noodles_vcf/variant/record/info/field/
key.rs

1//! VCF record info key.
2
3/// Ancestral allele (`AA`).
4pub const ANCESTRAL_ALLELE: &str = "AA";
5
6/// Allele count in genotypes, for each ALT allele, in the same order as listed (`AC`).
7pub const ALLELE_COUNT: &str = "AC";
8
9/// Total read depth for each allele (`AD`).
10pub const TOTAL_READ_DEPTHS: &str = "AD";
11
12/// Read depth for each allele on the forward strand (`ADF`).
13pub const FORWARD_STRAND_READ_DEPTHS: &str = "ADF";
14
15/// Read depth for each allele on the reverse strand (`ADR`).
16pub const REVERSE_STRAND_READ_DEPTHS: &str = "ADR";
17
18/// Allele frequency for each ALT allele in the same order as listed (`AF`).
19pub const ALLELE_FREQUENCIES: &str = "AF";
20
21/// Total number of alleles in called genotypes (`AN`).
22pub const TOTAL_ALLELE_COUNT: &str = "AN";
23
24/// RMS base quality (`BQ`).
25pub const BASE_QUALITY: &str = "BQ";
26
27/// Cigar string describing how to align an alternate allele to the reference allele (`CIGAR`).
28pub const CIGAR: &str = "CIGAR";
29
30/// dbSNP membership (`DB`).
31pub const IS_IN_DB_SNP: &str = "DB";
32
33/// Combined depth across samples (`DP`).
34pub const TOTAL_DEPTH: &str = "DP";
35
36/// HapMap2 membership (`H2`).
37pub const IS_IN_HAP_MAP_2: &str = "H2";
38
39/// HapMap3 membership (`H3`).
40pub const IS_IN_HAP_MAP_3: &str = "H3";
41
42/// RMS mapping quality (`MQ`).
43pub const MAPPING_QUALITY: &str = "MQ";
44
45/// Number of MAPQ == 0 reads (`MQ0`).
46pub const ZERO_MAPPING_QUALITY_COUNT: &str = "MQ0";
47
48/// Number of samples with data (`NS`).
49pub const SAMPLES_WITH_DATA_COUNT: &str = "NS";
50
51/// Strand bias (`SB`).
52pub const STRAND_BIAS: &str = "SB";
53
54/// Somatic mutation (`SOMATIC`).
55pub const IS_SOMATIC_MUTATION: &str = "SOMATIC";
56
57/// Validated by follow-up experiment (`VALIDATED`).
58pub const IS_VALIDATED: &str = "VALIDATED";
59
60/// 1000 Genomes membership (`1000G`).
61pub const IS_IN_1000_GENOMES: &str = "1000G";
62
63/// Imprecise structural variation (`IMPRECISE`).
64pub const IS_IMPRECISE: &str = "IMPRECISE";
65
66/// Indicates a novel structural variation (`NOVEL`).
67pub const IS_NOVEL: &str = "NOVEL";
68
69/// End position of the variant described in this record (`END`).
70///
71/// Deprecated in VCF 4.5.
72pub const END_POSITION: &str = "END";
73
74/// Type of structural variant (`SVTYPE`).
75///
76/// Deprecated in VCF 4.4.
77pub const SV_TYPE: &str = "SVTYPE";
78
79/// Difference in length between REF and ALT alleles (`SVLEN`).
80pub const SV_LENGTHS: &str = "SVLEN";
81
82/// Confidence interval around POS for imprecise variants (`CIPOS`).
83pub const POSITION_CONFIDENCE_INTERVALS: &str = "CIPOS";
84
85/// Confidence interval around END for imprecise variants (`CIEND`).
86pub const END_CONFIDENCE_INTERVALS: &str = "CIEND";
87
88/// Length of base pair identical micro-homology at event breakpoints (`HOMLEN`).
89pub const MICROHOMOLOGY_LENGTHS: &str = "HOMLEN";
90
91/// Sequence of base pair identical micro-homology at event breakpoints (`HOMSEQ`).
92pub const MICROHOMOLOGY_SEQUENCES: &str = "HOMSEQ";
93
94/// ID of the assembled alternate allele in the assembly file (`BKPTID`).
95pub const BREAKPOINT_IDS: &str = "BKPTID";
96
97/// Mobile element info of the form NAME,START,END,POLARITY (`MEINFO`).
98pub const MOBILE_ELEMENT_INFO: &str = "MEINFO";
99
100/// Mobile element transduction info of the form CHR,START,END,POLARITY (`METRANS`).
