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@helrick helrick commented Aug 27, 2025

Introduces a feature to visualise CIGAR string insertions and deletions to alignment tracks as referenced in #31

For example, by adding cigar_insertion_threshold (default None) and insertion_color (default "#4444FF"):

    {
      "type": "alignments",
      "file": "/path/to/sample.bam",
      "label": "",
      "cigar_insertion_threshold": 50,
      "insertion_color": "#4444FF",
      "height": 50,
      "margin_above": 1.5,
      "bounding_box": true,
      "fontscale": 1.2,
      "hgap_bp": 30,
      "vgap_frac": 0.3,
      "link_color": "#999999",
      "link_lw": 0.5,
      "group_by": "none",
      "color_by": "none"
    },
image

and by adding cigar_deletion_threshold (default None) and deletion_color (default "#FF4444"):

    {
      "type": "alignments",
      "file": "/path/to/sample.bam",
      "label": "",
      "cigar_deletion_threshold": 50,
      "deletion_color": "#FF4444",
      "height": 50,
      "margin_above": 1.5,
      "bounding_box": true,
      "fontscale": 1.2,
      "hgap_bp": 30,
      "vgap_frac": 0.3,
      "read_color": "#cccccc",
      "splitread_color": "#FF9F00",
      "link_color": "#999999",
      "link_lw": 0.5,
      "link_splitreads": true,
      "group_by": "none",
      "color_by": "none"
    },
image

@e-sollier
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@helrick thanks for the PR! I'll try to take a look at it in the coming week. Would you be able to share a bam file (at least a subset) and your config file so that I can test myself?

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2 participants