noodles-util 0.71.0

noodles support utilities
Documentation 
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88

use std::io;

use noodles_bcf as bcf;
use noodles_core::Position;
use noodles_vcf as vcf;

/// A variant record.
#[derive(Clone, Debug)]
pub enum Record {
    /// A VCF record.
    Vcf(vcf::Record),
    /// A BCF record.
    Bcf(bcf::Record),
}

impl vcf::variant::Record for Record {
    fn reference_sequence_name<'a, 'h: 'a>(
        &'a self,
        header: &'h vcf::Header,
    ) -> io::Result<&'a str> {
        match self {
            Self::Vcf(record) => vcf::variant::Record::reference_sequence_name(record, header),
            Self::Bcf(record) => vcf::variant::Record::reference_sequence_name(record, header),
        }
    }

    fn variant_start(&self) -> Option<io::Result<Position>> {
        match self {
            Record::Vcf(record) => vcf::variant::Record::variant_start(record),
            Record::Bcf(record) => vcf::variant::Record::variant_start(record),
        }
    }

    fn ids(&self) -> Box<dyn vcf::variant::record::Ids + '_> {
        match self {
            Record::Vcf(record) => vcf::variant::Record::ids(record),
            Record::Bcf(record) => vcf::variant::Record::ids(record),
        }
    }

    fn reference_bases(&self) -> Box<dyn vcf::variant::record::ReferenceBases + '_> {
        match self {
            Record::Vcf(record) => vcf::variant::Record::reference_bases(record),
            Record::Bcf(record) => vcf::variant::Record::reference_bases(record),
        }
    }

    fn alternate_bases(&self) -> Box<dyn vcf::variant::record::AlternateBases + '_> {
        match self {
            Record::Vcf(record) => vcf::variant::Record::alternate_bases(record),
            Record::Bcf(record) => vcf::variant::Record::alternate_bases(record),
        }
    }

    fn quality_score(&self) -> Option<io::Result<f32>> {
        match self {
            Record::Vcf(record) => vcf::variant::Record::quality_score(record),
            Record::Bcf(record) => vcf::variant::Record::quality_score(record),
        }
    }

    fn filters(&self) -> Box<dyn vcf::variant::record::Filters + '_> {
        match self {
            Record::Vcf(record) => vcf::variant::Record::filters(record),
            Record::Bcf(record) => vcf::variant::Record::filters(record),
        }
    }

    fn info(&self) -> Box<dyn vcf::variant::record::Info + '_> {
        match self {
            Record::Vcf(record) => vcf::variant::Record::info(record),
            Record::Bcf(record) => vcf::variant::Record::info(record),
        }
    }

    fn samples(&self) -> io::Result<Box<dyn vcf::variant::record::Samples + '_>> {
        match self {
            Record::Vcf(record) => vcf::variant::Record::samples(record),
            Record::Bcf(record) => vcf::variant::Record::samples(record),
        }
    }
}

impl Default for Record {
    fn default() -> Self {
        Self::Vcf(vcf::Record::default())
    }
}