rsomics_vcf_grep/
lib.rs

1use std::fs::File;
2use std::io::{BufRead, BufReader, BufWriter, Write};
3use std::path::Path;
4
5use regex::Regex;
6use rsomics_common::{Result, RsomicsError};
7
8pub fn grep(input: &Path, pattern: &str, invert: bool, output: &mut dyn Write) -> Result<u64> {
9    let re =
10        Regex::new(pattern).map_err(|e| RsomicsError::InvalidInput(format!("bad regex: {e}")))?;
11    let file = File::open(input)
12        .map_err(|e| RsomicsError::InvalidInput(format!("{}: {e}", input.display())))?;
13    let reader = BufReader::new(file);
14    let mut out = BufWriter::with_capacity(64 * 1024, output);
15    let mut count: u64 = 0;
16
17    for line in reader.lines() {
18        let line = line.map_err(RsomicsError::Io)?;
19        if line.starts_with('#') {
20            writeln!(out, "{line}").map_err(RsomicsError::Io)?;
21            continue;
22        }
23        let matches = re.is_match(&line);
24        if matches != invert {
25            writeln!(out, "{line}").map_err(RsomicsError::Io)?;
26            count += 1;
27        }
28    }
29
30    out.flush().map_err(RsomicsError::Io)?;
31    Ok(count)
32}
rsomics_vcf_grep/lib.rs

rsomics_vcf_grep/
lib.rs
