redirect sam to standard output for piping

[EA2106-Universite-Francois-Rabelais]

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]

Hi,

-o /dev/stdout should do it!

Sincerely,

Markus

[EA2106-Universite-Francois-Rabelais]

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,

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-o /dev/stdout should do it! Sincerely, Markus — You are receiving this because you authored the thread. Reply to this email directly, [ #10 (comment) | view it on GitHub ] , or [ https://github.com/notifications/unsubscribe-auth/AECRNXUMEZZNEADNKVX3563TFTDRVANCNFSM4Z26EGLA | unsubscribe ] .

[MarkusRainerSchmidt]

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