libprosic 0.4.0

A library for calling of genomic variants using a latent variable model.
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
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103

#![cfg_attr(feature="flame_it", feature(plugin))]
#![cfg_attr(feature="flame_it", plugin(flamer))]
// activate flame for the whole crate

extern crate bio;
extern crate rust_htslib;
#[macro_use]
extern crate log;
extern crate rgsl;
extern crate itertools;
extern crate itertools_num;
#[macro_use]
extern crate approx;
extern crate rusty_machine;
extern crate ordered_float;
extern crate ndarray;
extern crate rustc_serialize;
#[macro_use]
extern crate quick_error;
extern crate csv;
#[macro_use]
extern crate lazy_static;
extern crate statrs;

#[cfg(feature="flame_it")]
extern crate flame;

pub mod model;
pub mod estimation;
pub mod call;
pub mod utils;
pub mod pairhmm;
pub mod constants;

pub use model::sample::Sample;
pub use model::likelihood;
pub use model::priors;
pub use model::sample::InsertSize;

use std::ascii::AsciiExt;


quick_error! {
    #[derive(Debug)]
    pub enum BCFError {
        MissingTag(name: String) {
            description("unexpected missing tag")
            display("expected tag {} missing from BCF record", name)
        }
        InvalidRecord(msg: String) {
            description("invalid record")
            display("{}", msg)
        }
    }
}


/// Event to call.
pub trait Event {
    fn name(&self) -> &str;

    fn tag_name(&self, prefix: &str) -> String {
        format!("{}_{}", prefix, self.name().to_ascii_uppercase())
    }

    fn header_entry(&self, prefix: &str, desc: &str) -> String {
        format!(
            "##INFO=<ID={tag_name},Number=A,Type=Float,\
            Description=\"{desc} {name} variant\">",
            name=self.name(),
            desc=desc,
            tag_name=&self.tag_name(prefix)
        )
    }
}


/// Complement of other given events (i.e. 1 - Pr(other events)).
pub struct ComplementEvent {
    /// event name
    pub name: String
}


impl Event for ComplementEvent {
    fn name(&self) -> &str {
        &self.name
    }
}


/// A simple event that just has a name.
pub struct SimpleEvent {
    /// event name
    pub name: String
}


impl Event for SimpleEvent {
    fn name(&self) -> &str {
        &self.name
    }
}