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oushujun / LTR_retriever

LTR_retriever is a highly accurate and sensitive program for identification of LTR retrotransposons; The LTR Assembly Index (LAI) is also included in this package.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5813529/
GNU General Public License v3.0
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Is a writable `$genome` necessary? #176

Closed GallVp closed 3 weeks ago

GallVp commented 1 month ago

Hi @oushujun

Is a writable $genome necessary? This can cause problems in pipelines such as Plant-Food-Research-Open/assemblyqc where multiple tools are executed on the same genome. Changing the original file can result in misleading results by the other programs and reduce reproducibility. Thank you!

https://github.com/oushujun/LTR_retriever/blob/d4d72a2e3edd0033b9aeb4c54c718ff8e52911d7/LTR_retriever#L312

GallVp commented 1 month ago

I see, this is related to https://github.com/oushujun/LTR_retriever/pull/125

GallVp commented 1 month ago

This issue was resolved by RepeatMasker on Nov 2, 2022. Please see,

https://github.com/rmhubley/RepeatMasker/commit/3d83626710649d98222da7e0940a756138878fc0

https://github.com/rmhubley/RepeatMasker/blob/3d83626710649d98222da7e0940a756138878fc0/RepeatMasker#L741-L743

I guess it is safe now to remove the writable file check?

https://github.com/oushujun/LTR_retriever/blob/d4d72a2e3edd0033b9aeb4c54c718ff8e52911d7/LTR_retriever#L312

oushujun commented 3 weeks ago

Thank you for checking this out. I have removed this component.

Shujun