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Addition of tests that compare hgvs to vcf translation between this and Ensembl Variant Recoder #18

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h-joshi opened this issue Nov 14, 2023 · 2 comments
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Addition of tests that compare hgvs to vcf translation between this and Ensembl Variant Recoder #18

h-joshi opened this issue Nov 14, 2023 · 2 comments

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@h-joshi
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h-joshi commented Nov 14, 2023 •
edited

Persist pre-computed variant recoder output using http://asia.ensembl.org/Homo_sapiens/Tools/VR for hgvs_vcf_valid.tsv and hgvs_vcf_invalid.tsv
@h-joshi h-joshi changed the title Addition of tests that compare hgvs to vcf translation between this and Ensembl VEP Addition of tests that compare hgvs to vcf translation between this and Ensembl Variant Recoder Nov 14, 2023
PeterKnealeCMRI added a commit that referenced this issue Nov 14, 2023
@PeterKnealeCMRI
Issue #18. Add pre-computed outputs for the valid files
865b2ef
@PeterKnealeCMRI
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@h-joshi I didnt do the invalid ones as I presume they would all fail to decode properly?

@h-joshi
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h-joshi commented Nov 15, 2023

@h-joshi I didnt do the invalid ones as I presume they would all fail to decode properly?

Yup they should all fail to decode

PeterKnealeCMRI added a commit that referenced this issue Nov 27, 2023
@PeterKnealeCMRI
Issue #18. Add pre-computed outputs for the valid files (#19)
070aeea 
* Issue #18. Add pre-computed outputs for the valid files

* Add readme

* Add readme

* Handle lookup failures

* Update to use two sources

* Update to use two sources

* Add tests that use the ensembl and variant validator files as inputs for comparison

* Refactor tests

* Add commend to execute tests

* Perform comparison tests

* Add instructions for diff

* add http retries

* Add resiliency

* Add complete comparison files
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@h-joshi @PeterKnealeCMRI