Updates to VarDictJava and VarDictJavaEndToEnd

[nh13]

• support the -K option to include the count of Ns in the total depth: https://github.com/AstraZeneca-NGS/VarDictJava/pull/88

• support outputting all sites, including reference sites, not just sites with alternate alternate alleles.

[codecov-io]

Codecov Report

Merging #318 into master will not change coverage. The diff coverage is n/a.

@@           Coverage Diff           @@
##           master     #318   +/-   ##
=======================================
  Coverage   91.37%   91.37%           
=======================================
  Files          31       31           
  Lines        1136     1136           
  Branches      102      102           
=======================================
  Hits         1038     1038           
  Misses         98       98

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[clintval]

I submitted this PR just now:

AstraZeneca-NGS/VarDict#58

[nh13]

@tfenne both AstraZeneca-NGS/VarDict#58 and AstraZeneca-NGS/VarDictJava#88 have been merged, so I think this is ready to go.