Optimize AbstractBAMFileIndex#query with test

[lbergelson]

Description

Adding a test to https://github.com/samtools/htsjdk/pull/1396

Things to think about before submitting:

• [x] Make sure your changes compile and new tests pass locally.
• [x] Add new tests or update existing ones:
  • A bug fix should include a test that previously would have failed and passes now.
  • New features should come with new tests that exercise and validate the new functionality.
• [ ] Extended the README / documentation, if necessary
• [ ] Check your code style.
• [ ] Write a clear commit title and message
  • The commit message should describe what changed and is targeted at htsjdk developers
  • Breaking changes should be mentioned in the commit message.

[lbergelson]

@tomwhite I've added a test ontop of your branch. I couldn't push directly to yours so I've just opened a different Pr.

[codecov-io]

Codecov Report

Merging #1397 into master will increase coverage by 0.716%. The diff coverage is 100%.

@@               Coverage Diff               @@
##              master     #1397       +/-   ##
===============================================
+ Coverage     68.046%   68.761%   +0.716%     
- Complexity      8370      9116      +746     
===============================================
  Files            573       573               
  Lines          33886     36026     +2140     
  Branches        5662      6256      +594     
===============================================
+ Hits           23058     24772     +1714     
- Misses          8640      8978      +338     
- Partials        2188      2276       +88

Impacted Files	Coverage Δ	Complexity Δ
src/main/java/htsjdk/samtools/CSIIndex.java	71.622% <ø> (ø)	59 <0> (ø)	:arrow_down:
...ain/java/htsjdk/samtools/AbstractBAMFileIndex.java	85.207% <100%> (+0.451%)	50 <0> (+2)	:arrow_up:
...htsjdk/samtools/util/nio/DeleteOnExitPathHook.java	78.947% <0%> (-10.526%)	3% <0%> (-1%)
.../main/java/htsjdk/samtools/SAMValidationError.java	93.805% <0%> (-2.349%)	11% <0%> (+2%)
src/main/java/htsjdk/samtools/BAMSBIIndexer.java	73.333% <0%> (-1.667%)	1% <0%> (ø)
src/main/java/htsjdk/tribble/Tribble.java	100% <0%> (ø)	16% <0%> (+8%)	:arrow_up:
src/main/java/htsjdk/tribble/util/TabixUtils.java	0% <0%> (ø)	0% <0%> (ø)	:arrow_down:
...c/main/java/htsjdk/samtools/util/IntervalList.java	72.311% <0%> (+0.131%)	105% <0%> (+41%)	:arrow_up:
src/main/java/htsjdk/samtools/SamFiles.java	92.857% <0%> (+0.174%)	30% <0%> (+15%)	:arrow_up:
src/main/java/htsjdk/samtools/BAMFileReader.java	69.003% <0%> (+0.537%)	52% <0%> (ø)	:arrow_down:
... and 27 more

[tomwhite]

Thanks for adding a test @lbergelson