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fulcrumgenomics / dagr

A scala based DSL and framework for writing and executing bioinformatics pipelines as Directed Acyclic GRaphs
MIT License
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Allow callers of Var2VcfValid to turn on printing of a variant's END tag #398

Closed clintval closed 3 years ago

clintval commented 3 years ago

Do you know why historically this was hardcoded to false?

codecov-commenter commented 3 years ago

Codecov Report

Merging #398 (3f9ea4d) into master (f639abd) will not change coverage. The diff coverage is n/a.

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@@           Coverage Diff           @@
##           master     #398   +/-   ##
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  Coverage   91.40%   91.40%           
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  Files          31       31           
  Lines        1187     1187           
  Branches       83       83           
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  Hits         1085     1085           
  Misses        102      102
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clintval commented 3 years ago

To follow up. I have non-exhaustively tested VarDictJava's ability to correctly calculate the END tag on a large collection of simple variants (SNV, MNV, insertion, deletion) and on simple symbolics (INS, INV, DUP). Given that downstream tooling wants the END tag for symbolics, it is a good idea to include it:

• END : end position of the variant described in this record (for use with symbolic alleles)

Source: https://samtools.github.io/hts-specs/VCFv4.2.pdf

Thank you for the merge!