CRAM: Refactor Encodings and Codecs

[jmthibault79]

Description

Encodings and Codecs are better encapsulated: final fields and constructors over random-access

removed AbstractBitCodec and BitCodec

• base interface is now CramCodec
• codecs are fully instantiated with all necessary streams so the interface is simply read()/write() -- removed unused skip(), readInto(), numberOfBits() methods
• bit-based core codecs inherit from abstract CoreBitCodec and live in encoding.core
• byte-based external codecs inherit from abstract ExternalCodec and live in encoding.external
• NullCodec is neither and ByteArrayLenCodec is both, so both implement CramCodec directly

"Experimental" codecs are those which are not supported by htslib and will be removed from the spec

• all are CoreBitCodecs in encoding.core.experimental
• a warning will be logged if one is instantiated (by an unusual file input?)

moved compression classes out of the encoding package to prevent confusion

rethrowing IOExceptions as RuntimeExceptions

rearranged the Huffman classes to better isolate the base codecs

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 #1224 into master will increase coverage by 0.538%. The diff coverage is 61.043%.

@@               Coverage Diff               @@
##              master     #1224       +/-   ##
===============================================
+ Coverage     69.031%   69.568%   +0.538%     
- Complexity      8077      8120       +43     
===============================================
  Files            539       543        +4     
  Lines          32616     32650       +34     
  Branches        5510      5538       +28     
===============================================
+ Hits           22515     22714      +199     
+ Misses          7894      7729      -165     
  Partials        2207      2207

Impacted Files	Coverage Δ	Complexity Δ
...ava/htsjdk/samtools/cram/compression/rans/E04.java	96.875% <ø> (ø)	5 <0> (?)
...a/htsjdk/samtools/cram/compression/rans/Utils.java	57.895% <ø> (ø)	3 <0> (?)
...va/htsjdk/samtools/cram/compression/rans/RANS.java	79.545% <ø> (ø)	17 <0> (?)
...oding/reader/MultiRefSliceAlignmentSpanReader.java	100% <ø> (ø)	6 <0> (ø)	:arrow_down:
...ain/java/htsjdk/samtools/cram/structure/Block.java	62.5% <ø> (ø)	30 <0> (ø)	:arrow_down:
...s/cram/encoding/core/huffmanUtils/HuffmanCode.java	90.244% <ø> (ø)	7 <0> (?)
...ava/htsjdk/samtools/cram/compression/rans/E14.java	88.679% <ø> (ø)	3 <0> (?)
...s/cram/encoding/core/huffmanUtils/HuffmanLeaf.java	100% <ø> (ø)	1 <0> (?)
...samtools/cram/compression/ExternalCompression.java	88.571% <ø> (ø)	11 <0> (?)
...jdk/samtools/cram/structure/CompressionHeader.java	90.506% <ø> (-0.119%)	27 <0> (-1)
... and 97 more

[jmthibault79]

Based on spec conversations, I made some changes to this PR:

• moving Gamma and SubExponential encodings from Experimental to Core and adding appropriate tests
• giving a meaningful order to DataSeries