INNER CODE UNIT · Rust

get_target_depth

mbhall88/rasusa · src/alignment/mod.rs:58

    fn get_target_depth(&self, is_paired: bool) -> u32 {
        if is_paired {
            // divide the original target by 2 because we will add the mates back later
            (self.coverage / 2).max(1) // in case we hit 0
        } else {
            self.coverage
        }
    }

    // a helper function to scan the file linearly to find mates, only relevent on paired end illumina data
    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)?;

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