Fix error in genotype given alleles mode when input alleles have genotypes #5341
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…ven allele variants have genotypes
ldgauthier
approved these changes
Oct 22, 2018
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...I mean tomorrow's release. |
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@droazen added a quick unit test that failed without my change but passes now. look ok? |
Codecov Report
@@ Coverage Diff @@
## master #5341 +/- ##
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+ Coverage 86.821% 86.825% +0.004%
- Complexity 30197 30199 +2
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Files 1845 1845
Lines 139825 139852 +27
Branches 15412 15412
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+ Hits 121398 121427 +29
- Misses 12818 12819 +1
+ Partials 5609 5606 -3
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droazen
approved these changes
Oct 23, 2018
EdwardDixon
pushed a commit
to EdwardDixon/gatk
that referenced
this pull request
Nov 9, 2018
…types (broadinstitute#5341) * fix issue of alleles not being replaced with star alleles when the given allele variants have genotypes * add unit test to replaceWithSpanDelVC
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Fixes #5336
HaplotypeCallerGenotypingEngine.replaceWithSpanDelVCreplaces the given allelesVariantContextobjects with new VCs in which the alleles have been replaced with star alleles to represent spanning deletions. However, if the input variant records had genotypes, the original (non-star) deletion alleles were still being retained, causing a downstream error. This fixes that issue.