Prutha Kulkarni and me were working on this today. A NullPointerException occurred on Mac (Prutha's pc) as well. We were able to fix it by using 'fileChooser.CANCEL_OPTION' and fileChooser.APPROVE_OPTION to handle the cases when a file is not selected and a file is selected respectively.
But these solutions did not work for Windows. The exceptions occurring for Windows are attached for this ticket. We will continue working on this.
Prof. Ann Loraine

Prutha Kulkarni and me have tried many options as follows:
1) We tried to debug the code using Logger
2) We tried to use try and catch to catch the NullPointerException
3) We tried creating a new app from scratch to replicate biojava-2bit-reader and while doing this, we tried to use an alternative FileChooser which was already implemented in genometry module.
After trying the above steps, we still were not able to fix it and are having a doubt whether the exceptions occur on my system. So, we are asking others to check it on their systems as well and are waiting for their response.

Pawan Bole and Srishti Tiwari tried installing and running this app on their laptops. Srishti Tiwari did not get repeated NPEs while Pawan Bole saw the repeated NPEs behaviour.

I have pushed the changes including 'fileChooser.CANCEL_OPTION' and ' fileChooser.APPROVE_OPTION' on Wednesday.
https://bitbucket.org/skulka2710/shamika-2bit-reader/branch/IGBF-2278#diff

The NullPointerExceptions occur when we try to open a dialog box using FileChooser, and get an absolute path for the file chosen. If no file is chosen, a NullPointerException occurred. This was fixed using the above two options. However, we are unable to find a fix for the other repeated NPEs occurring due to dialog box using FileChooser as of now. Due to repeatedly occurring NPEs (on Windows), we need to restart the IGB to make it work normally.

Thank you Shamika Gajanan Kulkarni for investigating.

I will take a look next. Am creating a new ticket to capture that task and moving this to Done.