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Fix for missing INFO.STRANDS tag for TRA features in breakpoint split view #4232

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merged 2 commits into from Feb 22, 2024

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cmdcolin
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this fix will not have the "directional feet" that the strands tag helps with, but it at least does not crash :)

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fixes usage with some DELLY VCF, potentially (as a follow on) can use a different tag from DELLY called "CT" which says "5to3" and "5to5" as an equivalent to STRAND

Fixes #4188

Fix follows from office hours meeting

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codecov bot commented Feb 22, 2024

Codecov Report

Attention: Patch coverage is 0% with 11 lines in your changes are missing coverage. Please review.

Project coverage is 62.67%. Comparing base (c53e444) to head (e9c2a34).

Files Patch % Lines
.../BreakpointSplitView/components/Translocations.tsx 0.00% 11 Missing ⚠️
Additional details and impacted files
@@            Coverage Diff             @@
##             main    #4232      +/-   ##
==========================================
- Coverage   62.76%   62.67%   -0.10%     
==========================================
  Files        1084     1084              
  Lines       31316    31324       +8     
  Branches     7474     7478       +4     
==========================================
- Hits        19655    19631      -24     
- Misses      11486    11521      +35     
+ Partials      175      172       -3     

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@cmdcolin cmdcolin changed the title Fix handling of missing INFO.STRANDS tag for breakpoint split view Fix for missing INFO.STRANDS tag for TRA features in breakpoint split view Feb 22, 2024
@cmdcolin
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newer versions of delly now output proper VCF breakend spec so i'm not super inclined to go through the full support of the "CT" tag aforementioned but will see if it ends up being needed...it also applies to DEL/INV i think too

@cmdcolin cmdcolin merged commit ba46c26 into main Feb 22, 2024
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@cmdcolin cmdcolin deleted the strands_missing branch February 22, 2024 22:37
@cmdcolin cmdcolin added the bug Something isn't working label Feb 28, 2024
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Error to launch split window for TRA in structural variant track
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