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iqbal-lab-org / gramtools

Genome inference from a population reference graph
MIT License
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Rename kmer size parameter #111

Closed ffranr closed 6 years ago

ffranr commented 6 years ago

The existence of the kmer index should be hidden from a user. It is an internal gramtools tool. Trying to explain what it is just adds complexity. Therefore, the kmer size parameter should probably be renamed. It's new name could reflect it's effect on gramtools rather than what it is.

ffranr commented 6 years ago

@iqbal-lab mentioned this in another issue:

Ideas for what this could be called:

--map_seed <integer between 1 and 20> gramtools stores a mapping from seeds/kmers in the graph to suffix-array intervals, to accelerate quasimapping (purely performance, identical results). Longer seeds cost more RAM but accelerate quasimapping.

--sa_index_cache ...same text here...

ffranr commented 6 years ago

The default kmer size now causes the kmer index to be built without analyzing the PRG for kmers. This means that users should not ordinarily set this parameter at all. It no longer makes sense to modify the name.

I would like to avoid naming it anything unclear since it's not critical.