Tips of reads can overlap in X by fractions of a base

[adamnovak]

In this view, reads crossing an expanded gap between nodes can get bumped down a lane because they overlap other reads in X by a few pixels, not an entire base. See this image:

Read lines should always start and end exactly on base boundaries. There shouldn't be apparently random slop of a few pixels here or there.

[adamnovak]

I looked at these more and the reads are indeed overlapping by exactly 1 SVG pixel unit. The X + width of the final rectangle in that blue read on the right is 1 more than the X of the first rectangle of that red read it bumps into.

We probably need to look at the functions that compute read start and end X coordinates:

sequenceTubeMap/src/util/tubemap.js

Lines 2656 to 2680 in 56d3c4b

	function getReadXStart(read) {
	const node = nodes[read.path[0].node];
	if (read.path[0].isForward) {
	// read starts in forward direction
	return getXCoordinateOfBaseWithinNode(node, read.firstNodeOffset);
	}
	// read starts in backward direction
	return getXCoordinateOfBaseWithinNode(
	node,
	node.sequenceLength - read.firstNodeOffset
	);
	}
	function getReadXEnd(read) {
	const node = nodes[read.path[read.path.length - 1].node];
	if (read.path[read.path.length - 1].isForward) {
	// read ends in forward direction
	return getXCoordinateOfBaseWithinNode(node, read.finalNodeCoverLength);
	}
	// read ends in backward direction
	return getXCoordinateOfBaseWithinNode(
	node,
	node.sequenceLength - read.finalNodeCoverLength
	);
	}

But I have no idea where we're getting the 1 pixel of overlap.

[adamnovak]

To follow the view link, you should be able to start your local tube map and then click it. The node I am looking at is near the middle of the rendered visualization.

[adamnovak]

Actually, the problem might be here:

sequenceTubeMap/src/util/tubemap.js

Lines 3787 to 3788 in 56d3c4b

	.attr("width", (d) => d.xEnd - d.xStart + 1)
	.attr("height", (d) => d.yEnd - d.yStart + 1)

We generate the rectangle list entries with exactly coinciding start and end coordinates, and then we add a +1 when we go to draw the SVG elements for them for some reason.