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iqbal-lab-org / pandora

Pan-genome inference and genotyping with long noisy or short accurate reads
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Confusuing option in seq2path #230

Open mbhall88 opened 4 years ago

mbhall88 commented 4 years ago

There is an option --flag in seq2path subcommand which seems to have a conflicting behaviour. The previous comment/description for it was

"output success/fail rather than the node path"

But when I look at the code it seems to still output the node path... I've not used this subcommand before so I was wondering is someone who has used it can clarify this flag (@leoisl)?

iqbal-lab commented 4 years ago

Is it for checking whether a sequence really does lie entirely in the graph?

leoisl commented 4 years ago

I've never used this command...

rmcolq commented 4 years ago

Not read the thread, but I think this was useful for development of mixture genotyping, not so useful for other people.

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-------- Original message -------- From: leoisl notifications@github.com Date: 21/09/2020 10:56 (GMT+00:00) To: rmcolq/pandora pandora@noreply.github.com Cc: Subscribed subscribed@noreply.github.com Subject: Re: [rmcolq/pandora] Confusuing option in seq2path (#230)

I've never used this command...

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mbhall88 commented 4 years ago

I'm not questioning the command itself, just the --flag option as it doesn't (seem to) do what it claims to do.