KEG G-based-positive-gold-standard.tsv -x /mnt/picea/storage/reference/goldStandard/Picea-a bies_KEGG-based-negative-gold-standard.tsv -a 1000

I got the following error:

[ ERROR ][ 2020-03-14T15:41:47 ][ seidr ]: option '--network' cannot be sp ecified more than once

[bschiffthaler]

This is because you specify -n, but the network can also be positional. Your -a is a switch so the CLI thinks the 1000 is also an argument to network. It's possible to code around that in boost::program_options, but this is intended behaviour

[nicolasDelhomme]

Then I think the man page (seidr roc) should say so. It says that -n is required, so I do not expect any positional argument :-)

I think it might get others confused too ;-)

On 14 Mar 2020, at 18:41, Bastian Schiffthaler notifications@github.com wrote:

This is because you specify -n, but the network can also be positional. Your -a is a switch so the CLI thinks the 1000 is also an argument to network. It's possible to code around that in boost::program_options, but this is intended behaviour

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[bschiffthaler]

Forgot to tag, this is mentioned in the usage message now since 720c6a5b415e5296fbc8a1efe4f74daba93ad0e8