How to get tags

[Liripo]

How to get CB and UB tags:
my code:

use noodles::bam::record::data;
use noodles::bam::{self, record};
use anyhow::Result;
use std::fs::File;
use std::io::Write;

pub fn read_bam_tags(bam_file: &str,csv_out: &str) -> Result<()> {
    let mut reader = bam::io::indexed_reader::Builder::default().build_from_path(bam_file)?;

    // Skip the BAM header
    reader.read_header()?;

    let mut csv_writer = File::create(csv_out)?;
    writeln!(csv_writer, "CB,UB")?;


    for result in reader.records() {
        let record = result?;
        if record.flags().is_unmapped() || record.flags().is_secondary() {
            continue;
        }
        let cb = [b'C',b'B'];
        let cb_value = record.data().get(&cb);
        let ub = [b'U',b'B'];
        let ub_value = record.data().get(&ub);
        writeln!("{},{}",cb_value,ub_value);
    }

    Ok(())
}

fn main() -> Result<()> {
    read_bam_tags("Aligned.sortedByCoord.out.bam","test.csv")
}

[zaeleus]

Data::get returns an Option<io::Result<Value<'_>>>. You will need to handle 1) whether the tag exists, 2) any decode error, and 3) whether the tag type is expected. Using the cell barcode ID (CB) tag for example:

let cb = data
    .get(&Tag::CELL_BARCODE_ID)
    .transpose()?
    .and_then(|value| match value {
        Value::String(s) => Some(s),
        _ => None,
    })
    .unwrap_or_default();

If the tag is missing or the wrong type, this returns an empty string. This example can also be used for your UB tag.