upgrading to htsjdk 2.16.1

[lbergelson]

No description provided.

[lbergelson]

@jonn-smith Could you review this one when you get a chance?

[jonn-smith]

Looks fine to me.

The constructor for BlockCompressedOutputStream seems a little funky. I feel like there must be a way to avoid the cast (i.e. just have one constructor with either a Path or a File). But that's an HTSJDK issue.

Feel free to merge when tests pass.

[codecov-io]

Codecov Report

Merging #5168 into master will not change coverage.
The diff coverage is 100%.

@@             Coverage Diff             @@
##              master     #5168   +/-   ##
===========================================
  Coverage     86.742%   86.742%           
  Complexity     29470     29470           
===========================================
  Files           1818      1818           
  Lines         136436    136436           
  Branches       15125     15125           
===========================================
  Hits          118347    118347           
  Misses         12649     12649           
  Partials        5440      5440

Impacted Files	Coverage Δ	Complexity Δ
...oadinstitute/hellbender/tools/GatherVcfsCloud.java	70.811% <100%> (ø)	40 <0> (ø)	⬇️
...adinstitute/hellbender/utils/spark/SparkUtils.java	84.524% <100%> (ø)	21 <2> (ø)	⬇️
...broadinstitute/hellbender/utils/GenotypeUtils.java	94.872% <100%> (ø)	12 <0> (ø)	⬇️

[lbergelson]

@jonn-smith We don't want to break backwards compatibility by removing the old constructors but we do want the new constructors, so we're stuck with 2 until we pull the switch to kill the file constructors.