INNER CODE UNIT · Rust

recover_mates

mbhall88/rasusa · src/alignment/mod.rs:68

    fn recover_mates(
        &self,
        survivor_names: &mut NameSet,
        header: &Header,
        writer: &mut AlignmentWriter,
    ) -> Result<()> {
        info!("Recovering mates (last segment records)");
        let mut reader = build_alignment_reader(&self.aln, self.threads)?;

        let _ = reader.read_header()?; // skip header

        for result in reader.records(header) {
            let record = result.context("Failed to parse BAM record")?;

            // only care about the last segment (read 2)
            if !record.flags()?.is_last_segment() {
                continue;
            }

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