8bb827838c60d008d1cd5124b050021a3b7734dc,cnvlib/diagram.py,,create_diagram,#,29

Before Change

    // Label genes where copy ratio value exceeds threshold
    cnarr = cnarr.shift_xx(male_reference)
    if cnarr_is_seg:
        gainloss = []
    elif segarr:
        segarr = segarr.shift_xx(male_reference)
        gainloss = reports.gainloss_by_segment(cnarr, segarr, threshold)
    else:

After Change

    // NB: If multiple segments cover the same gene (gene contains breakpoints),
    // all those segments are marked as "hits".  We"ll uniquify them.
    // TODO - use different logic to only label the gene"s signficant segment(s)
    seen_genes = set()

    // Consolidate genes & coverage values as chromosome features
    features = collections.defaultdict(list)
    strand = 1 if do_both else None  // Draw on the chr. right half or full width
    chrom_sizes = plots.chromosome_sizes(cnarr)
    if not cnarr_is_seg:
        cnarr = cnarr.squash_genes()
    for row in cnarr:
        if row.start - 1 >= 0 and row.end <= chrom_sizes[row.chromosome]:  // Sanity check
            if row.gene in gene_labels and row.gene not in seen_genes:
                seen_genes.add(row.gene)
                feat_name = row.gene
                if "," in feat_name:
                    // TODO - line-wrap multi-gene labels (reportlab won"t do \n)
                    feat_name = feat_name.replace(",", ", ")
            else:
                feat_name = None
            features[row.chromosome].append(
                (row.start - 1, row.end, strand, feat_name,
                 colors.Color(*plots.cvg2rgb(row.log2, not cnarr_is_seg))))
    if do_both:

Instances