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Move GenomicsDB to 1.0.3 for Importer fix to Issue 5449 #5899

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merged 1 commit into from
Apr 23, 2019

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nalinigans
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@nalinigans nalinigans commented Apr 22, 2019

@ldgauthier found a bug in GenomicsDBImport with overlapping deletions, specifically with the * allele and the deletion spanning the interval specified - see #5449 (comment). The fix for this issue(thanks @mlathara) is in 1.0.3 of GenomicsDB.

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codecov-io commented Apr 22, 2019

Codecov Report

Merging #5899 into master will increase coverage by 0.001%.
The diff coverage is n/a.

@@               Coverage Diff               @@
##              master     #5899       +/-   ##
===============================================
+ Coverage     86.838%   86.838%   +0.001%     
- Complexity     32323     32324        +1     
===============================================
  Files           1991      1991               
  Lines         149327    149327               
  Branches       16483     16483               
===============================================
+ Hits          129672    129673        +1     
+ Misses         13647     13646        -1     
  Partials        6008      6008
Impacted Files Coverage Δ Complexity Δ
...lotypecaller/readthreading/ReadThreadingGraph.java 88.725% <0%> (-0.245%) 159% <0%> (ø)
...nder/utils/runtime/StreamingProcessController.java 68.72% <0%> (+0.948%) 34% <0%> (+1%) ⬆️

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We have included unit tests for wildstar allele and the deletion spanning the interval in GenomicsDB. @ldgauthier, can you please confirm that this solves the issue?

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@ldgauthier ldgauthier left a comment

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I reran my exact use case and it works perfectly. Thanks for the quick turnaround!

@droazen droazen merged commit c644e20 into master Apr 23, 2019
@droazen droazen deleted the nalini_issue_5449 branch April 23, 2019 17:59
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4 participants