search

hall-lab / speedseq

A flexible framework for rapid genome analysis and interpretation
MIT License
314 stars 117 forks source link

Compressing temporary files #90

Open inti opened 8 years ago

inti commented 8 years ago

Hi, Why are temporary files not compressed? It is due to impact of performance? would it be possible to add an option to opt for compressed output to reduce disk usage?

thanks in advance,

cc2qe commented 8 years ago

can you just clarify which module you're running. Do you mean for variant calling (speedseq var and speedseq somatic) or for alignment?

The temp VCF files for variant calling could be compressed, but they shouldn't be very big anyway

inti commented 8 years ago

I am running variant calling. I guess big depends on the system being used and the dataset being analysed. Compression would help on my case.

Thanks a a lot!

On Sep 21, 2016, at 3:01 PM, Colby Chiang notifications@github.com wrote:

can you just clarify which module you're running. Do you mean for variant calling (speedseq var and speedseq somatic) or for alignment?

The temp VCF files for variant calling could be compressed, but they shouldn't be very big anyway

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/hall-lab/speedseq/issues/90#issuecomment-248692772, or mute the thread https://github.com/notifications/unsubscribe-auth/AAXApYjpuE4MXdB-rr5LLyvv7QBrOpAhks5qsXDkgaJpZM4KBjo7.