SNV frequency-based substitution matrix construction for CRAM writer

[athos]

This PR introduces a new feature to the CRAM writer, allowing it to construct a substitution matrix that takes into account the observed frequencies of SNVs.

The change introduces a substitution matrix builder, which works similarly to the existing tag dictionary builder used for constructing the tag dictionary. The substitution matrix builder provides two main functions:

• assign-code!: This function is called during preprocessing for each :subst read feature in the records and returns a unique base substitution code (BS code) for every pair of ref and alt bases
• build-subst-matrix: After preprocessing, this function is called to generate the substitution matrix based on the SNV frequency information gathered by assign-code!

Note that since BS codes cannot be assigned until all records within a container are scanned, assign-code! initially returns a unique reference (not the actual BS code) for each SNV. When build-subst-matrix is invoked, BS codes are assigned for each SNV, and the references are accordingly updated all at once. This implementation is intended to reduce the overhead of scanning each :subst read features again to assign the final BS codes after the records are fully processed.

BS code assignment follows a simple frequency-based method: the most frequently observed alt base for each ref base is assigned BS code 0, the next most frequent is assigned code 1, and so forth.

[codecov]

Codecov Report

Attention: Patch coverage is 91.30435% with 4 lines in your changes missing coverage. Please review.

Project coverage is 89.96%. Comparing base (943f181) to head (b07d48d).
Report is 2 commits behind head on master.

Files with missing lines	Patch %	Lines
src/cljam/io/cram/encode/subst_matrix.clj	89.74%	0 Missing and 4 partials ⚠️

Additional details and impacted files

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- Coverage   89.97%   89.96%   -0.01%     
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  Files         102      103       +1     
  Lines        9236     9271      +35     
  Branches      481      485       +4     
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+ Hits         8310     8341      +31     
  Misses        445      445              
- Partials      481      485       +4     

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[alumi]

Thank you for implementing the feature! LGTM 👍

[r6eve]

LGTM including the comments.