Method from_record

src/plot.rs:613–665

Creates a Read from a given rust_htslib bam record

(
        record: rust_htslib::bam::record::Record,
        ref_path: P,
        target: &str,
        aux_tags: &Option<Vec<String>>,
    )

impl Read {
    /// Creates a Read from a given rust_htslib bam record
    fn from_record<P: AsRef<Path> + std::fmt::Debug>(
        record: rust_htslib::bam::record::Record,
        ref_path: P,
        target: &str,
        aux_tags: &Option<Vec<String>>,
    ) -> Result<Option<Read>> {
        let read_seq = record
            .seq()
            .as_bytes()
            .iter()
            .map(|u| char::from(*u))
            .collect_vec();
        if read_seq.is_empty() && record.cigar().iter().next().is_some() {
            warn!(
                "Skipping read '{}': empty sequence but non-empty CIGAR string ('{}').",
                String::from_utf8_lossy(record.qname()),
                record.cigar(),
            );
            return Ok(None);
        }
        let ref_length = get_fasta_length(&ref_path.as_ref().to_path_buf(), target)?;
        let read_start = record.pos() - record.cigar().leading_softclips();
        let read_end = record.reference_end() + record.cigar().trailing_softclips();

        let record = if read_start < 0 || read_end > ref_length as i64 {
            clip_read(record, ref_length)?
        } else {
            record
        };
        let region = cli::Region {
            target: target.to_string(),
            start: record.pos() - record.cigar().leading_softclips(),
            end: record.reference_end() + record.cigar().trailing_softclips(),
        };
        let ref_seq = read_fasta(ref_path, &region)?;
        let mpos = if record.is_paired() {
            record.mpos()
        } else {
            -1
        };
        Ok(Some(Read {
            name: String::from_utf8(record.qname().to_vec())?,
            cigar: PlotCigar::from_cigar(record.cigar(), read_seq, ref_seq)?,
            position: record.pos() - record.cigar().leading_softclips(),
            flags: record.flags(),
            mapq: record.mapq(),
            row: None,
            end_position: record.reference_end(),
            mpos,
            aux: AuxRecord::new(&record, aux_tags),
            raw_cigar: record.cigar().to_string(),
        }))
    }

    /// Sets the row of the Read
    fn set_row(&mut self, row: u32) {