WIP: Progress toward Container encapsulation

[jmthibault79]

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 #1348 into master will increase coverage by 0.051%. The diff coverage is 82.474%.

@@               Coverage Diff               @@
##              master     #1348       +/-   ##
===============================================
+ Coverage     67.848%   67.899%   +0.051%     
- Complexity      8283      8316       +33     
===============================================
  Files            563       564        +1     
  Lines          33706     33747       +41     
  Branches        5657      5656        -1     
===============================================
+ Hits           22869     22914       +45     
+ Misses          8659      8656        -3     
+ Partials        2178      2177        -1

Impacted Files	Coverage Δ	Complexity Δ
src/main/java/htsjdk/samtools/CRAMCRAIIndexer.java	80.952% <0%> (ø)	9 <0> (ø)	:arrow_down:
src/main/java/htsjdk/samtools/CRAMBAIIndexer.java	81.034% <0%> (ø)	17 <5> (ø)	:arrow_down:
...jdk/samtools/cram/build/CramContainerIterator.java	88.889% <100%> (ø)	10 <0> (ø)	:arrow_down:
...mtools/cram/build/CramContainerHeaderIterator.java	100% <100%> (ø)	2 <1> (ø)	:arrow_down:
src/main/java/htsjdk/samtools/CRAMFileReader.java	76.02% <100%> (ø)	53 <0> (ø)	:arrow_down:
...a/htsjdk/samtools/cram/build/ContainerFactory.java	96.296% <100%> (-0.255%)	5 <0> (ø)
...va/htsjdk/samtools/cram/build/ContainerParser.java	96.774% <100%> (ø)	10 <4> (ø)	:arrow_down:
...ava/htsjdk/samtools/CRAMContainerStreamWriter.java	71.73% <33.333%> (-0.61%)	54 <0> (ø)
src/main/java/htsjdk/samtools/CRAMIterator.java	81.752% <50%> (+0.134%)	31 <4> (ø)	:arrow_down:
...va/htsjdk/samtools/cram/structure/ContainerIO.java	65.574% <59.375%> (+2.24%)	10 <5> (ø)	:arrow_down:
... and 6 more

[cmnbroad]

Mined this for container header changes, and container is now encapsulated in my refactoring branch.