"View chimeric alignments in split screen" feature not aligning properly

[ryan-moreno]

In some cases, I believe that the "View chimeric alignments in split screen" feature is zooming to the wrong endpoint on the supplementary read. Here is an example:

In this case, the read maps to both the positive strand of chr6 and the negative strand of chr18. As is shown (correctly) in the "Supplementary Reads Diagram," this means that the read went from "left to right" (in terms of the reference genome) on chr6 and then went from "right to left" on chr18. In this case, I would expect the screen showing chr18 to be centered on the "right" of the read, since this is the position in the read that connects to chr6.

Steps to reproduce:

• Pull up a bam file in IGV
• Find a read that maps to two chromosomes and zoom to the main alignment (in this case, the main alignment was on chr6)
• Right click on the read and select "View chimeric alignments in split screen"

Expected: The screen splits, with each half-screen centered on the position that connects to the other chromosome.

Actual: The screen showing the main alignment correctly centers on the position that connects to the other chromosome, but the screen showing the supplementary alignment centers on the incorrect end of the read.

[jrobinso]

@lbergelson Comments?

[lbergelson]

@ryan-moreno Thanks for pointing this out. It's a good point. I'll update it.