CRAM indexing tests and associated fixes and updates

[jmthibault79]

Description

Adding better test coverage for CRAM indexing, which inspired:

• a CRAIQuery class with the necessary fields from CRAIEntry for querying
• AlignmentSpan immutability and distinguishing between mapped and unmapped read counts
• Recording mapped, unmapped, and unplaced read counts per slice
• requiring Coordinate-Sorted for CRAM BAI generation

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)

[codecov-io]

Codecov Report

Merging #1276 into master will increase coverage by 0.246%. The diff coverage is 80.365%.

@@               Coverage Diff               @@
##              master     #1276       +/-   ##
===============================================
+ Coverage     67.626%   67.873%   +0.246%     
- Complexity      8229      8265       +36     
===============================================
  Files            562       562               
  Lines          33617     33800      +183     
  Branches        5642      5684       +42     
===============================================
+ Hits           22734     22941      +207     
+ Misses          8708      8681       -27     
- Partials        2175      2178        +3

Impacted Files	Coverage Δ	Complexity Δ
src/main/java/htsjdk/samtools/CRAMIterator.java	81.752% <ø> (ø)	31 <0> (ø)	:arrow_down:
...samtools/cram/structure/CramCompressionRecord.java	92.969% <ø> (ø)	113 <0> (ø)	:arrow_down:
...a/htsjdk/samtools/cram/build/ContainerFactory.java	96.667% <100%> (-0.108%)	5 <0> (ø)
...oding/reader/MultiRefSliceAlignmentSpanReader.java	100% <100%> (ø)	6 <3> (+1)	:arrow_up:
...va/htsjdk/samtools/cram/build/ContainerParser.java	96.774% <100%> (+2.435%)	10 <0> (-8)	:arrow_down:
src/main/java/htsjdk/samtools/CRAMCRAIIndexer.java	79.167% <100%> (+0.443%)	9 <1> (ø)	:arrow_down:
...jdk/samtools/cram/structure/CompressionHeader.java	90.303% <100%> (+0.059%)	29 <1> (+1)	:arrow_up:
...va/htsjdk/samtools/cram/structure/ContainerIO.java	61.728% <100%> (ø)	13 <0> (ø)	:arrow_down:
...rc/main/java/htsjdk/samtools/BAMIndexMetaData.java	77.67% <100%> (+3.838%)	22 <2> (ø)	:arrow_down:
src/main/java/htsjdk/samtools/cram/CRAIIndex.java	88.406% <100%> (+5.69%)	26 <12> (-1)	:arrow_down:
... and 10 more

[cmnbroad]

Thanks @jmthibault79 for all the iteration on this one.