vcf/header/record/value/map/format/definition: Add VCF 4.5 format def…

…initions
zaeleus · Jul 1, 2024 · 81c9589 · 81c9589
1 parent 3444007
commit 81c9589
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diff --git a/noodles-vcf/CHANGELOG.md b/noodles-vcf/CHANGELOG.md
@@ -10,6 +10,9 @@
     reference-alternate bases (`LR`), local samples (`LG`), ploidy (`P`), and
     base modifications (`M`).
 
+  * vcf/header/record/value/map/format/definition: Add VCF 4.5 format
+    definitions.
+
   * vcf/variant/record/samples/keys/key: Add VCF 4.5 format keys.
 
 ## 0.60.0 - 2024-06-17

diff --git a/noodles-vcf/src/header/record/value/map/format/definition.rs b/noodles-vcf/src/header/record/value/map/format/definition.rs
@@ -2,6 +2,7 @@
 
 mod v4_3;
 mod v4_4;
+mod v4_5;
 
 use crate::header::{
     record::value::map::format::{Number, Type},
@@ -13,6 +14,7 @@ pub(crate) fn definition(
     key: &str,
 ) -> Option<(Number, Type, &'static str)> {
     match (file_format.major(), file_format.minor()) {
+        (4, 5) => v4_5::definition(key),
         (4, 4) => v4_4::definition(key),
         (4, 3) => v4_3::definition(key),
         _ => None,

