gtars_core/models/
fragments.rs

1use std::str::FromStr;
2
3use anyhow::Result;
4
5use crate::models::Region;
6
7#[allow(unused)]
8pub struct Fragment {
9    pub chr: String,
10    pub start: u32,
11    pub end: u32,
12    pub barcode: String,
13    pub read_support: u32,
14}
15
16impl FromStr for Fragment {
17    type Err = anyhow::Error;
18
19    fn from_str(s: &str) -> Result<Self> {
20        let parts: Vec<&str> = s.split_whitespace().collect();
21        // dont check file integrity right now
22        // if parts.len() != 6 {
23        //     anyhow::bail!(
24        //         "Error parsing fragment file line: {}. Is your fragment file malformed? Found {} parts.",
25        //         s,
26        //         parts.len()
27        //     )
28        // }
29
30        let start = parts[1].parse::<u32>()?;
31        let end = parts[2].parse::<u32>()?;
32        let read_support = parts[4].parse::<u32>()?;
33
34        Ok(Fragment {
35            chr: parts[0].to_string(),
36            start,
37            end,
38            barcode: parts[3].to_string(),
39            read_support,
40        })
41    }
42}
43
44impl From<Fragment> for Region {
45    fn from(val: Fragment) -> Self {
46        Region {
47            chr: val.chr,
48            start: val.start,
49            end: val.end,
50            rest: None,
51        }
52    }
53}
gtars_core/models/fragments.rs

gtars_core/models/
fragments.rs
