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

Before Change

        cnarr = cnarr.squash_genes()
    for row in cnarr:
        if row.start - 1 >= 0 and row.end <= chrom_sizes[row.chromosome]:  // Sanity check
            feat_name = row.gene if row.gene in gene_labels else 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:

After Change

    cnarr = cnarr.shift_xx(male_reference)
    if cnarr_is_seg:
        sel = cnarr.data[(cnarr.data.log2.abs() >= threshold) &
                          ~cnarr.data.gene.isin(params.IGNORE_GENE_NAMES)]
        gainloss = [(s.gene, s.chromosome, s.start, s.end, s.log2, s.probes)
                    for s in sel.itertuples(index=False)]
    elif segarr:
        segarr = segarr.shift_xx(male_reference)
        gainloss = reports.gainloss_by_segment(cnarr, segarr, threshold)

Instances