IGV Panel

[shihabdider]

Some remaining features for the IGV Panel.

• Add a debounce to the zoom/translation on view port (for all tracks)
• Make SNV events zoom into the mutation (i.e remove the padding that encapsulates the whole gene instead replace with a padding of 250bp with the mutation centered)
  See:
  

  case-report/src/helpers/utility.js

  Lines 1032 to 1050 in 039554c

  	if (["SNV", "DEL"].includes(event.vartype)) {
  	// center the SNV in the plot while encapsulating its gene in the
  	// window
  	try {
  	const snvMatch = regex.exec(event.Variant_g);
  	const snvStartPoint = parseInt(snvMatch[2]);
  	const snvEndPoint = parseInt(snvMatch[3]);
  	const geneStartPoint = parseInt(startPoint);
  	const geneEndPoint = parseInt(endPoint);
  	let padding =
  	snvStartPoint - geneStartPoint > geneEndPoint - snvEndPoint
  	? snvStartPoint - geneStartPoint
  	: geneEndPoint - snvEndPoint;
  	padding += 1000;
  	startPoint = parseInt(snvStartPoint - padding);
  	endPoint = parseInt(snvEndPoint + padding);
  	location = event.Variant_g;
  	actualLocation = `${chromosome}:${startPoint}-${chromosome}:${endPoint}`;

  
  Just set padding to 250 instead of computing it based on gene position.
• set sort by base as the default view
  add "sort": { option: "BASE" }, to

  case-report/src/components/igvPlot/index.js

  Lines 27 to 38 in 11caac0

  	const igvOptions = {
  	genome: "hg19",
  	locus: domainToLoci(chromoBins, domain),
  	tracks: [
  	{
  	name,
  	url,
  	indexURL,
  	format,
  	},
  	],
  	};

• (low-priority) Make the center line toggle in the IGV Panel also display a center line in the other tracks
• (low-priority) make double-clicking on a mutations point center all tracks (including IGV panel) on that mutation's location (without changing the zoom level). Essentially this would be similar to a call to the handler that translates the view port on user mouse drag. When the user double-clicks on a mutation point, it should be as if the user had dragged their mouse to make the mutation point the center of the view port.

[xanthopoulakis]

@shihabdider , I managed to resolve the bullet items 1, 2, and 5, for the othes (3, 4) I will probably need to pick your brains