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Reference data includes bwa indices under incorrect name #108
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I'm not sure whether the format of the indices ever changed in bwa, but I can see how maybe we should try to stay on the safe side. |
bwa hasn't, minimap2 did at some point, but I agree that the change in 0.10.0 was mostly out of caution. |
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Several bugfixes included since beta1: - Do not fail when merging empty files (ngless-toolkit#113) - Fix version in install-reference mode (ngless-toolkit#107) - Update --create-reference-pack mode (ngless-toolkit#108) - Reset terminal colors after error for `--download-demo` mode - Add --trace argument to all modes
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Many bugfixes and improvements since `1.3.0` - Do not fail when merging empty files (ngless-toolkit#113) - Fix version in install-reference mode (ngless-toolkit#107) - Update --create-reference-pack mode (ngless-toolkit#108) - Reset terminal colors after error for `--download-demo` mode - Add --trace argument to all modes - Newer version of megahit - Builtin gmgc module - Faster internals
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Since ngless 0.10.0 index files created by bwa are versioned
reference.fa-bwa-0.7.17.gz.bwt
instead ofreference.fa.gz.bwt
.The bundled reference genomes (
hg19
,mm10.p5
, ...) includebwa
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.
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