about viral_read_report and summary_integration file

[PavitaKae]

Is it possible to link the results in the files viral_read_report, summary_integration, and the generated images? Specifically, can we identify which reads in the viral_read_report file correspond to the integration positions of interest in the summary_integration file, and also determine which images represent these positions?

[zstephens]

This should be straightforward to do, I'll try to implement this soon. Much of this code is overdue for updates and cleanup (e.g. transitioning from python2 --> python3), and I think I'll merge the read plotting functions into the final combine_reports script so that the figures can be annotated with which cluster (integration site) they are associated with.

[PavitaKae]

Thank you for your quick response. Adding the integration site ID to the reads report and the same ID to the images would be excellent.

Since this feature is not yet available, may I ask a few additional questions? In the images, do the shades of blue on the left and right represent read1 and read2, or do they correspond to the same read? Additionally, when an integration site is detected, can we assume that the virus has integrated its entire genome, or is it possible that only a portion has been integrated?