Feature request: junction reads

[olgabot]

Thanks for making biodalliance, I'm really enjoying it. It would be very helpful for people in the splicing community to add the option to see the junction reads when loading bam files, like IGV does here:

[dasmoth]

Yes, that would be a great addition

[fgypas]

Do you have plans to implement this feature in the near future?

[dasmoth]

I've not had a chance to work on it myself, but I believe @drpowell has given this a try -- there's a little more about it on the Google Group/mailing list.

[drpowell]

I added parsing of the split read in the CIGAR string, and display of the reads in the alignment. But I've not worked at all on the sashami style plot. To add proper support for the split reads also need to fix the density estimate when zoomed out. The current approximation effectively ignores the CIGAR string which is generally fine - but not when split reads are involved