Remove VariantContexts from most fgbio tools

[kstromhaug]

Changes to

VariantMask
UpdateVcfContigNames
JointVariantContextIterator
ByIntervalListVariantContextIterator
AssessPhasing
ErrorRateByReadPosition

To remove VariantContexts and other elements of HTSJDK

and associated tests

MakeMixtureVcf has a modified line so that everything will compile, but still passes all tests which is a little concerning.

[codecov-commenter]

Codecov Report

Merging #836 (c81cca1) into main (bb36b51) will increase coverage by 0.12%.
The diff coverage is 98.75%.

@@            Coverage Diff             @@
##             main     #836      +/-   ##
==========================================
+ Coverage   95.58%   95.71%   +0.12%     
==========================================
  Files         122      125       +3     
  Lines        7068     7282     +214     
  Branches      511      490      -21     
==========================================
+ Hits         6756     6970     +214     
  Misses        312      312              

Flag	Coverage Δ
unittests	95.71% <98.75%> (+0.12%)	⬆️

Flags with carried forward coverage won't be shown. Click here to find out more.

Impacted Files	Coverage Δ
.../fulcrumgenomics/vcf/MakeTwoSampleMixtureVcf.scala	97.61% <0.00%> (ø)
.../fulcrumgenomics/bam/ErrorRateByReadPosition.scala	97.00% <100.00%> (ø)
.../scala/com/fulcrumgenomics/vcf/AssessPhasing.scala	97.74% <100.00%> (+0.03%)	⬆️
...ics/vcf/ByIntervalListVariantContextIterator.scala	92.00% <100.00%> (ø)
...crumgenomics/vcf/JointVariantContextIterator.scala	90.00% <100.00%> (+3.33%)	⬆️
...com/fulcrumgenomics/vcf/UpdateVcfContigNames.scala	100.00% <100.00%> (ø)
...in/scala/com/fulcrumgenomics/vcf/VariantMask.scala	100.00% <100.00%> (ø)
.../fulcrumgenomics/umi/ReviewConsensusVariants.scala	95.96% <0.00%> (-1.62%)	⬇️
.../scala/com/fulcrumgenomics/bam/api/SamWriter.scala	100.00% <0.00%> (ø)
...fulcrumgenomics/umi/CallDuplexConsensusReads.scala	100.00% <0.00%> (ø)
... and 5 more

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