fix: Sec and Stop coincide in SEPHS2

[tedil]

supersedes #213

in HGNC:19686, the last amino acid is actually translated to selenocysteine, but is practically interpreted as stop as well.

[coderabbitai]

Walkthrough

The changes in this pull request focus on enhancing the logic for handling alternative sequences related to genetic variants in the src/mapper/altseq.rs file. Key modifications include improvements to methods such as AltTranscriptData::new, incorporate_delins, and build_altseq, which now feature more detailed handling of specific cases, including selenocysteine and stop codons. Additionally, error handling has been refined to better manage invalid sequences and variant processing conditions, reflecting a deeper understanding of genetic sequence complexities.

Changes

File	Change Summary
src/mapper/altseq.rs	Enhanced logic in AltTranscriptData::new for handling selenocysteine and stop codons.
	Updated incorporate_delins for improved processing of deletions and insertions, especially frameshift variants.
	Modified build_altseq for accurate construction of variant sequence data and better categorization.
	Improved error handling for invalid sequences and processing conditions.
	Updated method signatures for AltTranscriptData::new, AltSeqBuilder::build_altseq, and AltSeqToHgvsp::create_variant to accommodate new logic.

Poem

In the meadow where sequences play,
A rabbit hops, brightening the day.
With logic refined, variants now sing,
Selenocysteine's dance, oh what joy it brings!
Through codons and frameshifts, we leap and we bound,
In the world of genetics, new wonders abound! 🐇✨

---

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[coderabbitai]

Actionable comments posted: 0

🧹 Outside diff range and nitpick comments (2)

src/mapper/altseq.rs (2)

159-171: Consider handling selenocysteine cases more robustly

The heuristic introduced for handling cases where selenocysteine ('U') coincides with a stop codon may not cover all scenarios. Consider enhancing the logic to check against known protein_accession cases or making the handling configurable to ensure correctness across different sequences.

---

Line range hint 304-304: Replace panic! with proper error handling

Using panic! in production code can lead to unexpected crashes. It's advisable to return an error instead, allowing the calling function to handle it gracefully.

Apply this diff to replace the panic! with an error return:

- _ => panic!("Can only work with concrete ref/alt"),
+ _ => return Err(Error::InvalidVariant("Expected concrete ref/alt in NaEdit".to_string())),

📜 Review details

Configuration used: CodeRabbit UI
Review profile: CHILL

📥 Commits

Reviewing files that changed from the base of the PR and between b85d04b and d8b8017.

📒 Files selected for processing (1)

• src/mapper/altseq.rs (1 hunks)

🔇 Additional comments (1)

src/mapper/altseq.rs (1)

Line range hint 942-949: Correctly truncating the alternative sequence after stop codons

The added code appropriately truncates the alternative sequence at the first occurrence of a stop codon ('*' or 'X'), which ensures that the resulting protein sequence is accurate and does not include residues beyond the stop codon.

[codecov]

Codecov Report

Attention: Patch coverage is 75.00000% with 1 line in your changes missing coverage. Please review.

Project coverage is 92.19%. Comparing base (3901274) to head (011e6f5).
Report is 1 commits behind head on main.

Files with missing lines	Patch %	Lines
src/mapper/altseq.rs	75.00%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #214      +/-   ##
==========================================
- Coverage   92.20%   92.19%   -0.01%     
==========================================
  Files          18       18              
  Lines       11440    11443       +3     
==========================================
+ Hits        10548    10550       +2     
- Misses        892      893       +1     

Files with missing lines	Coverage Δ
src/mapper/altseq.rs	95.28% <75.00%> (-0.11%)	⬇️