Investigate: Error in navigation for Quick-Search Box

As per my observations I figured that ID - NM_004019.2 is unavailable in 9.1.6 for human genome.

[~aloraine] - Any suggestions?

Nowlan Freese - if you are available, could you take a look?

9.1.6 is pulling the annotation from: http://lorainelab-quickload.scidas.org/quickload/H_sapiens_Dec_2013/H_sapiens_Dec_2013_ncbiRefSeqCurated.bed.gz
9.1.4 is pulling the annotation from: http://igbquickload.org/quickload/H_sapiens_Dec_2013/H_sapiens_Dec_2013_ncbiRefSeqCurated.bed.gz

The 9.1.6 annotation is the human annotation from October of 2020.
The 9.1.4 annotation is the human annotation from March of 2019.

Searching for DMD works correctly when the March 2019 annotation is used.
Searching for DMD does not work when the October 2020 annotation is used.

When I compared the files there are a few differences in the gene IDs, but I did not see anything that would explain why the quick search is behaving oddly. Would need to further investigate why these two files lead to this difference.

There does not appear to be any difference in the search functionality between 9.1.6 and 9.1.4.

Updated igbquickload.org with the latest files from the subversion repository https://svn.bioviz.org/viewvc. After that doing, we observe identical behavior with 9.1.4 and 9.1.6. Next step: Create an "investigate" ticket to determine cause.

In a nutshell, the basic problem is that when a user enters DMD in the "Quick Search" box, two options appear: "GSDMD" and "DMD". When the user selects "DMD", IGB zooms-and-scrolls to the location of GSDMD and not DMD.

Why this is happening needs to be determined. Please see attached files.

Previous issues investigating search functionality in IGB:

https://jira.transvar.org/browse/IGBF-1096
https://jira.transvar.org/browse/IGBF-2032

My observations on IGB 9.1.8:

I downloaded the attached annotation files from the ticket.
I selected Species as “Homo Sapiens” and Genome version as “H_sapien_2013”.
I unticked RefSeq curated tab under IGB Quickload in configure box menu.

I opened below files one by one.

When I selected "DMD" in quick search box for annotation files (Load mode as genome)
• H_sapiens_Dec_2013_ncbiRefSeqCurated_MARCH-2019.bed
• H_sapiens_Dec_2013_ncbiRefSeqCurated_MARCH-2019_SMALL.bed

In the advanced search box, IGB navigated to DMD as expected but

When I selected “DMD” in quick search box for annotation files (Load mode as genome)
• H_sapiens_Dec_2013_ncbiRefSeqCurated_OCTOBER-2020.bed
• H_sapiens_Dec_2013_ncbiRefSeqCurated_OCTOBER-2020_SMALL.bed

In the advanced search box, IGB navigated to GSDMD instead of DMD.

I will continue investigating in the code base of IGB quick search box for its odd behavior.

As per Dr. Freese's guidance I investigated MapRangeBox.java file which is a code for quick search box of IGB. There are 6 search functions with different search criteria's for string . I think we can try altering those search criteria's to check if we are getting the expected results.

Dr. Loraine please suggest on the same.