vcf/header/record/value/map/info/definition: Add VCF 4.5 info definit…

…ions

noodles-vcf/CHANGELOG.md

@@ -1,5 +1,11 @@
 # Changelog
 
+## Unreleased
+
+### Added
+
+  * vcf/header/record/value/map/info/definition: Add VCF 4.5 info definitions.
+
 ## 0.62.0 - 2024-08-04
 
 ### Added

noodles-vcf/src/header/record/value/map/info/definition.rs

@@ -2,6 +2,7 @@
 
 mod v4_3;
 mod v4_4;
+mod v4_5;
 
 use crate::header::{
     record::value::map::info::{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,

noodles-vcf/src/header/record/value/map/info/definition/v4_5.rs

@@ -0,0 +1,201 @@
+use crate::{
+    header::record::value::map::info::{Number, Type},
+    variant::record::info::field::key,
+};
+
+pub(super) fn definition(key: &str) -> Option<(Number, Type, &'static str)> {
+    match key {
+        key::ANCESTRAL_ALLELE => Some((Number::Count(1), Type::String, "Ancestral allele")),
+        key::ALLELE_COUNT => Some((
+            Number::AlternateBases,
+            Type::Integer,
+            "Allele count in genotypes, for each ALT allele, in the same order as listed",
+        )),
+        key::TOTAL_READ_DEPTHS => Some((
+            Number::ReferenceAlternateBases,
+            Type::Integer,
+            "Total 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::ALLELE_FREQUENCIES => Some((
+            Number::AlternateBases,
+            Type::Float,
+            "Allele frequency for each ALT allele in the same order as listed (estimated from primary data, not called genotypes)",
+        )),
+        key::TOTAL_ALLELE_COUNT => Some((
+            Number::Count(1),
+            Type::Integer,
+            "Total number of alleles in called genotypes",
+        )),
+        key::BASE_QUALITY => Some((Number::Count(1), Type::Float, "RMS base quality")),
+        key::CIGAR => Some((
+            Number::AlternateBases,
+            Type::String,
+            "Cigar string describing how to align an alternate allele to the reference allele",
+        )),
+        key::IS_IN_DB_SNP => Some((Number::Count(0), Type::Flag, "dbSNP membership")),
+        key::TOTAL_DEPTH => Some((
+            Number::Count(1),
+            Type::Integer,
+            "Combined depth across samples",
+        )),
+        key::IS_IN_HAP_MAP_2 => Some((Number::Count(0), Type::Flag, "HapMap2 membership")),
+        key::IS_IN_HAP_MAP_3 => Some((Number::Count(0), Type::Flag, "HapMap3 membership")),
+        key::MAPPING_QUALITY => Some((Number::Count(1), Type::Float, "RMS mapping quality")),
+        key::ZERO_MAPPING_QUALITY_COUNT => {
+            Some((Number::Count(1), Type::Integer, "Number of MAPQ == 0 reads"))
+        }
+        key::SAMPLES_WITH_DATA_COUNT => Some((
+            Number::Count(1),
+            Type::Integer,
+            "Number of samples with data",
+        )),
+        key::STRAND_BIAS => Some((Number::Count(4), Type::Integer, "Strand bias")),
+        key::IS_SOMATIC_MUTATION => Some((
+            Number::Count(0),
+            Type::Flag,
+            "Somatic mutation (for cancer genomics)",
+        )),
+        key::IS_VALIDATED => Some((
+            Number::Count(0),
+            Type::Flag,
+            "Validated by follow-up experiment",
+        )),
+        key::IS_IN_1000_GENOMES => {
+            Some((Number::Count(0), Type::Flag, "1000 Genomes membership"))
+        }
+
+        key::IS_IMPRECISE => Some((
+            Number::Count(0),
+            Type::Flag,
+            "Imprecise structural variation",
+        )),
+        key::IS_NOVEL => Some((
+            Number::Count(0),
+            Type::Flag,
+            "Indicates a novel structural variation",
+        )),
+        key::END_POSITION => Some((
+            Number::Count(1),
+            Type::Integer,
+            "Deprecated. Present for backwards compatibility with earlier versions of VCF.",
+        )),
+        key::SV_TYPE => Some((Number::Count(1), Type::String, "Type of structural variant")),
+        key::SV_LENGTHS => Some((Number::AlternateBases, Type::Integer, "Length of structural variant")),
+        key::POSITION_CONFIDENCE_INTERVALS => Some((
+            Number::Unknown,
+            Type::Integer,
+            "Confidence interval around POS for symbolic structural variants",
+        )),
+        key::END_CONFIDENCE_INTERVALS => Some((
+            Number::Unknown,
+            Type::Integer,
+            "Confidence interval around the inferred END for symbolic structural variants",
