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refactor: umi intervalbed #837

Merged
merged 5 commits into from
Dec 17, 2021
Merged

refactor: umi intervalbed #837

merged 5 commits into from
Dec 17, 2021

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ashwini06
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This PR:

While calling UMI variants using TNscope, use the panel-defined regions to restrict calls.
Fixes : #821

Review and tests:

  • Tests pass
  • Code review
  • New code is executed and covered by tests, and test approve

@ashwini06 ashwini06 changed the base branch from master to develop December 13, 2021 12:22
@ashwini06 ashwini06 changed the title Fix/umi intervalbed Fix: umi intervalbed Dec 13, 2021
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codecov bot commented Dec 13, 2021

Codecov Report

Merging #837 (1b81a73) into develop (86e1b36) will increase coverage by 0.00%.
The diff coverage is 100.00%.

Impacted file tree graph

@@           Coverage Diff            @@
##           develop     #837   +/-   ##
========================================
  Coverage    99.61%   99.61%           
========================================
  Files           29       29           
  Lines         1814     1815    +1     
========================================
+ Hits          1807     1808    +1     
  Misses           7        7           
Flag Coverage Δ
unittests 99.61% <100.00%> (+<0.01%) ⬆️

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Impacted Files Coverage Δ
BALSAMIC/constants/workflow_params.py 100.00% <ø> (ø)
BALSAMIC/utils/models.py 100.00% <100.00%> (ø)

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@ashwini06 ashwini06 changed the title Fix: umi intervalbed refactor: umi intervalbed Dec 13, 2021
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hassanfa commented Dec 13, 2021

@ashwini06 in regular SNV calling, the padding is 100bp. Probably you might take this into account.

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Kudos, SonarCloud Quality Gate passed!    Quality Gate passed

Bug A 0 Bugs
Vulnerability A 0 Vulnerabilities
Security Hotspot A 0 Security Hotspots
Code Smell A 0 Code Smells

No Coverage information No Coverage information
0.0% 0.0% Duplication

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👍 👍

BALSAMIC/utils/models.py Show resolved Hide resolved
@ashwini06 ashwini06 merged commit 9f68b5e into develop Dec 17, 2021
@ashwini06 ashwini06 deleted the fix/umi_intervalbed branch December 17, 2021 14:42
@ashwini06 ashwini06 restored the fix/umi_intervalbed branch December 17, 2021 14:43
@ashwini06 ashwini06 deleted the fix/umi_intervalbed branch December 17, 2021 14:45
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Successfully merging this pull request may close these issues.

[UMIworkflow]: Problems with UMI-called variants from outside panel design
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