Test for gene model with multiple exons and unusual SO terms

Author: dariober

packages/jbrowse-plugin-apollo/.gitignore

@@ -4,3 +4,6 @@
 cypress/videos
 cypress/screenshots
 cypress/downloads
+cypress-image-diff-html-report
+cypress-image-diff-screenshots/comparison
+cypress-image-diff-screenshots/diff

packages/jbrowse-plugin-apollo/cypress-image-diff-screenshots/baseline/simpleVisual.cy.ts-gene-model.png

@@ -6,18 +6,11 @@ describe('Simple tests for visuals', () => {
     cy.deleteAssemblies()
   })
   it('Shows correct gene model', () => {
-    cy.addAssemblyFromGff(
-      'stopcodon.gff3',
-      'test_data/cdsChecks/stopcodon.gff3',
-    )
-    cy.selectAssemblyToView('stopcodon.gff3')
-    cy.searchFeatures('gene08', 1)
+    cy.addAssemblyFromGff('so_types.gff3', 'test_data/so_types.gff3')
+    cy.selectAssemblyToView('so_types.gff3')
+    cy.searchFeatures('TGGT1_200010', 1)
     cy.wait(5000) // Wait for the gene model to render. It would be better to ensure some element of the canvas is actually there
 
     cy.get('canvas[data-testid="overlayCanvas"]').compareSnapshot('gene-model')
-
-    cy.get('canvas[data-testid="seqTrackOverlayCanvas"]').compareSnapshot(
-      'sixframe',
-    )
   })
 })

packages/jbrowse-plugin-apollo/cypress-image-diff-screenshots/baseline/simpleVisual.cy.ts-sixframe.png

@@ -3,8 +3,9 @@ chr1	VEuPathDB	protein_coding_gene	1	200	.	-	.	ID=TGGT1_200010
 chr1	VEuPathDB	mRNA_with_frameshift	1	200	.	-	.	ID=TGGT1_200010-t26_1;Parent=TGGT1_200010
 chr1	VEuPathDB	interior_exon	1	50	.	-	.	ID=exon_TGGT1_200010-t26_1-E2;Parent=TGGT1_200010-t26_1
 chr1	VEuPathDB	interior_exon	70	100	.	-	.	ID=exon_TGGT1_200010-t26_1-E1;Parent=TGGT1_200010-t26_1
-chr1	VEuPathDB	CDS	1	50	.	-	1	ID=TGGT1_200010-t26_1-p1-CDS2;Parent=TGGT1_200010-t26_1
+chr1	VEuPathDB	CDS	1	50	.	-	1	ID=TGGT1_200010-t26_1-p1-CDS1;Parent=TGGT1_200010-t26_1
 chr1	VEuPathDB	CDS	70	100	.	-	0	ID=TGGT1_200010-t26_1-p1-CDS1;Parent=TGGT1_200010-t26_1
+chr1	VEuPathDB	five_prime_UTR	160	200	.	-	0	ID=UTR;Parent=TGGT1_200010-t26_1
 ##FASTA
 >chr1
 cattgttgcggagttgaacaacggcattacgaacacttccgtctctcacttttatacgat