Update Handling of Sequence Variants (Part 8): Point LoadRnaXML to new VariantApplicationMethod#972
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trishorts wants to merge 45 commits into
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Update Handling of Sequence Variants (Part 8): Point LoadRnaXML to new VariantApplicationMethod#972trishorts wants to merge 45 commits into
trishorts wants to merge 45 commits into
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…iant proteins when they dont explicitly call for them
Codecov Report❌ Patch coverage is Additional details and impacted files@@ Coverage Diff @@
## master #972 +/- ##
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- Coverage 81.00% 80.91% -0.10%
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Files 269 269
Lines 38826 38957 +131
Branches 4241 4272 +31
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+ Hits 31450 31521 +71
- Misses 6640 6678 +38
- Partials 736 758 +22
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current LoadRnaXml has two int variables: maxVariantsForCombinatorics =4 and minAlleleDepth = 1. VariantApplication now has three consensusPlusVariantIsoforms = 1, minAlleleDepth = 0 and maxVariantsPerIsoform = 0. This PR changes LoadRnaXML to call use all three variables. It also calls the new GetConsensusAndVariantBioPolymers method in VariantApplication
this may break some tests in MM where variants are expected but none are called for. The former LoadXML called for 4 with a min depth of 1. defaults now are zero.