remove caching of alleles in AbstractVCFCodec

[lbergelson]

This replaces https://github.com/samtools/htsjdk/pull/1264 and responds to my own comments.

[codecov-io]

Codecov Report

Merging #1282 into master will increase coverage by 0.439%. The diff coverage is 90%.

@@              Coverage Diff               @@
##             master     #1282       +/-   ##
==============================================
+ Coverage     67.49%   67.929%   +0.439%     
- Complexity     8150      8483      +333     
==============================================
  Files           558       561        +3     
  Lines         33365     34324      +959     
  Branches       5608      5848      +240     
==============================================
+ Hits          22518     23316      +798     
- Misses         8658      8796      +138     
- Partials       2189      2212       +23

Impacted Files	Coverage Δ	Complexity Δ
...main/java/htsjdk/variant/vcf/AbstractVCFCodec.java	73.765% <100%> (+0.759%)	86 <0> (-4)	:arrow_down:
...ain/java/htsjdk/variant/variantcontext/Allele.java	77.703% <86.667%> (+0.497%)	95 <9> (+7)	:arrow_up:
...c/main/java/htsjdk/samtools/util/SnappyLoader.java	78.571% <0%> (-2.198%)	9% <0%> (ø)
src/main/java/htsjdk/samtools/SamReader.java	81.818% <0%> (-0.94%)	0% <0%> (ø)
...va/htsjdk/samtools/SAMSequenceDictionaryCodec.java	86.957% <0%> (-0.543%)	8% <0%> (+2%)
src/main/java/htsjdk/samtools/util/CigarUtil.java	30.303% <0%> (-0.466%)	14% <0%> (ø)
...java/htsjdk/samtools/cram/ref/ReferenceSource.java	46.364% <0%> (-0.425%)	19% <0%> (ø)
...htsjdk/tribble/readers/LongLineBufferedReader.java	29.944% <0%> (-0.342%)	15% <0%> (ø)
...ain/java/htsjdk/samtools/util/MergingIterator.java	85.417% <0%> (-0.298%)	18% <0%> (+7%)
...ava/htsjdk/samtools/CRAMContainerStreamWriter.java	70.612% <0%> (-0.289%)	54% <0%> (ø)
... and 35 more

[lbergelson]

@pshapiro4broad Could you review this branch?