updating to htsjdk 2.14.1

[lbergelson]

htsjdk 2.13.2 -> 2.14.1

[cmnbroad]

@lbergelson The old File SequenceDictionaryExtractor methods are still there right ? If not we should upgrade picard as well.

[lbergelson]

They're still there, just deprecated.

[cmnbroad]

Looks like these were just deprecated, so they should be ok. 👍 when tests pass.

[codecov-io]

Codecov Report

Merging #4210 into master will decrease coverage by 0.007%.
The diff coverage is 33.333%.

@@              Coverage Diff               @@
##              master    #4210       +/-   ##
==============================================
- Coverage     78.477%   78.47%   -0.007%     
+ Complexity     16424    16423        -1     
==============================================
  Files           1041     1041               
  Lines          59099    59099               
  Branches        9673     9673               
==============================================
- Hits           46379    46375        -4     
- Misses          8978     8981        +3     
- Partials        3742     3743        +1

Impacted Files	Coverage Δ	Complexity Δ
...llbender/utils/test/SimpleIntervalTestFactory.java	0% <0%> (ø)	0 <0> (ø)	⬇️
...kers/variantutils/UpdateVCFSequenceDictionary.java	86.957% <100%> (ø)	14 <0> (ø)	⬇️
...e/hellbender/engine/spark/SparkContextFactory.java	71.233% <0%> (-2.74%)	11% <0%> (ø)
...oadinstitute/hellbender/utils/gcs/BucketUtils.java	78.71% <0%> (-1.29%)	39% <0%> (ø)
...park/sv/discovery/alignment/AlignmentInterval.java	89.272% <0%> (-0.383%)	73% <0%> (-1%)
...utils/smithwaterman/SmithWatermanIntelAligner.java	90% <0%> (+10%)	3% <0%> (ø)	⬇️