CRAM: Refactor and Test Slice

[jmthibault79]

Description

Encapsulate Slice and make immutable

• extract immutable SliceHeader class
• create immutable IndexableSlice subclass with indexing metadata
• create immutable SliceBAIMetadata class and update index-consuming methods to take this as input instead of slice
• make CRAIEntry immutable and add a method to convert to a SliceBAIMetadata

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 #1242 into master will increase coverage by 0.159%. The diff coverage is 82.441%.

@@               Coverage Diff               @@
##              master     #1242       +/-   ##
===============================================
+ Coverage     69.376%   69.535%   +0.159%     
- Complexity      8140      8325      +185     
===============================================
  Files            547       549        +2     
  Lines          32622     33199      +577     
  Branches        5515      5654      +139     
===============================================
+ Hits           22632     23085      +453     
- Misses          7772      7865       +93     
- Partials        2218      2249       +31

Impacted Files	Coverage Δ	Complexity Δ
.../samtools/cram/build/CompressionHeaderFactory.java	90.842% <ø> (ø)	66 <0> (ø)	:arrow_down:
...java/htsjdk/samtools/cram/structure/Container.java	81.25% <100%> (ø)	7 <0> (ø)	:arrow_down:
...oding/reader/MultiRefSliceAlignmentSpanReader.java	100% <100%> (ø)	6 <2> (ø)	:arrow_down:
src/main/java/htsjdk/samtools/CRAMIterator.java	78.676% <100%> (-1.044%)	32 <0> (-1)
...amtools/cram/encoding/writer/CramRecordWriter.java	89.063% <100%> (ø)	26 <0> (ø)	:arrow_down:
.../samtools/cram/structure/slice/SliceAlignment.java	86.207% <100%> (ø)	10 <4> (?)
...jdk/samtools/cram/structure/CompressionHeader.java	90.244% <100%> (ø)	28 <0> (ø)	:arrow_down:
...amtools/cram/encoding/reader/CramRecordReader.java	85.256% <100%> (ø)	26 <0> (ø)	:arrow_down:
...c/main/java/htsjdk/samtools/cram/build/CramIO.java	83.721% <100%> (ø)	20 <1> (ø)	:arrow_down:
...amtools/cram/structure/slice/SliceBAIMetadata.java	100% <100%> (ø)	9 <9> (?)
... and 28 more

[jmthibault79]

Closing this while we work through the spec implications here: https://github.com/samtools/hts-specs/issues/370