CRAM: revert #1326 and fix tests and comments

[jmthibault79]

Description

Please explain the changes you made here. Explain the motivation for making this change. What existing problem does the pull request solve?

Checklist

• [x] Code compiles correctly
• [x] New tests covering changes and new functionality
• [x] All tests passing
• [x] Extended the README / documentation, if necessary
• [ ] Is not backward compatible (breaks binary or source compatibility)

[jmthibault79]

1326 was based on a misunderstanding of values in the CRAM Container Header. https://github.com/samtools/hts-specs/pull/398 is the companion PR for the spec.

[codecov-io]

Codecov Report

Merging #1341 into master will decrease coverage by 0.003%. The diff coverage is 80.488%.

@@               Coverage Diff               @@
##              master     #1341       +/-   ##
===============================================
- Coverage     67.848%   67.846%   -0.003%     
  Complexity      8273      8273               
===============================================
  Files            562       562               
  Lines          33678     33675        -3     
  Branches        5653      5653               
===============================================
- Hits           22850     22847        -3     
  Misses          8653      8653               
  Partials        2175      2175

Impacted Files	Coverage Δ	Complexity Δ
...n/java/htsjdk/samtools/cram/structure/SliceIO.java	83.333% <ø> (ø)	14 <0> (ø)	:arrow_down:
...mtools/cram/build/CramContainerHeaderIterator.java	100% <100%> (ø)	2 <0> (ø)	:arrow_down:
src/main/java/htsjdk/samtools/CRAMFileReader.java	76.02% <100%> (ø)	53 <0> (ø)	:arrow_down:
...jdk/samtools/cram/structure/ContainerHeaderIO.java	74.545% <100%> (ø)	7 <0> (ø)	:arrow_down:
...rc/main/java/htsjdk/samtools/BAMIndexMetaData.java	77.67% <100%> (ø)	22 <0> (ø)	:arrow_down:
src/main/java/htsjdk/samtools/CRAMBAIIndexer.java	81.034% <100%> (ø)	17 <0> (ø)	:arrow_down:
...ain/java/htsjdk/samtools/cram/structure/Slice.java	67.593% <100%> (ø)	43 <0> (ø)	:arrow_down:
src/main/java/htsjdk/samtools/cram/CRAIIndex.java	88.571% <100%> (ø)	26 <0> (ø)	:arrow_down:
...va/htsjdk/samtools/cram/structure/ContainerIO.java	63.333% <57.143%> (-0.601%)	10 <0> (ø)
src/main/java/htsjdk/samtools/cram/CRAIEntry.java	73.684% <71.429%> (ø)	25 <1> (ø)	:arrow_down:
... and 2 more