101pub const MOBILE_ELEMENT_TRANSDUCTION_INFO: &str = "METRANS";
102
103/// ID of this element in Database of Genomic Variation (`DBVID`).
104pub const DBV_ID: &str = "DBVID";
105
106/// ID of this element in DBVAR (`DBVARID`).
107pub const DB_VAR_ID: &str = "DBVARID";
108
109/// ID of this element in DBRIP (`DBRIPID`).
110pub const DB_RIP_ID: &str = "DBRIPID";
111
112/// ID of mate breakends (`MATEID`).
113pub const MATE_BREAKEND_IDS: &str = "MATEID";
114
115/// ID of partner breakend (`PARID`).
116pub const PARTNER_BREAKEND_ID: &str = "PARID";
117
118/// ID of event associated to breakend (`EVENT`).
119pub const BREAKEND_EVENT_ID: &str = "EVENT";
120
121/// Type of associated event (`EVENTTYPE`).
122///
123/// Added in VCF 4.4.
124pub const EVENT_TYPE: &str = "EVENTTYPE";
125
126/// Confidence interval around the inserted material between breakends (`CILEN`).
127pub const BREAKEND_CONFIDENCE_INTERVALS: &str = "CILEN";
128
129/// Read Depth of adjacency (`DPADJ`).
130///
131/// Removed in VCF 4.4.
132pub const ADJACENT_READ_DEPTHS: &str = "DPADJ";
133
134/// Copy number of segment containing breakend (`CN`).
135pub const BREAKEND_COPY_NUMBER: &str = "CN";
136
137/// Copy number of adjacency (`CNADJ`).
138///
139/// Removed in VCF 4.4.
140pub const ADJACENT_COPY_NUMBER: &str = "CNADJ";
141
142/// Confidence interval around copy number for the segment (`CICN`).
143pub const COPY_NUMBER_CONFIDENCE_INTERVALS: &str = "CICN";
144
145/// Confidence interval around copy number for the adjacency (`CICNADJ`).
146///
147/// Removed in VCF 4.4.
148pub const ADJACENT_COPY_NUMBER_CONFIDENCE_INTERVALS: &str = "CICNADJ";
149
150/// Claim made by the structural variant call (`SVCLAIM`).
151///
152/// Valid values are D, J, DJ for abundance, adjacency and both respectively.
153///
154/// Added in VCF 4.4.
155pub const SV_CLAIM: &str = "SVCLAIM";
156
157/// Total number of repeat sequences in this allele (`RN`).
158///
159/// Added in VCF 4.4.
160pub const TOTAL_REPEAT_SEQUENCE_COUNTS: &str = "RN";
161
162/// Repeat unit sequence of the corresponding repeat sequence (`RUS`).
163///
164/// Added in VCF 4.4.
165pub const REPEAT_UNIT_SEQUENCES: &str = "RUS";
166
167/// Repeat unit length of the corresponding repeat sequence (`RUL`).
168///
169/// Added in VCF 4.4.
170pub const REPEAT_UNIT_LENGTHS: &str = "RUL";
171
172/// Repeat unit count of corresponding repeat sequence (`RUC`).
173///
174/// Added in VCF 4.4.
175pub const REPEAT_UNIT_COUNTS: &str = "RUC";
176
177/// Total number of bases in the corresponding repeat sequence (`RB`).
178///
179/// Added in VCF 4.4.
180pub const TOTAL_REPEAT_SEQUENCE_BASE_COUNTS: &str = "RB";
181
182/// Confidence interval around RUC (`CIRUC`).
183///
184/// Added in VCF 4.4.
185pub const REPEAT_UNIT_COUNT_CONFIDENCE_INTERVALS: &str = "CIRUC";
186
187/// Confidence interval around RB (`CIRB`).
188///
189/// Added in VCF 4.4.
190pub const TOTAL_REPEAT_SEQUENCE_BASE_COUNT_CONFIDENCE_INTERVALS: &str = "CIRB";
191
192/// Number of bases in each individual repeat unit (`RUB`).
193///
194/// Added in VCF 4.4.
