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bioinformatics-centre / BayesTyper

A method for variant graph genotyping based on exact alignment of k-mers
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Running BayesTyper with a different kmer length #15

Closed stephaniemyan closed 5 years ago

stephaniemyan commented 5 years ago

Hi,

I'm interested in running BayesTyper with a kmer length other than the default, as in supplementary section S13 of this paper: http://science.sciencemag.org/content/358/6363/655.

After running KMC3 with -k31, I attempted to run BayesTyper's makeBloom function, and got an error that I assume comes from the discrepancy in kmer lengths.

[13/03/2019 13:31:03] You are using BayesTyperTools (v1.4)

[13/03/2019 13:31:03] Running BayesTyperTools (v1.4) makeBloom ...

bayesTyperTools: /isdata/kroghgrp/jasi/bayesTyper/code/releases/v1.4_static/BayesTyper-1.4/src/bayesTyperTools/MakeBloom.cpp:213: kmer_bloom_t* MakeBloom::kmc2bloomThreaded(const string&, float, uint): Assertion `kmc_table_info.kmer_length == kmer_size' failed.
Aborted

There doesn't seem to be an immediate option for adjusting kmer length when running makeBloom. Do you know how I would be able to do this?

Thanks, Steph

stephaniemyan commented 5 years ago

Never mind, I just found this page: https://github.com/bioinformatics-centre/BayesTyper/wiki/Building-BayesTyper-from-source.