search

gmarcais / Jellyfish

A fast multi-threaded k-mer counter
Other
463 stars 136 forks source link

count: unrecognized option '--both-strands' #10

Closed moskalenko closed 10 years ago

moskalenko commented 10 years ago

I built jellyfish 2.1.1. However, it looks like the 'count --both-strands' option is not available even though it's listed in the documentation and many external programs that use jellyfish depend on it.

jellyfish count --both-strands count: unrecognized option '--both-strands'

gmarcais commented 10 years ago

The switch it still present, it is -C or --canonical. The short form (-C) was already present if version 1.x. The long form has been renamed. --both-strands was taken from meryl, the mer counter of Celera, but the name never pleased me much. Canonical is better in my opinion.

Maybe I should add --both-strands as a alias.

moskalenko commented 10 years ago

I eventually found --canonical. I was trying to set up the 'Agalma' pipeline when I ran into it. So, I just switched to Jellyfish 1.1.11.

Thanks,

Alex

On Apr 2, 2014, at 9:16 PM, gmarcais notifications@github.com wrote:

The switch it still present, it is -C or --canonical. The short form (-C) was already present if version 1.x. The long form has been renamed. --both-strands was taken from meryl, the mer counter of Celera, but the name never pleased me much. Canonical is better in my opinion.

Maybe I should add --both-strands as a alias.

— Reply to this email directly or view it on GitHub.