Synthetic Route 2 epi-tag test (CC0-1.0; invented data)
1. Load reference.gff3 in Create gene-maps from annotations; select geneA.
2. Keep the default 500-bp flank, exons selected, and full span/CDS off. A boundary-clipping notice is expected for this small invented reference.
3. Choose Gene structure + data and Epi-tags as Signal display.
4. Select all 17 gene-epi-sample-*.bedgraph files, then analyze/populate and Create chromoMap.
5. Expect 17 sample chromosome sets followed by the gene structure (18 sets). Sample bodies are hidden; the gene body remains visible. Each sample has three tagged 2-bp windows: one lollipop, one lollipop plus triangle, and one lollipop. The empty checkpoint window has no tag.
6. Read gene-epi-tags-expected.json for exact coordinates per sample. Values vary but tag shape encodes annotation count, not methylation magnitude.
7. Change a sample Tag color under per-set Epi-tags, or change its plot to Line in Visualise. Route 2 sets plotting defaults as well as creating tables; all remain editable.
