This is happening probably because when users open a bed file, IGB creates a local cache for the file. The cache contains a directory for every sequence listed in the file. However, some genome assemblies (like blueberry) are in draft form only and consist of many thousands of scaffolds. Hiral (or some-one) probably implemented a safeguard to prevent IGB from making lots of directories for these draft assemblies.

Change the error message to:

"The file contains data for too many sequences; some may not be shown. If this is a problem, please compress and index the file using tabix. For more information, contact the IGB Support Team."

Then add a button that says: "Contact IGB Support Team" and another button that says "OK"

If the users clicks "Contact IGB Support Team" a Web browser opens to http://bioviz.org/igb/contact.html.

If the user clicks "OK" or the window close button (on Mac, upper left) then the dialog should close.

Also, check that the message is not shown when a user converts the file to compressed, tabix-indexed form.

For now only the error message has been updated.
https://bitbucket.org/lorainelab/integrated-genome-browser/pull-request/106/igbf-33/diff

Testers
Only the message has been changed. Other changes will be introduced in next sprint with IGBF-154

Story: IGBF-33 (Improve error message when user opens Bed file with lots of sequences)
Date: August 15, 2014

Intro:
When using the blueberry genome and opening this attached file ["BlueberrySSR.bed.gz" (attached to the JIRA issue)] IGB displays a dialog and prints a console message with text:
-------------------------------------------------------
ERROR: File contains too many contigs; some will not be shown.
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This error is not helpful because it doesn't tell the user how to fix the problem. The error message has been changed and is now ready for testing.

Story IGBF-33 was tested on:
*IGB Version: 8.2.0
-(My Office Mac) Mac OS X Version 10.9.3 using JAVA RE 1.8.0_05-b13 Java HotSpot ™ 64-Bit Server

The story was tested using this workflow:
1) I opened IGB and slected the blueberry genome.
2) I opened the file "BlueberrySSR.bed.gz" (attached to the JIRA issue).
3) I checked to see if the error message had been changed to "The file contains data for too many sequences; some may not be shown. If this is a problem, please compress and index the file using tabix."

Observed:
The error message had been changed to "The file contains data for too many sequences; some may not be shown. If this is a problem, please compress and index the file using tabix."

Summary:
Story IGBF-33 was tested on my Mac. My observations were in accordance with the IGB Team's expectations. There will be more to test relating to this issue in IGBF-154.