Since ngless 0.10.0 index files created by bwa are versioned reference.fa-bwa-0.7.17.gz.bwt instead of reference.fa.gz.bwt.
The bundled reference genomes (hg19, mm10.p5, ...) include bwa indices but only in the non-versioned format.
As such, we should either create versioned indices (or symlinks to the appropriate versions) or delete the indices and let them be created by ngless.
In the long run we may want to delete indices entirely as it simplifies packaging and distribution of reference data for every new ngless version. As-is, leaving the indices in the reference package only wastes space on the users' end.
Since ngless 0.10.0 index files created by bwa are versioned
reference.fa-bwa-0.7.17.gz.bwtinstead ofreference.fa.gz.bwt.The bundled reference genomes (
hg19,mm10.p5, ...) includebwaindices but only in the non-versioned format.As such, we should either create versioned indices (or symlinks to the appropriate versions) or delete the indices and let them be created by
ngless.In the long run we may want to delete indices entirely as it simplifies packaging and distribution of reference data for every new ngless version. As-is, leaving the indices in the reference package only wastes space on the users' end.