Automatic read name generation for CRAM records

[athos]

This PR enables the CRAM reader to automatically generate read names (QNAMEs) when they are absent in CRAM records.

Specification

According to section §10.3 of the CRAM specification v3.1:

• If the RN field in the compression header's preservation map of a slice is set to true, the decoder will decode read names from the RN data series
• If the RN field is set to false and a record has a detached flag (0x2) set in the CF field, the decoder will also decode its read name from the RN data series
• For all other records, the decoder will automatically generate read names
  • Although the CRAM specification does not define a specific method for generating read names, it suggests that names "are typically based on the file name and a numeric ID of the read, utilizing the record counter field from the slice header block"
  • Also, the decoder must generate consistent read names for mate reads

Due to the last condition, read name generation must occur after resolving mate reads.

Implementation

This PR adds a "qname generator" to the CRAM reader. A qname generator is responsible for generating read names based on the file name and the global record counter. If the RN field is set to false in the compression header, the CRAM record decoder generates read names by calling the qname generator after mate read resolution.

The format for generated read names is <file name>:<counter>, which is aligned with htslib. The <file name> will be tweaked from the actual file name to ensure it complies with the specification for QNAMEs in SAM, meaning it does not contain characters outside the [!-?A-~] range and does not exceed 254 characters in length.

Note

The PR also includes new test code based on the 1001_name.cram test file from hts-specs.

[codecov]

Codecov Report

Attention: Patch coverage is 84.84848% with 5 lines in your changes are missing coverage. Please review.

Project coverage is 88.39%. Comparing base (82e16ed) to head (69e852a).

Files	Patch %	Lines
src/cljam/io/cram/core.clj	66.66%	5 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##           master     #308      +/-   ##
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- Coverage   88.40%   88.39%   -0.02%     
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  Files          95       95              
  Lines        8228     8255      +27     
  Branches      506      506              
==========================================
+ Hits         7274     7297      +23     
- Misses        448      452       +4     
  Partials      506      506              

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[alumi]

Thank you for the PR.
I have reviewed the implementation based on the spec.
Everything looks good to me 👍

[athos]

Rebased onto the latest master branch.

[athos]

Rebased onto the latest master branch.

[athos]

Rebased onto the latest master branch.

[ToshimitsuArai]

Sorry for the late review 🙏
Thank you and checked for the PR, LGTM 👍