Dot sometimes inverts the y-axis: why and when?

[MrTomRod]

Hi Maria

I have a problem with Dot: sometimes, it inverts the y-axis.

Normally, Dot and nucmer/mummerplot agree:

[left: FAM19036_FAM19038; right: FAM19038_FAM19036]

But sometimes, they do not:

[left: FAM19036_FAM14217; right: FAM14217_FAM19036]

The problem is that if the y-axis is inverted, the annotation track does not match the plot any more.

There are two potential solutions for me:

1. Make Dot always agree with mummer/nucmer (preferred)
2. Tell me how to predict when Dot inverts the y-axis, so that I can invert the annotation track

Here is the relevant data so you can reproduce the issue: https://cloud.roder.casa/s/t7ByZCajS6pdw2B

I would be very glad if you could fix the issue or give me a few hints, it would safe me a lot of time.

Best, Thomas

[MrTomRod]

I figured it out. The trick is to look which contigs are inverted in the coords.idx file, and to invert the annotations on that contig so that the annotations match the plot. I created a fork of this repo that contains my solutions: https://github.com/MrTomRod/dot