Use ReferenceContext for CramCompressionRecord sequenceId and mateSequenceID

[jmthibault79]

Description

Part of an attempt to replace all reference IDs / sequenceIDs with ReferenceContexts.

Note: It was necessary to move one CRAMComplianceTest from Full Verification to Partial Verification.

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 #1332 into master will decrease coverage by 0.011%. The diff coverage is 93.75%.

@@               Coverage Diff               @@
##              master     #1332       +/-   ##
===============================================
- Coverage     67.822%   67.811%   -0.011%     
+ Complexity      8253      8252        -1     
===============================================
  Files            562       562               
  Lines          33644     33642        -2     
  Branches        5640      5640               
===============================================
- Hits           22818     22813        -5     
- Misses          8654      8656        +2     
- Partials        2172      2173        +1

Impacted Files	Coverage Δ	Complexity Δ
...ava/htsjdk/samtools/cram/ref/ReferenceContext.java	91.667% <ø> (ø)	22 <0> (ø)	:arrow_down:
...ava/htsjdk/samtools/cram/build/CramNormalizer.java	81.143% <100%> (ø)	56 <0> (ø)	:arrow_down:
src/main/java/htsjdk/samtools/CRAMIterator.java	81.752% <100%> (ø)	31 <0> (ø)	:arrow_down:
...samtools/cram/structure/CramCompressionRecord.java	92.913% <100%> (-0.055%)	113 <5> (ø)
...jdk/samtools/cram/build/Sam2CramRecordFactory.java	85.256% <100%> (ø)	49 <0> (ø)	:arrow_down:
...jdk/samtools/cram/build/Cram2SamRecordFactory.java	93.162% <100%> (ø)	29 <0> (ø)	:arrow_down:
...oding/reader/MultiRefSliceAlignmentSpanReader.java	100% <100%> (ø)	6 <0> (ø)	:arrow_down:
...amtools/cram/encoding/writer/CramRecordWriter.java	89.231% <100%> (ø)	26 <0> (ø)	:arrow_down:
src/main/java/htsjdk/samtools/CRAMBAIIndexer.java	80.663% <100%> (ø)	17 <0> (ø)	:arrow_down:
...amtools/cram/encoding/reader/CramRecordReader.java	85.256% <100%> (ø)	26 <0> (ø)	:arrow_down:
... and 3 more

[cmnbroad]

Closing in favor of the refactoring branch.