fix: ensure FORMAT sample order is in-sync with header sample order #671
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Actionable comments posted: 1
🔭 Outside diff range comments (2)
src/annotate/strucvars/mod.rs (2)
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363-368: Remove duplicate FORMAT field definition.The FORMAT field "src" is defined twice with identical parameters. This is redundant and should be removed.
- "src", // FIXME this is clearly the same format as above?! - Map::<Format>::new( - FormatNumber::Count(1), - Type::Integer, - "Split-end variant support", - ),
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2184-2190: Improve error handling in coordinate filling.The function uses unwrap/expect which could be replaced with proper error handling and more descriptive messages.
- .expect("chromosome not canonical"); + .ok_or_else(|| anyhow::anyhow!("Chromosome {} is not in the canonical set", &tsv_record.chromosome))?; - .expect("Telomeric breakend not supported") + .ok_or_else(|| anyhow::anyhow!("Telomeric breakends are not supported in this implementation"))?
🧹 Nitpick comments (2)
src/annotate/strucvars/mod.rs (2)
429-443: Consider improving pedigree handling implementation.The implementation could be enhanced in a few ways:
- The debug message could include more context about why the sample was skipped
- The HashMap conversion could be more concise using
into_iter()- let individuals = pedigree - .individuals - .values() - .map(|i| (i.name.clone(), i)) - .collect::<HashMap<_, _>>(); + let individuals: HashMap<_, _> = pedigree.individuals.values().map(|i| (&i.name, i)).collect(); for sample in header.sample_names() { let individual = individuals.get(sample); if individual.is_none() { - tracing::debug!("Sample {} not part of the pedigree, skipping.", sample); + tracing::debug!("Sample {} not found in pedigree definition, skipping sample.", sample); continue; }
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1201-1288: Add missing documentation for struct fields.Several fields in the VarFishStrucvarTsvRecord struct lack documentation. Consider adding documentation for all fields to improve code maintainability.
Example for a few fields:
/// A record, as written out to a VarFish TSV file. #[derive(Debug, Default, Serialize, Deserialize, Clone, PartialEq)] pub struct VarFishStrucvarTsvRecord { /// The genome assembly/build. pub release: String, /// Chromosome name of start position. pub chromosome: String, + /// Numeric representation of the chromosome (1-22, X=23, Y=24, M=25) pub chromosome_no: u32, + /// UCSC bin for efficient interval queries pub bin: u32, // ... other fields }
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src/annotate/strucvars/mod.rs(5 hunks)
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- GitHub Check: Testing
- GitHub Check: Schema
- GitHub Check: Linting
- GitHub Check: build-and-push-image
Fixes #668
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New Features
Refactor