noodles_vcf/variant/record/samples/keys/
key.rs

1//! Variant record samples key.
2
3/// Read depth for each allele (`AD`).
4pub const READ_DEPTHS: &str = "AD";
5
6/// Read depth for each allele on the forward strand (`ADF`).
7pub const FORWARD_STRAND_READ_DEPTHS: &str = "ADF";
8
9/// Read depth for each allele on the reverse strand (`ADR`).
10pub const REVERSE_STRAND_READ_DEPTHS: &str = "ADR";
11
12/// Read depth (`DP`).
13pub const READ_DEPTH: &str = "DP";
14
15/// Expected alternate allele counts (`EC`).
16pub const EXPECTED_ALTERNATE_ALLELE_COUNTS: &str = "EC";
17
18/// Length of <*> reference block (`LEN`).
19///
20/// Added in VCF 4.5.
21pub const LENGTH: &str = "LEN";
22
23/// Filter indicating if this genotype was "called" (`FT`).
24pub const FILTER: &str = "FT";
25
26/// Genotype likelihoods (`GL`).
27pub const GENOTYPE_LIKELIHOODS: &str = "GL";
28
29/// Genotype posterior probabilities (`GP`).
30pub const GENOTYPE_POSTERIOR_PROBABILITIES: &str = "GP";
31
32/// Conditional genotype quality (`GQ`).
33pub const CONDITIONAL_GENOTYPE_QUALITY: &str = "GQ";
34
35/// Genotype (`GT`).
36pub const GENOTYPE: &str = "GT";
37
38/// Haplotype quality (`HQ`).
39pub const HAPLOTYPE_QUALITY: &str = "HQ";
40
41/// Reserved (`LA`).
42///
43/// Added in VCF 4.5.
44pub const RESERVED_LA: &str = "LA";
45
46/// 1-based indices into ALT, indicating which alleles are relevant (local) for the current sample
47/// (`LAA`).
48///
49/// Added in VCF 4.5.
50pub const LOCAL_ALTERNATIVE_ALLELE: &str = "LAA";
51
52/// Local-allele representation of AD (`LAD`).
53///
54/// Added in VCF 4.5.
55pub const LOCAL_READ_DEPTHS: &str = "LAD";
56
57/// Local-allele representation of ADF (`LADF`).
58///
59/// Added in VCF 4.5.
60pub const LOCAL_FORWARD_STRAND_READ_DEPTHS: &str = "LADF";
61
62/// Local-allele representation of ADR (`LADR`).
63///
64/// Added in VCF 4.5.
65pub const LOCAL_REVERSE_STRAND_READ_DEPTHS: &str = "LADR";
66
67/// Local-allele representation of EC (`LEC`).
68///
69/// Added in VCF 4.5.
70pub const LOCAL_EXPECTED_ALTERNATE_ALLELE_COUNTS: &str = "LEC";
71
72/// Local-allele representation of GL (`LGL`).
73///
74/// Added in VCF 4.5.
75pub const LOCAL_GENOTYPE_LIKELIHOODS: &str = "LGL";
76
77/// Local-allele representation of GP (`LGP`).
78///
79/// Added in VCF 4.5.
80pub const LOCAL_GENOTYPE_POSTERIOR_PROBABILITIES: &str = "LGP";
81
82/// Local-allele representation of PL (`LPL`).
83///
84/// Added in VCF 4.5.
85pub const LOCAL_ROUNDED_GENOTYPE_LIKELIHOODS: &str = "LPL";
86
87/// Local-allele representation of PP (`LPP`).
88///
89/// Added in VCF 4.5.
90pub const LOCAL_ROUNDED_GENOTYPE_POSTERIOR_PROBABILITIES: &str = "LPP";
91
92/// RMS mapping quality (`MQ`).
93pub const MAPPING_QUALITY: &str = "MQ";
94
95/// Phred-scaled genotype likelihoods rounded to the closest integer (`PL`).
96pub const ROUNDED_GENOTYPE_LIKELIHOODS: &str = "PL";
97
98/// Phred-scaled genotype posterior probabilities rounded to the closest integer (`PP`).
99pub const ROUNDED_GENOTYPE_POSTERIOR_PROBABILITIES: &str = "PP";
100
101/// Phasing quality (`PQ`).
102pub const PHASING_QUALITY: &str = "PQ";
103
104/// Phase set (`PS`).
105pub const PHASE_SET: &str = "PS";
106
107/// Phase set list (`PSL`).
108///
109/// Added in VCF 4.4.
110pub const PHASE_SET_LIST: &str = "PSL";
111
112/// Phase set list ordinal (`PSO`).
113///
114/// Added in VCF 4.4.
115pub const PHASE_SET_LIST_ORDINALS: &str = "PSO";
116
117/// Phase set list quality (`PSQ`).
118///
119/// Added in VCF 4.4.
120pub const PHASE_SET_LIST_QUALITIES: &str = "PSQ";
121
122/// Copy number genotype for imprecise events (`CN`).
