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
// 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::error::Error;
use crate::coverage::CoverageConfig;
use crate::genome::Genome;
use crate::track_generic::GenericMutableTrack;
use crate::track_simple::SimpleTrack;
/* -------------------------------------------------------------------------- */
impl SimpleTrack {
pub fn coverage_from_bam(
config : CoverageConfig,
filenames_treatment: &Vec<&str>,
filenames_control : &Vec<&str>,
fraglen_treatment : &Vec<usize>,
fraglen_control : &Vec<usize>,
genome : Genome,
) -> Result<SimpleTrack, Box<dyn Error>> {
let mut track1 = SimpleTrack::alloc("treatment".to_string(), genome.clone(), config.initial_value, config.bin_size);
if !filenames_control.is_empty() {
// Control data
let mut track2 = SimpleTrack::alloc("control".to_string(), genome.clone(), config.initial_value, config.bin_size);
GenericMutableTrack::coverage_from_bam(
config,
GenericMutableTrack::wrap(&mut track1),
Some(GenericMutableTrack::wrap(&mut track2)),
filenames_treatment,
filenames_control,
fraglen_treatment,
fraglen_control)?;
} else {
GenericMutableTrack::coverage_from_bam(
config,
GenericMutableTrack::wrap(&mut track1),
None,
filenames_treatment,
filenames_control,
fraglen_treatment,
fraglen_control)?;
};
Ok(track1)
}
}