Allow callers of Var2VcfValid to turn on printing of a variant's END tag

[clintval]

Do you know why historically this was hardcoded to false?

[codecov-commenter]

Codecov Report

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

@@           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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[nh13]

I do not know why it was set to false previously. @tfenne do you recall? VarDictJava has evolved quite well over the years, so it could have been an issue there, or the fact we were looking only at small variants?

[clintval]

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!