Use Integer.parseInt over Integer.valueOf to avoid unnecessary boxing…

[tomwhite]

... as reported by SpotBugs.

See https://spotbugs.readthedocs.io/en/stable/bugDescriptions.html#bx-boxing-unboxing-to-parse-a-primitive-dm-boxed-primitive-for-parsing

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)

[lbergelson]

👍 Thanks @tomwhite

[lbergelson]

Oh, tests are failing...

[lbergelson]

I can't tell what's failing from the log... I'll rerun and see if it goes away.

[codecov-io]

Codecov Report

Merging #1275 into master will not change coverage.
The diff coverage is 72%.

@@            Coverage Diff            @@
##             master    #1275   +/-   ##
=========================================
  Coverage     67.49%   67.49%           
  Complexity     8150     8150           
=========================================
  Files           558      558           
  Lines         33365    33365           
  Branches       5608     5608           
=========================================
  Hits          22518    22518           
  Misses         8658     8658           
  Partials       2189     2189

Impacted Files	Coverage Δ	Complexity Δ
...main/java/htsjdk/tribble/example/CountRecords.java	0% <0%> (ø)	0 <0> (ø)	⬇️
...main/java/htsjdk/samtools/cram/common/Version.java	36% <0%> (ø)	7 <0> (ø)	⬇️
...n/java/htsjdk/variant/variantcontext/Genotype.java	59.036% <0%> (ø)	80 <0> (ø)	⬇️
...sjdk/tribble/readers/PositionalBufferedStream.java	53.465% <0%> (ø)	24 <0> (ø)	⬇️
...va/htsjdk/tribble/example/ProfileIndexReading.java	0% <0%> (ø)	0 <0> (ø)	⬇️
.../htsjdk/variant/variantcontext/VariantContext.java	77.714% <100%> (ø)	246 <0> (ø)	⬇️
src/main/java/htsjdk/samtools/SamFlagField.java	92.308% <100%> (ø)	12 <0> (ø)	⬇️
.../htsjdk/samtools/reference/FastaSequenceIndex.java	63.38% <100%> (ø)	12 <0> (ø)	⬇️
...main/java/htsjdk/variant/vcf/AbstractVCFCodec.java	73.006% <100%> (ø)	90 <0> (ø)	⬇️
...samtools/cram/compression/ExternalCompression.java	62.963% <100%> (ø)	14 <1> (ø)	⬇️
... and 5 more

[lbergelson]

Seems to be a mysterious non-deterministic issue. I don't think this change caused it.