+        )),
+        key::MICROHOMOLOGY_LENGTHS => Some((
+            Number::AlternateBases,
+            Type::Integer,
+            "Length of base pair identical micro-homology at breakpoints",
+        )),
+        key::MICROHOMOLOGY_SEQUENCES => Some((
+            Number::AlternateBases,
+            Type::String,
+            "Sequence of base pair identical micro-homology at breakpoints",
+        )),
+        key::BREAKPOINT_IDS => Some((
+            Number::AlternateBases,
+            Type::String,
+            "ID of the assembled alternate allele in the assembly file",
+        )),
+        key::MOBILE_ELEMENT_INFO => Some((
+            Number::Unknown,
+            Type::String,
+            "Mobile element info of the form NAME,START,END,POLARITY",
+        )),
+        key::MOBILE_ELEMENT_TRANSDUCTION_INFO => Some((
+            Number::Unknown,
+            Type::String,
+            "Mobile element transduction info of the form CHR,START,END,POLARITY",
+        )),
+        key::DBV_ID => Some((
+            Number::AlternateBases,
+            Type::String,
+            "ID of this element in Database of Genomic Variation",
+        )),
+        key::DB_VAR_ID => Some((Number::AlternateBases, Type::String, "ID of this element in DBVAR")),
+        key::DB_RIP_ID => Some((Number::AlternateBases, Type::String, "ID of this element in DBRIP")),
+        key::MATE_BREAKEND_IDS => Some((Number::AlternateBases, Type::String, "ID of mate breakend")),
+        key::PARTNER_BREAKEND_ID => Some((Number::AlternateBases, Type::String, "ID of partner breakend")),
+        key::BREAKEND_EVENT_ID => Some((Number::AlternateBases, Type::String, "ID of associated event")),
+        key::EVENT_TYPE => Some((Number::AlternateBases, Type::String, "Type of associated event")),
+        key::BREAKEND_CONFIDENCE_INTERVALS => Some((
+            Number::Unknown,
+            Type::Integer,
+            "Confidence interval for the SVLEN field",
+        )),
+        key::BREAKEND_COPY_NUMBER => {
+            Some((Number::AlternateBases, Type::Float, "Copy number of CNV/breakpoint"))
+        }
+        key::COPY_NUMBER_CONFIDENCE_INTERVALS => Some((
+            Number::Unknown,
+            Type::Float,
+            "Confidence interval around copy number",
+        )),
+        key::SV_CLAIM => Some((
+            Number::AlternateBases,
+            Type::String,
+            "Claim made by the structural variant call. Valid values are D, J, DJ for abundance, adjacency and both respectively",
+        )),
+        key::TOTAL_REPEAT_SEQUENCE_COUNTS => Some((
+            Number::AlternateBases,
+            Type::Integer,
+            "Total number of repeat sequences in this allele",
+        )),
+        key::REPEAT_UNIT_SEQUENCES => Some((
+            Number::Unknown,
+            Type::String,
+            "Repeat unit sequence of the corresponding repeat sequence",
+        )),
+        key::REPEAT_UNIT_LENGTHS => Some((
+            Number::Unknown,
+            Type::Integer,
+            "Repeat unit length of the corresponding repeat sequence",
+        )),
+        key::REPEAT_UNIT_COUNTS => Some((
+            Number::Unknown,
+            Type::Float,
+            "Repeat unit count of corresponding repeat sequence",
+        )),
+        key::TOTAL_REPEAT_SEQUENCE_BASE_COUNTS => Some((
+            Number::Unknown,
+            Type::Integer,
+            "Total number of bases in the corresponding repeat sequence",
+        )),
+        key::REPEAT_UNIT_COUNT_CONFIDENCE_INTERVALS => Some((
+            Number::Unknown,
+            Type::Float,
+            "Confidence interval around RUC",
+        )),
+        key::TOTAL_REPEAT_SEQUENCE_BASE_COUNT_CONFIDENCE_INTERVALS => Some((
+            Number::Unknown,
+            Type::Integer,
+            "Confidence interval around RB",
+        )),
+        key::REPEAT_UNIT_BASE_COUNTS => Some((
+            Number::Unknown,
+            Type::Integer,
+            "Number of bases in each individual repeat unit",
+        )),
+
+        _ => None,
+    }
+}

noodles-vcf/src/variant/record/info/field/key.rs

@@ -67,6 +67,8 @@ pub const IS_IMPRECISE: &str = "IMPRECISE";
 pub const IS_NOVEL: &str = "NOVEL";
 
 /// End position of the variant described in this record (`END`).
+///
+/// Deprecated in VCF 4.5.
 pub const END_POSITION: &str = "END";
 
 /// Type of structural variant (`SVTYPE`).