Support writing a CRAI index from CRAMContainerStreamWriter

[tomwhite]

Description

This is to make it possible to write CRAI indexes from CRAMContainerStreamWriter, not just BAI indexes (as is the case currently). This is needed by disq-bio/disq#97.

This PR introduces AbstractCRAMIndexer that is the common base class of CRAMBAIIndexer and CRAMCRAIIndexer; and adds a constructor to CRAMContainerStreamWriter that takes an AbstractCRAMIndexer.

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 #1351 into master will increase coverage by 0.013%.
The diff coverage is 100%.

@@               Coverage Diff               @@
##              master     #1351       +/-   ##
===============================================
+ Coverage     67.848%   67.861%   +0.013%     
- Complexity      8283      8286        +3     
===============================================
  Files            563       563               
  Lines          33706     33710        +4     
  Branches        5657      5656        -1     
===============================================
+ Hits           22869     22876        +7     
+ Misses          8659      8657        -2     
+ Partials        2178      2177        -1

Impacted Files	Coverage Δ	Complexity Δ
src/main/java/htsjdk/samtools/CRAMBAIIndexer.java	81.034% <ø> (ø)	17 <0> (ø)	⬇️
...ava/htsjdk/samtools/CRAMContainerStreamWriter.java	72.458% <100%> (+0.117%)	55 <2> (+1)	⬆️
src/main/java/htsjdk/samtools/CRAMCRAIIndexer.java	81.818% <100%> (+0.866%)	10 <1> (+1)	⬆️
...antcontext/writer/VariantContextWriterBuilder.java	82.803% <0%> (+0.11%)	60% <0%> (ø)	⬇️
...samtools/util/AsyncBlockCompressedInputStream.java	76% <0%> (+4%)	13% <0%> (+1%)	⬆️

[tomwhite]

cc @cmnbroad

[cmnbroad]

Thx for making the common class/interface. Looks pretty good - just a request to factor out some duplicated test code.

[tomwhite]

Thanks for all the feedback @pshapiro4broad and @cmnbroad. I've addressed all the points in a new commit.