diff --git a/noodles-vcf/src/header/record/value/map/format/definition/v4_5.rs b/noodles-vcf/src/header/record/value/map/format/definition/v4_5.rs
@@ -0,0 +1,162 @@
+use crate::{
+    header::record::value::map::format::{Number, Type},
+    variant::record::samples::keys::key,
+};
+
+pub(super) fn definition(key: &str) -> Option<(Number, Type, &'static str)> {
+    match key {
+        key::READ_DEPTHS => Some((
+            Number::ReferenceAlternateBases,
+            Type::Integer,
+            "Read depth for each allele",
+        )),
+        key::FORWARD_STRAND_READ_DEPTHS => Some((
+            Number::ReferenceAlternateBases,
+            Type::Integer,
+            "Read depth for each allele on the forward strand",
+        )),
+        key::REVERSE_STRAND_READ_DEPTHS => Some((
+            Number::ReferenceAlternateBases,
+            Type::Integer,
+            "Read depth for each allele on the reverse strand",
+        )),
+        key::READ_DEPTH => Some((Number::Count(1), Type::Integer, "Read depth")),
+        key::EXPECTED_ALTERNATE_ALLELE_COUNTS => Some((
+            Number::AlternateBases,
+            Type::Integer,
+            "Expected alternate allele counts",
+        )),
+        key::LENGTH => Some((
+            Number::Count(1),
+            Type::Integer,
+            "Length of <*> reference block",
+        )),
+        key::FILTER => Some((
+            Number::Count(1),
+            Type::String,
+            r#"Filter indicating if this genotype was "called""#,
+        )),
+        key::GENOTYPE_LIKELIHOODS => Some((Number::Samples, Type::Float, "Genotype likelihoods")),
+        key::GENOTYPE_POSTERIOR_PROBABILITIES => Some((
+            Number::Samples,
+            Type::Float,
+            "Genotype posterior probabilities",
+        )),
+        key::CONDITIONAL_GENOTYPE_QUALITY => Some((
+            Number::Count(1),
+            Type::Integer,
+            "Conditional genotype quality",
+        )),
+        key::GENOTYPE => Some((Number::Count(1), Type::String, "Genotype")),
+        key::HAPLOTYPE_QUALITY => Some((Number::Count(2), Type::Integer, "Haplotype quality")),
+        key::RESERVED_LA => Some((Number::Unknown, Type::Integer, "Reserved")),
+        key::LOCAL_ALTERNATIVE_ALLELE => Some((
+            Number::Unknown,
+            Type::Integer,
+            "1-based indices into ALT, indicating which alleles are relevant (local) for the current sample",
+        )),
+        key::LOCAL_READ_DEPTHS => Some((
+            Number::LocalReferenceAlternateBases,
+            Type::Integer,
+            "Local-allele representation of AD",
+        )),
+        key::LOCAL_FORWARD_STRAND_READ_DEPTHS => Some((
+            Number::LocalReferenceAlternateBases,
+            Type::Integer,
+            "Local-allele representation of ADF",
+        )),
+        key::LOCAL_REVERSE_STRAND_READ_DEPTHS => Some((
+            Number::LocalReferenceAlternateBases,
+            Type::Integer,
+            "Local-allele representation of ADR",
+        )),
+        key::LOCAL_EXPECTED_ALTERNATE_ALLELE_COUNTS => Some((
+            Number::LocalAlternateBases,
+            Type::Integer,
+            "Local-allele representation of EC",
+        )),
+        key::LOCAL_GENOTYPE_LIKELIHOODS => Some((
+            Number::LocalSamples,
+            Type::Integer,
+            "Local-allele representation of GL",
+        )),
+        key::LOCAL_GENOTYPE_POSTERIOR_PROBABILITIES => Some((
+            Number::LocalSamples,
+            Type::Integer,
+            "Local-allele representation of GP",
+        )),
+        key::LOCAL_ROUNDED_GENOTYPE_LIKELIHOODS => Some((
+            Number::LocalSamples,
+            Type::Integer,
+            "Local-allele representation of PL",
+        )),
+        key::LOCAL_ROUNDED_GENOTYPE_POSTERIOR_PROBABILITIES => Some((
+            Number::LocalSamples,
+            Type::Integer,
+            "Local-allele representation of PP",
+        )),
+        key::MAPPING_QUALITY => Some((Number::Count(1), Type::Integer, "RMS mapping quality")),
+        key::ROUNDED_GENOTYPE_LIKELIHOODS => Some((
+            Number::Samples,
+            Type::Integer,
+            "Phred-scaled genotype likelihoods rounded to the closest integer",
+        )),
+        key::ROUNDED_GENOTYPE_POSTERIOR_PROBABILITIES => Some((
+            Number::Samples,
+            Type::Integer,
+            "Phred-scaled genotype posterior probabilities rounded to the closest integer",
+        )),
+        key::PHASING_QUALITY => Some((Number::Count(1), Type::Integer, "Phasing quality")),
+        key::PHASE_SET => Some((Number::Count(1), Type::Integer, "Phase set")),
+        key::PHASE_SET_LIST => Some((Number::Ploidy, Type::String, "Phase set list")),
+        key::PHASE_SET_LIST_ORDINALS => Some((
+            Number::Ploidy,
+            Type::Integer,
+            "Phase set list ordinal",
+        )),
+        key::PHASE_SET_LIST_QUALITIES => Some((
+            Number::Ploidy,
+            Type::Integer,
+            "Phase set list quality",
+        )),
+
+        key::GENOTYPE_COPY_NUMBER => Some((Number::Count(1), Type::Float, "Copy number")),
+        key::COPY_NUMBER_CONFIDENCE_INTERVAL => Some((
+            Number::Count(2),
+            Type::Float,
+            "Confidence interval around copy number",
+        )),
+        key::GENOTYPE_COPY_NUMBER_QUALITY => Some((
+            Number::Count(1),
+            Type::Float,
+            "Copy number genotype quality",
+        )),
+        key::GENOTYPE_COPY_NUMBER_LIKELIHOODS => Some((
+            Number::Samples,
+            Type::Float,
+            "Copy number genotype likelihood",
+        )),
+        key::GENOTYPE_COPY_NUMBER_POSTERIOR_PROBABILITIES => Some((
+            Number::Samples,
+            Type::Float,
+            "Copy number posterior probabilities",
+        )),
+        key::NOVEL_VARIANT_QUALITY_SCORE => Some((
+            Number::Count(1),
+            Type::Integer,
+            "Phred style probability score that the variant is novel",
+        )),
+        key::HAPLOTYPE_ID => Some((
+            Number::Count(1),
+            Type::Integer,
+            "Unique haplotype identifier",
+        )),
+        key::ANCESTRAL_HAPLOTYPE_ID => Some((
+            Number::Count(1),
+            Type::Integer,
+            "Unique identifier of ancestral haplotype",
+        )),
+
+        _ => None,
+    }
+}