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Hotfix 1.5.x - fix MNV coordinates #197

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merged 5 commits into from
Feb 25, 2021

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julie-sullivan
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The MNV positions were incorrect. Here's an example:

ClinVar ID: 266834
chr13:32316508:GAC:ATCGATCGAT

Decomposed variants

Dragen CellBase output
13:32316508:G:ATCGATCG 13:32316508::ATCGATC
13:32316510:C:T 13:32316517:C:T << wrong

The coordinates are calculated with the start, and the index:

genomic start + current index = start

Previously the code was using the index for the right aligned string, which was "-------GAC"

32316508 + 9 (index of -------GAC) = 32316517 << incorrect

I've updated the code to use the index of the original "GAC"

32316508 + 2 (index of GAC) = 32316510 << correct

@imedina imedina added the bug label Jan 22, 2021
@imedina imedina requested a review from j-coll January 22, 2021 19:59
@imedina imedina merged commit f0f3ee6 into opencb:hotfix-1.5.x Feb 25, 2021
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