195pub const REPEAT_UNIT_BASE_COUNTS: &str = "RUB";
196
197#[cfg(test)]
198mod tests {
199    use super::*;
200
201    #[test]
202    fn test_values() {
203        assert_eq!(ANCESTRAL_ALLELE, "AA");
204        assert_eq!(ALLELE_COUNT, "AC");
205        assert_eq!(TOTAL_READ_DEPTHS, "AD");
206        assert_eq!(FORWARD_STRAND_READ_DEPTHS, "ADF");
207        assert_eq!(REVERSE_STRAND_READ_DEPTHS, "ADR");
208        assert_eq!(ALLELE_FREQUENCIES, "AF");
209        assert_eq!(TOTAL_ALLELE_COUNT, "AN");
210        assert_eq!(BASE_QUALITY, "BQ");
211        assert_eq!(CIGAR, "CIGAR");
212        assert_eq!(IS_IN_DB_SNP, "DB");
213        assert_eq!(TOTAL_DEPTH, "DP");
214        assert_eq!(IS_IN_HAP_MAP_2, "H2");
215        assert_eq!(IS_IN_HAP_MAP_3, "H3");
216        assert_eq!(MAPPING_QUALITY, "MQ");
217        assert_eq!(ZERO_MAPPING_QUALITY_COUNT, "MQ0");
218        assert_eq!(SAMPLES_WITH_DATA_COUNT, "NS");
219        assert_eq!(STRAND_BIAS, "SB");
220        assert_eq!(IS_SOMATIC_MUTATION, "SOMATIC");
221        assert_eq!(IS_VALIDATED, "VALIDATED");
222        assert_eq!(IS_IN_1000_GENOMES, "1000G");
223
224        assert_eq!(IS_IMPRECISE, "IMPRECISE");
225        assert_eq!(IS_NOVEL, "NOVEL");
226        assert_eq!(END_POSITION, "END");
227        assert_eq!(SV_TYPE, "SVTYPE");
228        assert_eq!(SV_LENGTHS, "SVLEN");
229        assert_eq!(POSITION_CONFIDENCE_INTERVALS, "CIPOS");
230        assert_eq!(END_CONFIDENCE_INTERVALS, "CIEND");
231        assert_eq!(MICROHOMOLOGY_LENGTHS, "HOMLEN");
232        assert_eq!(MICROHOMOLOGY_SEQUENCES, "HOMSEQ");
233        assert_eq!(BREAKPOINT_IDS, "BKPTID");
234        assert_eq!(MOBILE_ELEMENT_INFO, "MEINFO");
235        assert_eq!(MOBILE_ELEMENT_TRANSDUCTION_INFO, "METRANS");
236        assert_eq!(DBV_ID, "DBVID");
237        assert_eq!(DB_VAR_ID, "DBVARID");
238        assert_eq!(DB_RIP_ID, "DBRIPID");
239        assert_eq!(MATE_BREAKEND_IDS, "MATEID");
240        assert_eq!(PARTNER_BREAKEND_ID, "PARID");
241        assert_eq!(BREAKEND_EVENT_ID, "EVENT");
242        assert_eq!(BREAKEND_CONFIDENCE_INTERVALS, "CILEN");
243        assert_eq!(ADJACENT_READ_DEPTHS, "DPADJ");
244        assert_eq!(BREAKEND_COPY_NUMBER, "CN");
245        assert_eq!(ADJACENT_COPY_NUMBER, "CNADJ");
246        assert_eq!(COPY_NUMBER_CONFIDENCE_INTERVALS, "CICN");
247        assert_eq!(ADJACENT_COPY_NUMBER_CONFIDENCE_INTERVALS, "CICNADJ");
248        assert_eq!(SV_CLAIM, "SVCLAIM");
249        assert_eq!(TOTAL_REPEAT_SEQUENCE_COUNTS, "RN");
250        assert_eq!(REPEAT_UNIT_SEQUENCES, "RUS");
251        assert_eq!(REPEAT_UNIT_LENGTHS, "RUL");
252        assert_eq!(REPEAT_UNIT_COUNTS, "RUC");
253        assert_eq!(TOTAL_REPEAT_SEQUENCE_BASE_COUNTS, "RB");
254        assert_eq!(REPEAT_UNIT_COUNT_CONFIDENCE_INTERVALS, "CIRUC");
255        assert_eq!(
256            TOTAL_REPEAT_SEQUENCE_BASE_COUNT_CONFIDENCE_INTERVALS,
257            "CIRB"
258        );
259        assert_eq!(REPEAT_UNIT_BASE_COUNTS, "RUB");
260    }
261}
noodles_vcf/variant/record/info/field/key.rs

noodles_vcf/variant/record/info/field/
key.rs
