libprosic/
lib.rs

1extern crate bio;
2extern crate rust_htslib;
3#[macro_use]
4extern crate log;
5extern crate itertools;
6extern crate itertools_num;
7extern crate rgsl;
8#[macro_use]
9extern crate approx;
10extern crate ndarray;
11extern crate ordered_float;
12extern crate rusty_machine;
13extern crate serde;
14#[macro_use]
15extern crate serde_derive;
16#[macro_use]
17extern crate quick_error;
18extern crate csv;
19#[macro_use]
20extern crate lazy_static;
21extern crate regex;
22extern crate statrs;
23extern crate vec_map;
24
25#[macro_use]
26extern crate cached;
27
28pub mod call;
29pub mod constants;
30pub mod estimation;
31pub mod model;
32pub mod utils;
33
34pub use estimation::alignment_properties::{AlignmentProperties, InsertSize};
35pub use model::likelihood;
36pub use model::priors;
37pub use model::sample::Sample;
38
39quick_error! {
40    #[derive(Debug)]
41    pub enum BCFError {
42        MissingTag(name: String) {
43            description("unexpected missing tag")
44            display("expected tag {} missing from BCF record", name)
45        }
46        InvalidRecord(msg: String) {
47            description("invalid record")
48            display("{}", msg)
49        }
50    }
51}
52
53/// Event to call.
54pub trait Event {
55    fn name(&self) -> &str;
56
57    fn tag_name(&self, prefix: &str) -> String {
58        format!("{}_{}", prefix, self.name().to_ascii_uppercase())
59    }
60
61    fn header_entry(&self, prefix: &str, desc: &str) -> String {
62        format!(
63            "##INFO=<ID={tag_name},Number=A,Type=Float,\
64             Description=\"{desc} {name} variant\">",
65            name = self.name(),
66            desc = desc,
67            tag_name = &self.tag_name(prefix)
68        )
69    }
70}
71
72/// Complement of other given events (i.e. 1 - Pr(other events)).
73pub struct ComplementEvent {
74    /// event name
75    pub name: String,
76}
77
78impl Event for ComplementEvent {
79    fn name(&self) -> &str {
80        &self.name
81    }
82}
83
84/// A simple event that just has a name.
85pub struct SimpleEvent {
86    /// event name
87    pub name: String,
88}
89
90impl Event for SimpleEvent {
91    fn name(&self) -> &str {
92        &self.name
93    }
94}
libprosic/lib.rs

libprosic/
lib.rs
