kmer-size consistency between build and quasimap

iqbal-lab-org / gramtools

Genome inference from a population reference graph

MIT License

92 stars 15 forks source link

Closed martinghunt closed 6 years ago

martinghunt commented 6 years ago

I ran build using --kmer-size 5. Then with quasimap:

using --kmer-size 5 works fine and the reads get mapped
not using --kmer-size results in zero reads mapped. report.json has --kmer-size 15 in the command in "gramtools_cpp_quasimap" -> "command".

Does --kmer-size even need to be an option to quasimap? Seems like it's specified when running build.

ffranr commented 6 years ago

Will remove the --kmer-size option from quasimap. It used to be important to us when gramtools was in a different state.

Thank you for pointing that out.

ffranr commented 6 years ago

Fix implemented here: f4655b7f47c1e15a236f15fc6d1cf3afcbd6c567