123pub const GENOTYPE_COPY_NUMBER: &str = "CN";
124
125/// Confidence interval around copy number (`CICN`).
126///
127/// Added in VCF 4.4.
128pub const COPY_NUMBER_CONFIDENCE_INTERVAL: &str = "CICN";
129
130/// Copy number genotype quality for imprecise events (`CNQ`).
131pub const GENOTYPE_COPY_NUMBER_QUALITY: &str = "CNQ";
132
133/// Copy number genotype likelihood for imprecise events (`CNL`).
134pub const GENOTYPE_COPY_NUMBER_LIKELIHOODS: &str = "CNL";
135
136/// Copy number posterior probabilities (`CNP`).
137pub const GENOTYPE_COPY_NUMBER_POSTERIOR_PROBABILITIES: &str = "CNP";
138
139/// Phred style probability score that the variant is novel (`NQ`).
140pub const NOVEL_VARIANT_QUALITY_SCORE: &str = "NQ";
141
142/// Unique haplotype identifier (`HAP`).
143pub const HAPLOTYPE_ID: &str = "HAP";
144
145/// Unique identifier of ancestral haplotype (`AHAP`).
146pub const ANCESTRAL_HAPLOTYPE_ID: &str = "AHAP";
147
148#[cfg(test)]
149mod tests {
150    use super::*;
151
152    #[test]
153    fn test_fmt() {
154        assert_eq!(READ_DEPTHS, "AD");
155        assert_eq!(FORWARD_STRAND_READ_DEPTHS, "ADF");
156        assert_eq!(REVERSE_STRAND_READ_DEPTHS, "ADR");
157        assert_eq!(READ_DEPTH, "DP");
158        assert_eq!(EXPECTED_ALTERNATE_ALLELE_COUNTS, "EC");
159        assert_eq!(LENGTH, "LEN");
160        assert_eq!(FILTER, "FT");
161        assert_eq!(GENOTYPE_LIKELIHOODS, "GL");
162        assert_eq!(GENOTYPE_POSTERIOR_PROBABILITIES, "GP");
163        assert_eq!(CONDITIONAL_GENOTYPE_QUALITY, "GQ");
164        assert_eq!(GENOTYPE, "GT");
165        assert_eq!(HAPLOTYPE_QUALITY, "HQ");
166        assert_eq!(RESERVED_LA, "LA");
167        assert_eq!(LOCAL_ALTERNATIVE_ALLELE, "LAA");
168        assert_eq!(LOCAL_READ_DEPTHS, "LAD");
169        assert_eq!(LOCAL_FORWARD_STRAND_READ_DEPTHS, "LADF");
170        assert_eq!(LOCAL_REVERSE_STRAND_READ_DEPTHS, "LADR");
171        assert_eq!(LOCAL_EXPECTED_ALTERNATE_ALLELE_COUNTS, "LEC");
172        assert_eq!(LOCAL_GENOTYPE_LIKELIHOODS, "LGL");
173        assert_eq!(LOCAL_GENOTYPE_POSTERIOR_PROBABILITIES, "LGP");
174        assert_eq!(LOCAL_ROUNDED_GENOTYPE_LIKELIHOODS, "LPL");
175        assert_eq!(LOCAL_ROUNDED_GENOTYPE_POSTERIOR_PROBABILITIES, "LPP");
176        assert_eq!(MAPPING_QUALITY, "MQ");
177        assert_eq!(ROUNDED_GENOTYPE_LIKELIHOODS, "PL");
178        assert_eq!(ROUNDED_GENOTYPE_POSTERIOR_PROBABILITIES, "PP");
179        assert_eq!(PHASING_QUALITY, "PQ");
180        assert_eq!(PHASE_SET, "PS");
181        assert_eq!(PHASE_SET_LIST, "PSL");
182        assert_eq!(PHASE_SET_LIST_ORDINALS, "PSO");
183        assert_eq!(PHASE_SET_LIST_QUALITIES, "PSQ");
184
185        assert_eq!(GENOTYPE_COPY_NUMBER, "CN");
186        assert_eq!(COPY_NUMBER_CONFIDENCE_INTERVAL, "CICN");
187        assert_eq!(GENOTYPE_COPY_NUMBER_QUALITY, "CNQ");
188        assert_eq!(GENOTYPE_COPY_NUMBER_LIKELIHOODS, "CNL");
189        assert_eq!(GENOTYPE_COPY_NUMBER_POSTERIOR_PROBABILITIES, "CNP");
190        assert_eq!(NOVEL_VARIANT_QUALITY_SCORE, "NQ");
191        assert_eq!(HAPLOTYPE_ID, "HAP");
192        assert_eq!(ANCESTRAL_HAPLOTYPE_ID, "AHAP");
193    }
194}
noodles_vcf/variant/record/samples/keys/key.rs

noodles_vcf/variant/record/samples/keys/
key.rs
