redirect sam to standard output for piping

Open EA2106-Universite-Francois-Rabelais opened this issue 4 years ago • 3 comments

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,

Mar 26 '21 08:03 EA2106-Universite-Francois-Rabelais

Hi,

-o /dev/stdout should do it!

Sincerely,

Markus

Mar 26 '21 16:03 MarkusRainerSchmidt

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

— You are receiving this because you authored the thread. Reply to this email directly, [ https://github.com/ITBE-Lab/MA/issues/10#issuecomment-808372937 | view it on GitHub ] , or [ https://github.com/notifications/unsubscribe-auth/AECRNXUMEZZNEADNKVX3563TFTDRVANCNFSM4Z26EGLA | unsubscribe ] .

Mar 26 '21 20:03 EA2106-Universite-Francois-Rabelais

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

Mar 27 '21 10:03 MarkusRainerSchmidt