Add RANS Nx16 codec (Update CRAM Codecs to CRAM 3.1)

[yash-puligundla]

Description

This PR is part of an effort to upgrade CRAM to v3.1. It adds the RANS Nx16 implementation and adds changes to the existing RANS implementation to accommodate RANS Nx16.

List of Changes:

• Add RANS Nx16 Codec
• Add interfaces - RANSEncode, RANSDecode and RANSParams
• Restructured existing RANS code
  • Rename the existing RANS codec to RANS4x8
  • Change the structure of the ArithmeticDecoder
  • Move the code from E04, E14, D04, and D14 into the classes where it is used
• Add CRAMCodecCorpusTest to test RANS 4x8 and RANS Nx16 Codecs using test files from htscodecs
• Add more test cases to RANSTest to test RANS 4x8 and RANS Nx16 Codecs

Test fails:
CRAMCodecCorpusTest fails as they require the test files from htscodecs repo.

[cmnbroad]

Checkpointing what I have so far, which only covers test code.

[cmnbroad]

A few more minor comments.

[codecov-commenter]

Codecov Report

Merging #1618 (c63a253) into master (347c0ac) will increase coverage by 0.423%.
Report is 40 commits behind head on master.
The diff coverage is 95.548%.

❗ Current head c63a253 differs from pull request most recent head 1979264. Consider uploading reports for the commit 1979264 to get more accurate results

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Additional details and impacted files

@@               Coverage Diff               @@
##              master     #1618       +/-   ##
===============================================
+ Coverage     69.856%   70.279%   +0.423%     
- Complexity      9695      9907      +212     
===============================================
  Files            703       705        +2     
  Lines          37772     38427      +655     
  Branches        6139      6275      +136     
===============================================
+ Hits           26386     27006      +620     
- Misses          8929      8945       +16     
- Partials        2457      2476       +19     

Files	Coverage Δ
.../samtools/cram/compression/ExternalCompressor.java	74.074% <100.000%> (ø)
...tools/cram/compression/RANSExternalCompressor.java	76.000% <100.000%> (+5.167%)	⬆️
...tools/cram/compression/rans/ArithmeticDecoder.java	100.000% <100.000%> (ø)
...jdk/samtools/cram/compression/rans/RANSDecode.java	100.000% <100.000%> (ø)
...ools/cram/compression/rans/RANSDecodingSymbol.java	100.000% <100.000%> (ø)
...jdk/samtools/cram/compression/rans/RANSParams.java	100.000% <100.000%> (ø)
...s/cram/compression/rans/rans4x8/RANS4x8Params.java	100.000% <100.000%> (ø)
...cram/compression/rans/ransnx16/RANSNx16Params.java	100.000% <100.000%> (ø)
...s/cram/structure/CompressionHeaderEncodingMap.java	85.621% <100.000%> (ø)
...tsjdk/samtools/cram/structure/CompressorCache.java	92.000% <100.000%> (+0.696%)	⬆️
... and 8 more

... and 25 files with indirect coverage changes

[yash-puligundla]

Hi @cmnbroad I have addressed all the feedback so far. Please let me know if you notice anything. Thanks!

[cmnbroad]

Another checkpoint of what I have so far.

[cmnbroad]

Not even close to done, but checkpointing what I have - will resume when I get back from vacation.

[cmnbroad]

Still a little bit more to go, but almost done.

[cmnbroad]

In this round I mostly focused on the decoders - many of my comments apply to the encoders as well, but I didn't duplicate them there since there are quite a few. I'm stopping for now and will need to do another round once these issues are addressed.

[yash-puligundla]

@cmnbroad Thank you for your comments. I have addressed all of them so far. Ready for the next round of review.