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Feature/sniffle convert handling #300

Merged
merged 17 commits into from
Feb 3, 2022
Merged

Feature/sniffle convert handling #300

merged 17 commits into from
Feb 3, 2022

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zhemingfan
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Addressing issues described in Issue 294

  • Add support for uncertain types (e.g DEL/INS)
  • Add error handling of cases where breakpoints breakpoint start > breakpoint end
  • Add unit tests that includes aforementioned cases
  • Add support for handling INVDUP from Sniffles input

@zhemingfan zhemingfan self-assigned this Jan 26, 2022
@zhemingfan zhemingfan linked an issue Jan 26, 2022 that may be closed by this pull request
Long reads support for Sniffles files #294
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creisle
creisle reviewed Jan 26, 2022
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@zhemingfan zhemingfan added long read support Support for long read sequence data, e.g. from Oxford Nanopore or PacBio SV caller Tickets related to support for inputs from different SV callers labels Jan 29, 2022
@zhemingfan zhemingfan added this to the v3.0.0 milestone Jan 29, 2022
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codecov bot commented Jan 29, 2022 •
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Codecov Report

Merging #300 (2987227) into develop_v3 (841c364) will decrease coverage by 0.01%.
The diff coverage is 100.00%.

Impacted file tree graph

@@              Coverage Diff               @@
##           develop_v3     #300      +/-   ##
==============================================
- Coverage       87.12%   87.10%   -0.02%     
==============================================
  Files              53       53              
  Lines            8831     8835       +4     
  Branches         2291     2293       +2     
==============================================
+ Hits             7694     7696       +2     
- Misses            691      692       +1     
- Partials          446      447       +1
Flag Coverage Δ
unittests 87.10% <100.00%> (-0.02%) ⬇️

Flags with carried forward coverage won't be shown. Click here to find out more.

Impacted Files Coverage Δ
src/mavis/tools/constants.py 100.00% <ø> (ø)
src/mavis/tools/vcf.py 94.40% <100.00%> (+0.16%) ⬆️
src/mavis/breakpoint.py 90.64% <0.00%> (-0.65%) ⬇️

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@zhemingfan zhemingfan requested a review from creisle January 29, 2022 19:57
creisle
creisle reviewed Jan 30, 2022
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@zhemingfan zhemingfan requested a review from creisle February 1, 2022 19:16
@zhemingfan zhemingfan merged commit 5e49142 into develop_v3 Feb 3, 2022
@zhemingfan zhemingfan deleted the feature/sniffle-convert-handling branch February 3, 2022 20:11
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Reviewers

@creisle creisle creisle approved these changes

@calchoo calchoo Awaiting requested review from calchoo

@mattdoug604 mattdoug604 Awaiting requested review from mattdoug604

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@zhemingfan zhemingfan

Labels
long read support Support for long read sequence data, e.g. from Oxford Nanopore or PacBio SV caller Tickets related to support for inputs from different SV callers
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v3.0.0
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Successfully merging this pull request may close these issues.

Long reads support for Sniffles files
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@zhemingfan @creisle