search

uni-halle / gerbil

A fast and memory-efficient k-mer counter with GPU-support
MIT License
34 stars 14 forks source link

Enforcing fixed-length record output? #13

Closed mhorlacher closed 4 years ago

mhorlacher commented 4 years ago

First off, great tool!

Is there a way to enforce the program to write fixed-length output records, i.e. to always encode counts as int32?

Best, MH

merbert commented 4 years ago

I created a new branch, but haven't been able to check it yet. The desired result should now be generated with the new option '-o 32bit'.

mhorlacher commented 4 years ago

@merbert thanks, much appreciated! I will do some testing and then close this issue.

mhorlacher commented 4 years ago

@merbert Sorry for the late response. I did some testing and everything seems to work fine, so thanks again!

I had some troubles with Gerbil aborting as it found .fastq.gz as archives being corrupted, even though gzip -t returned OK on these archives and Gerbil worked fine with the decompressed files. I might open up another issue for this.