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/// This is a regular outer line doc comment, but it also contains a partial
/// Cargo manifest. Note the use of a *fenced* code block, and the
/// `cargo` "language".
///
/// ```cargo
/// [dependencies]
/// csv = "1.1"
/// serde = { version = "1.0", features = ["derive"] }
/// ```
use std::error::Error;
use std::io::{BufWriter, Write};
use std::fs::File;
use serde::Deserialize;
static BED: &[u8] = b"chrom1 1 15 foo 454 -
chrom1 40 45 bar 2 +
chrom2 4 45 baz 2 -
";
#[derive(Debug, Deserialize)]
struct BedRecord {
chrom: String,
start: u64,
end: u64,
name: Option<String>,
score: Option<u16>,
strand: Option<char>,
}
fn main() -> Result<(), Box<dyn Error>> {
let f_out = File::create(&snakemake.output[0])?;
let mut ostream = BufWriter::new(f_out);
println!("Loaded");
let keep_strand = match &snakemake.params.keep {
s if s.len() == 1 => Some(s.chars().next().unwrap() as char),
_ => None,
};
println!("Reading BED file...");
let mut rdr = csv::ReaderBuilder::new().has_headers(false).delimiter(b'\t').from_reader(BED);
for result in rdr.deserialize() {
// Notice that we need to provide a type hint for automatic
// deserialization.
let record: BedRecord = result?;
let l = record.end - record.start;
if record.strand == keep_strand {
write!(&mut ostream, "{}\t{}\n", record.chrom, l)?;
}
}
println!("Output written to {}", &snakemake.output[0]);
Ok(())
}
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