Add HtsgetBAMFileReader

[andersleung]

Description

Add a new SamReader type that is able to request reads from HTSget sources, as well as classes defining the content of an HTSget request and response. This change allows consumers of the htsjdk library to use HTSget sources like any other type of reads source.

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
• [x] Check your code style.
• [x] 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.

[codecov-commenter]

Codecov Report

Merging #1494 into master will increase coverage by 0.046%. The diff coverage is 72.156%.

@@               Coverage Diff               @@
##              master     #1494       +/-   ##
===============================================
+ Coverage     69.279%   69.325%   +0.046%     
- Complexity      8764      8888      +124     
===============================================
  Files            590       601       +11     
  Lines          34755     35433      +678     
  Branches        5800      5901      +101     
===============================================
+ Hits           24078     24564      +486     
- Misses          8386      8538      +152     
- Partials        2291      2331       +40     

Impacted Files	Coverage Δ	Complexity Δ
...rc/main/java/htsjdk/samtools/SamReaderFactory.java	65.487% <18.750%> (-3.381%)	7.000 <0.000> (ø)
src/main/java/htsjdk/samtools/SamReader.java	79.348% <25.000%> (-2.470%)	0.000 <0.000> (ø)
.../util/htsget/HtsgetMalformedResponseException.java	28.571% <28.571%> (ø)	1.000 <1.000> (?)
src/main/java/htsjdk/samtools/BAMFileReader.java	69.501% <50.000%> (+1.036%)	50.000 <1.000> (-2.000)	:arrow_up:
...rc/main/java/htsjdk/samtools/SamInputResource.java	65.432% <53.846%> (-2.451%)	20.000 <3.000> (+3.000)	:arrow_down:
...ava/htsjdk/samtools/util/htsget/HtsgetRequest.java	61.905% <61.905%> (ø)	34.000 <34.000> (?)
...dk/samtools/util/SAMRecordPrefetchingIterator.java	74.667% <74.667%> (ø)	13.000 <13.000> (?)
...main/java/htsjdk/samtools/HtsgetBAMFileReader.java	75.799% <75.799%> (ø)	24.000 <24.000> (?)
...sjdk/samtools/util/htsget/HtsgetErrorResponse.java	80.000% <80.000%> (ø)	4.000 <4.000> (?)
src/main/java/htsjdk/samtools/QueryInterval.java	71.429% <90.909%> (+4.762%)	24.000 <5.000> (+5.000)
... and 22 more

[lbergelson]

@andersleung 👍