The code parsing and supporting "useq" files in IGB has been removed from the codebase. Commit

• Remove the following comment in GeneralLoadUtils.java

  Get GenomeVersion for USEQ file format.

• Check line 54 of TrackDefaultView.java for use of "useq".

• Should we remove the following useq test files?

  core/genometry/src/test/resources/data/useq/chr17_H_sapiens_Mar_2006_Graph.useq
  core/genometry/src/test/resources/data/useq/chr17_H_sapiens_Mar_2006_Region.useq
  core/genometry/src/test/resources/data/useq/chr17_H_sapiens_Mar_2006_StrandedReadCoverage_Graph.useq

• I'm also seeing a lot of imports being replaced with "". This seems like the IDE automatically making the change and I think we should not change them to "".

I removed the above useq references in addition to Karthik's changes and pushed my branch (https://bitbucket.org/nfreese/nowlanfork-igb/branch/IGBF-3146).

Add the additional changes and removed import errors. Commit

We have fixed the issue with Karthik's branch, here is the new commit: https://bitbucket.org/KarthikRavee91/karthikfork-igb/commits/70b1c45edfb1f1169ebdef6bcc85844a94d73f5a

Testing on Mac OS 12.5
Reset preferences to default and delete the .igb folder.

Attempting to load the attached useq file into the H_sapiens_Mar_2006 genome resulted in a "Format not recognized" error. This is the appropriate behavior.
In the A_thaliana_Jun_2009 genome, loaded the RNA-Seq > Auxin arf19 > Graph - Scaled > Col-0 control scaled coverage graph file successfully.
In the Graph tab, used Single-Graph Operations to successfully copy and divide the graph.
In the Graph tab, used Multi-Graph Operations to successfully Sum two graphs.

Since I can find no files in IGB that include mention of useq and the other IGB graph functionality does not appear to be affected, ready for pull request.

PR submitted: https://bitbucket.org/lorainelab/integrated-genome-browser/pull-requests/905

Merged.

Master branch is built and ready for testing.

Testing master branch installer on Mac OS 12.5
Reset preferences to default and delete the .igb folder.

Attempting to load the attached useq file into the H_sapiens_Mar_2006 genome resulted in a "Format not recognized" error. This is the appropriate behavior.
In the A_thaliana_Jun_2009 genome, loaded the RNA-Seq > Auxin arf19 > Graph - Scaled > Col-0 control scaled coverage graph file successfully.

Closing ticket.