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
// Copyright (C) 2024 Philipp Benner
//
// Permission is hereby granted, free of charge, to any person obtaining a copy
// of this software and associated documentation files (the “Software”), to deal
// in the Software without restriction, including without limitation the rights
// to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
// copies of the Software, and to permit persons to whom the Software is
// furnished to do so, subject to the following conditions:
//
// The above copyright notice and this permission notice shall be included in
// all copies or substantial portions of the Software.
//
// THE SOFTWARE IS PROVIDED “AS IS”, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
// IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
// FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
// AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
// LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
// OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
// SOFTWARE.
use std::fs::File;
use std::io::{self, BufRead, BufReader};
use std::str::FromStr;
use std::{cell::RefCell, rc::Rc};
use flate2::read::GzDecoder;
use crate::track_simple::SimpleTrack;
use crate::utility::is_gzip;
/* -------------------------------------------------------------------------- */
impl SimpleTrack {
pub fn read_bedgraph<R: BufRead>(&mut self, reader: R) -> io::Result<()> {
let mut cur_seq = &mut Rc::new(RefCell::new(vec![]));
let mut cur_name = String::new();
let bin_size = self.bin_size;
for line in reader.lines() {
let line = line?;
let fields: Vec<&str> = line.split_whitespace().collect();
if fields.is_empty() {
break;
}
if fields.len() != 4 {
return Err(io::Error::new(io::ErrorKind::InvalidInput, "BedGraph file must have four columns!"));
}
let from = usize::from_str(fields[1]).map_err(|_| io::Error::new(io::ErrorKind::InvalidInput, "Invalid integer in column 2"))?;
let to = usize::from_str(fields[2]).map_err(|_| io::Error::new(io::ErrorKind::InvalidInput, "Invalid integer in column 3"))?;
let value = f64::from_str(fields[3]).map_err(|_| io::Error::new(io::ErrorKind::InvalidInput, "Invalid float in column 4"))?;
let name = fields[0].to_string();
if name != cur_name {
cur_seq = self.data.entry(name.clone()).or_insert_with(
|| Rc::new(RefCell::new(vec![0.0; (to / bin_size) + 1]))
);
cur_name = name;
}
let mut s = cur_seq.borrow_mut();
if from >= s.len() * bin_size || to >= s.len() * bin_size {
continue;
}
for i in (from / bin_size)..(to / bin_size) {
s[i] = value;
}
}
Ok(())
}
pub fn import_bedgraph(&mut self, filename: &str) -> io::Result<()> {
let file = File::open(&filename)?;
let reader: Box<dyn BufRead> = if is_gzip(&filename) {
let decoder = GzDecoder::new(file);
Box::new(BufReader::new(decoder))
} else {
Box::new(BufReader::new(file))
};
self.read_bedgraph(reader)
}
}