Fix bug when loading indexed bgzip fasta file.

[lbergelson]

• There was a bug that prevented loading an indexed bgzip fasta file if the index location was specified but wasn't next to the fasta in the file system.
• Fixes #1290

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 #1311 into master will increase coverage by 0.912%. The diff coverage is 40%.

@@               Coverage Diff               @@
##              master     #1311       +/-   ##
===============================================
+ Coverage     67.728%   68.639%   +0.912%     
- Complexity      8225      8760      +535     
===============================================
  Files            560       562        +2     
  Lines          33493     35286     +1793     
  Branches        5637      6146      +509     
===============================================
+ Hits           22684     24220     +1536     
- Misses          8632      8824      +192     
- Partials        2177      2242       +65

Impacted Files	Coverage Δ	Complexity Δ
...rence/BlockCompressedIndexedFastaSequenceFile.java	74.359% <40%> (+4.089%)	8 <2> (ø)	:arrow_down:
...a/htsjdk/samtools/cram/build/ContainerFactory.java	95.238% <0%> (-1.732%)	10% <0%> (+4%)
...va/htsjdk/samtools/cram/build/ContainerParser.java	95.062% <0%> (-1.235%)	36% <0%> (+18%)
...oding/reader/MultiRefSliceAlignmentSpanReader.java	100% <0%> (ø)	10% <0%> (+5%)	:arrow_up:
...ava/htsjdk/samtools/cram/ref/ReferenceContext.java	91.667% <0%> (ø)	22% <0%> (?)
...htsjdk/samtools/cram/ref/ReferenceContextType.java	100% <0%> (ø)	1% <0%> (?)
...jdk/samtools/cram/build/Cram2SamRecordFactory.java	93.22% <0%> (+0.058%)	29% <0%> (ø)	:arrow_down:
src/main/java/htsjdk/samtools/cram/CRAIIndex.java	83.065% <0%> (+0.138%)	54% <0%> (+27%)	:arrow_up:
.../java/htsjdk/samtools/util/IntervalListWriter.java	88.235% <0%> (+0.235%)	9% <0%> (+4%)	:arrow_up:
src/main/java/htsjdk/samtools/util/Interval.java	64.13% <0%> (+0.494%)	51% <0%> (+25%)	:arrow_up:
... and 21 more

[lbergelson]

@pshapiro4broad Thanks for the review!