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Reference data includes bwa indices under incorrect name #108

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unode opened this issue May 28, 2019 · 2 comments
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Reference data includes bwa indices under incorrect name #108

unode opened this issue May 28, 2019 · 2 comments

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@unode
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unode commented May 28, 2019

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.

@luispedro
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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.

@unode
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unode commented May 29, 2019

bwa hasn't, minimap2 did at some point, but I agree that the change in 0.10.0 was mostly out of caution.

luispedro added a commit to luispedro/ngless that referenced this issue May 26, 2022
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
luispedro added a commit to luispedro/ngless that referenced this issue May 30, 2022
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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