A few fixes for issues found by spotbugs

[tomwhite]

Address more of #1267

Checklist

• Code compiles correctly
• New tests covering changes and new functionality
• All tests passing
• Extended the README / documentation, if necessary
• Is not backward compatible (breaks binary or source compatibility)

[codecov-io]

Codecov Report

Merging #1278 into master will increase coverage by 0.094%.
The diff coverage is 78.571%.

@@              Coverage Diff               @@
##             master     #1278       +/-   ##
==============================================
+ Coverage     67.49%   67.584%   +0.094%     
- Complexity     8150      8189       +39     
==============================================
  Files           558       558               
  Lines         33365     33375       +10     
  Branches       5608      5609        +1     
==============================================
+ Hits          22518     22556       +38     
+ Misses         8658      8637       -21     
+ Partials       2189      2182        -7

Impacted Files	Coverage Δ	Complexity Δ
...dk/variant/variantcontext/GenotypeLikelihoods.java	83.636% <0%> (-0.51%)	69 <0> (ø)
src/main/java/htsjdk/samtools/util/CigarUtil.java	30.769% <0%> (ø)	14 <0> (ø)	⬇️
...sjdk/tribble/readers/PositionalBufferedStream.java	53.465% <0%> (ø)	24 <0> (ø)	⬇️
.../htsjdk/samtools/reference/FastaSequenceIndex.java	63.889% <100%> (+0.509%)	13 <1> (+1)	⬆️
...tools/cram/encoding/readfeatures/Substitution.java	92.105% <100%> (+26.391%)	22 <2> (+12)	⬆️
...samtools/cram/structure/CramCompressionRecord.java	87.302% <100%> (+8.135%)	109 <3> (+21)	⬆️
...samtools/util/AsyncBlockCompressedInputStream.java	76% <100%> (+4%)	13 <1> (+1)	⬆️
src/main/java/htsjdk/samtools/util/HttpUtils.java	32.258% <0%> (-3.226%)	2% <0%> (-1%)
...tsjdk/samtools/reference/FastaReferenceWriter.java	91.129% <0%> (-0.071%)	41% <0%> (ø)
...va/htsjdk/samtools/SAMSequenceDictionaryCodec.java	87.5% <0%> (ø)	6% <0%> (ø)	⬇️
... and 7 more

[tomwhite]

Thanks for taking a look @jmthibault79

[jmthibault79]

Resolves #1220

[lbergelson]

Thank you @tomwhite and @jmthibault79