noodles_vcf/
record.rs

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
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
//! VCF record.

mod alternate_bases;
pub(crate) mod fields;
mod filters;
mod ids;
mod info;
pub mod samples;

use std::{fmt, io};

use noodles_core::Position;

use self::fields::Fields;
pub use self::{
    alternate_bases::AlternateBases, filters::Filters, ids::Ids, info::Info, samples::Samples,
};
use super::Header;

/// A VCF record.
#[derive(Clone, Default, Eq, PartialEq)]
pub struct Record(Fields);

impl Record {
    #[cfg(test)]
    pub(crate) fn fields(&self) -> &Fields {
        &self.0
    }

    pub(crate) fn fields_mut(&mut self) -> &mut Fields {
        &mut self.0
    }

    /// Returns the reference sequence name.
    pub fn reference_sequence_name(&self) -> &str {
        self.0.reference_sequence_name()
    }

    /// Returns the variant start position.
    pub fn variant_start(&self) -> Option<io::Result<Position>> {
        self.0.variant_start()
    }

    /// Returns the IDs.
    pub fn ids(&self) -> Ids<'_> {
        self.0.ids()
    }

    /// Returns the reference bases.
    pub fn reference_bases(&self) -> &str {
        self.0.reference_bases()
    }

    /// Returns the alternate bases.
    pub fn alternate_bases(&self) -> AlternateBases<'_> {
        self.0.alternate_bases()
    }

    /// Returns the quality score.
    pub fn quality_score(&self) -> Option<io::Result<f32>> {
        self.0.quality_score()
    }

    /// Returns the filters.
    pub fn filters(&self) -> Filters<'_> {
        self.0.filters()
    }

    /// Returns the info.
    pub fn info(&self) -> Info<'_> {
        self.0.info()
    }

    /// Returns the samples.
    pub fn samples(&self) -> Samples<'_> {
        self.0.samples()
    }
}

impl fmt::Debug for Record {
    fn fmt(&self, f: &mut fmt::Formatter<'_>) -> fmt::Result {
        f.debug_struct("Record")
            .field("reference_sequence_name", &self.reference_sequence_name())
            .field("variant_start", &self.variant_start())
            .field("ids", &self.ids())
            .field("reference_bases", &self.reference_bases())
            .field("alternate_bases", &self.alternate_bases())
            .field("quality_score", &self.quality_score())
            .field("filters", &self.filters())
            .field("info", &self.info())
            .field("samples", &self.samples())
            .finish()
    }
}

impl TryFrom<&[u8]> for Record {
    type Error = io::Error;

    fn try_from(buf: &[u8]) -> Result<Self, Self::Error> {
        use crate::io::Reader;

        let mut reader = Reader::new(buf);
        let mut record = Self::default();
        reader.read_record(&mut record)?;
        Ok(record)
    }
}

impl crate::variant::Record for Record {
    fn reference_sequence_name<'a, 'h: 'a>(&'a self, _: &'h Header) -> io::Result<&'a str> {
        Ok(self.reference_sequence_name())
    }

    fn variant_start(&self) -> Option<io::Result<Position>> {
        self.variant_start()
    }

    fn ids(&self) -> Box<dyn crate::variant::record::Ids + '_> {
        Box::new(self.ids())
    }

    fn reference_bases(&self) -> Box<dyn crate::variant::record::ReferenceBases + '_> {
        Box::new(self.reference_bases())
    }

    fn alternate_bases(&self) -> Box<dyn crate::variant::record::AlternateBases + '_> {
        Box::new(self.alternate_bases())
    }

    fn quality_score(&self) -> Option<io::Result<f32>> {
        self.quality_score()
    }

    fn filters(&self) -> Box<dyn crate::variant::record::Filters + '_> {
        Box::new(self.filters())
    }

    fn info(&self) -> Box<dyn crate::variant::record::Info + '_> {
        Box::new(self.info())
    }

    fn samples(&self) -> io::Result<Box<dyn crate::variant::record::Samples + '_>> {
        Ok(Box::new(self.samples()))
    }
}