bam_builder/
wrappers.rs

1//! Helper wrappers over awkward [`rust_htslib`] types.
2#![warn(missing_docs)]
3use rust_htslib::bam::record::Aux;
4/// Wrapper type for a ReadGroupID.
5#[derive(Debug)]
6pub struct ReadGroupId(pub String);
7
8impl Default for ReadGroupId {
9    /// Default [`ReadGroupId`] is "A".
10    fn default() -> Self {
11        Self(String::from("A"))
12    }
13}
14
15/// Wrapper type for a Sample Name
16#[derive(Debug)]
17pub struct SampleName(pub String);
18
19impl Default for SampleName {
20    /// Default [`SampleName`] is "Sample1".
21    fn default() -> Self {
22        Self(String::from("Sample1"))
23    }
24}
25
26/// Wrapper for Aux that owns its own data. [`Aux::from`] is implemented in order
27/// to facilitate conversion between the wrapper and the underlying [`Aux`] type.
28#[derive(Clone, Debug)]
29pub enum AuxType {
30    /// Corresponds to [Aux::Integer].
31    Integer(i32),
32    /// Corresponds to [Aux::String], but as an owned String.
33    String(String),
34    /// Corresponds to [Aux::Float].
35    Float(f32),
36    /// Corresponds to [Aux::Char].
37    Char(u8),
38}
39
40impl<'a> From<&'a AuxType> for Aux<'a> {
41    /// Convert a ref [`AuxType`] to ref [`Aux`].
42    fn from(aux_type: &'a AuxType) -> Self {
43        match aux_type {
44            AuxType::Integer(x) => Aux::I32(*x),
45            AuxType::String(x) => Aux::String(x.as_str()),
46            AuxType::Float(x) => Aux::Float(*x),
47            AuxType::Char(x) => Aux::Char(*x),
48        }
49    }
50}
51
52/// Wrapper around strandedness of a read.
53#[derive(Clone, Debug)]
54pub enum Strand {
55    /// Forward strand.
56    Plus,
57    /// Reverse strand.
58    Minus,
59}
bam_builder/wrappers.rs

bam_builder/
wrappers.rs
