redirect sam to standard output for piping

EA2106-Universite-Francois-Rabelais commented 3 years ago

Dear ModularAligner team, thank you very much for your great job setting up a new read aligner. In order to include it into already existing pipelines, could it be possible to allow maCMD to write the .sam to standard output instead of writing to a file? processing tools could be piped in that way to speed up the process.

Thank you very much!

Best regards,

MarkusRainerSchmidt commented 3 years ago

Hi,

-o /dev/stdout should do it!

Sincerely,

Markus

EA2106-Universite-Francois-Rabelais commented 3 years ago

Thanks Markus, I will give a try. Just by curiosity, won't it be a problem if I start several mappings in parallel?

Thomas

De: "ITBE-Lab" @.> À: "ITBE-Lab/MA" @.> Cc: "Thomas Duge De Bernonville" @.>, "Author" @.> Envoyé: Vendredi 26 Mars 2021 17:59:54 Objet: Re: [ITBE-Lab/MA] redirect sam to standard output for piping (#10)

Hi,

-o /dev/stdout should do it!

Sincerely,

Markus

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MarkusRainerSchmidt commented 3 years ago

Hi,

as far as i know each process should have it's own /dev/stdout. https://unix.stackexchange.com/questions/574597/how-dev-stdout-is-pointing-to-different-process-separately-in-linux

Markus

ITBE-Lab / MA

redirect sam to standard output for piping #10