[Suggestion] Allow output to stdout

COMBINE-lab / pufferfish

An efficient index for the colored, compacted, de Bruijn graph

GNU General Public License v3.0

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[Suggestion] Allow output to stdout #21

Open apcamargo opened 3 years ago

apcamargo commented 3 years ago

Currently, the only way to get a bam file from puffalign is to write a sam and then convert it in a separate command. If puffalign could output to stdout it would be possible to pipe it into samtools to get a bam directly.

rob-p commented 3 years ago

This is a great suggestion. We'll work on it.

apcamargo commented 3 years ago

Thanks Rob!

I just started testing puffalign and I'm really excited with it. I may open some other issue tickets soon :)