Udaya Chinta (Inactive) added a comment - 27/Jan/25 7:40 PM While loading the GFF files that contain #FASTA code, I observed a NullPointerException. Upon checking the code, I identified the cause of the exception. The issue occurs because, while reading each line in the GFF file, the code reads the end of the line as a empty string but in code it is checking for null, which is causing the NullPointerException. The impact of this exception is that it prevents loading any tracks for files that contain #FASTA sections.

Udaya Chinta (Inactive) added a comment - 31/Jan/25 10:27 AM As part of this ticket I am working on investigating the conversion of gff to bed while saving the track. Currently I am understanding conversion logic.

Nowlan Freese added a comment - 05/Nov/25 3:45 PM See IGBF-3927 for additional discussion and documentation for GFF: https://gmod.org/wiki/GFF3

saideepthi jagarapu (Inactive) added a comment - 13/Nov/25 2:06 PM - edited Branch code changes: https://bitbucket.org/lorainelab-deepthi/integrated-genome-browser/branch/IGBF-4002 attn Nowlan Freese

Paige Kulzer added a comment - 14/Nov/25 10:18 AM - edited Fetched Deepthi's branch for testing on my Mac. The file prodigal_Lambda_phage_sequences.gff is now loading into IGB without error. However, when I attempt to load two GFF files at once, IGB throws the following error: 09:51:57.564 ERROR c.a.genometry.thread.CThreadWorker - class com.affymetrix.genometry.symloader.GFF3 cannot be cast to class com.affymetrix.genometry.quickload.QuickLoadSymLoader (com.affymetrix.genometry.symloader.GFF3 and com.affymetrix.genometry.quickload.QuickLoadSymLoader are in unnamed module of loader org.apache.felix.framework.BundleWiringImpl$BundleClassLoader @31889288) java.lang.ClassCastException: class com.affymetrix.genometry.symloader.GFF3 cannot be cast to class com.affymetrix.genometry.quickload.QuickLoadSymLoader (com.affymetrix.genometry.symloader.GFF3 and com.affymetrix.genometry.quickload.QuickLoadSymLoader are in unnamed module of loader org.apache.felix.framework.BundleWiringImpl$BundleClassLoader @31889288) at com.affymetrix.igb.view.load.GeneralLoadUtils$3.runInBackground(GeneralLoadUtils.java:1030) at com.affymetrix.igb.view.load.GeneralLoadUtils$3.runInBackground(GeneralLoadUtils.java:1009) at com.affymetrix.genometry.thread.CThreadWorker.doInBackground(CThreadWorker.java:73) at java.desktop/javax.swing.SwingWorker$1.call(SwingWorker.java:305) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:317) at java.desktop/javax.swing.SwingWorker.run(SwingWorker.java:342) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1144) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:642) at java.base/java.lang. Thread .run( Thread .java:1583) Loading these files into IGB individually does not throw this error. This is probably an edge case, but figured I'd bring it to your attention regardless. Also, I'm getting an error in the terminal upon closing IGB after loading in GFF file(s): ERROR: Bundle igb [39] EventDispatcher: Error during dispatch. (java.lang.IllegalStateException: Invalid BundleContext.) java.lang.IllegalStateException: Invalid BundleContext. at org.apache.felix.framework.BundleContextImpl.checkValidity(BundleContextImpl.java:491) at org.apache.felix.framework.BundleContextImpl.getService(BundleContextImpl.java:431) at com.affymetrix.common.ExtensionPointHandler.lambda$getOrCreateExtensionPoint$0(ExtensionPointHandler.java:46) at org.apache.felix.framework.EventDispatcher.invokeServiceListenerCallback(EventDispatcher.java:990) at org.apache.felix.framework.EventDispatcher.fireEventImmediately(EventDispatcher.java:838) at org.apache.felix.framework.EventDispatcher.fireServiceEvent(EventDispatcher.java:545) at org.apache.felix.framework.Felix.fireServiceEvent(Felix.java:4863) at org.apache.felix.framework.Felix.access$000(Felix.java:111) at org.apache.felix.framework.Felix$1.serviceChanged(Felix.java:440) at org.apache.felix.framework.ServiceRegistry.unregisterService(ServiceRegistry.java:170) at org.apache.felix.framework.ServiceRegistrationImpl.unregister(ServiceRegistrationImpl.java:146) at org.apache.felix.framework.ServiceRegistry.unregisterServices(ServiceRegistry.java:241) at org.apache.felix.framework.Felix.stopBundle(Felix.java:2847) at org.apache.felix.framework.Felix.setActiveStartLevel(Felix.java:1584) at org.apache.felix.framework.FrameworkStartLevelImpl.run(FrameworkStartLevelImpl.java:297) at java.base/java.lang. Thread .run( Thread .java:1583) Again, I'm not sure if this needs to be addressed since I'm not able to see this error while IGB's running. Interestingly, this isn't occurring with the test file attached to this ticket, but rather only with GFF files that have multiple FASTA sequences. General question after testing: Should Load Sequence work in IGB if a GFF file contains a ##FASTA section? I'm getting a pop-up that says "A genome sequence has not been selected. Loading sequence data is not possible." when I try to Load Sequence regardless of whether a GFF file contains a ##FASTA section or not. Upon closer inspection, though, files containing a single FASTA sequence do have their sequence loaded despite the pop-up! GFF files with multiple FASTA sequences do not. To reproduce my findings here, you can access GFF files with multiple FASTA sequences at the following Google Drive link: https://drive.google.com/drive/folders/1VV2xijrVRsBFacugGT1xZUwdns9t5CaG?usp=drive_link

Nowlan Freese added a comment - 18/Nov/25 4:19 PM - edited Testing Deepthi branch on Mac. Scenarios: Load fasta as custom sequence first. Attempt to load prodigal_Lambda_phage_sequences.gff as annotation - successful. No errors in log even when closing IGB. Load prodigal_Lambda_phage_sequences.gff without selecting a genome version or loading a separate fasta - successful. Note that the sequence loads with the Load Data button, which is the current behavior in IGB 10.1.0 when a fasta is opened in a genome that is already selected. No errors in log even when closing IGB. Load fasta as custom sequence first. Drag and drop two GFF files (no fasta included in the gff files) - successful. No errors in log even when closing IGB. Drag and drop two GFF files (no fasta included in the gff files) - successful. No errors in log even when closing IGB. So far all of the files provided by Dr. White are able to be loaded in IGB without any errors/issues. I'm continuing testing files with multiple sequence lines as the behavior is not exactly consistent so I am trying to figure out what is going on.

Paige Kulzer added a comment - 19/Nov/25 8:41 AM My apologies saideepthi jagarapu and Nowlan Freese , my clone of Deepthi's repo was not up to date with all of her latest commits. The errors I reported are not occurring now that I've pulled those changes.

Nowlan Freese added a comment - 24/Nov/25 3:23 PM The situations tested above are all working and I have found no errors in the log. The only adjacent issue I found was that if the GFF file contains multiple FASTA files, the provided sequences are only loaded in IGB for the last FASTA in the file. I have created IGBF-4362 to investigate the issue. Recommend pull request.

saideepthi jagarapu (Inactive) added a comment - 30/Nov/25 5:46 PM PR : https://bitbucket.org/lorainelab/integrated-genome-browser/pull-requests/1086

Ann Loraine added a comment - 01/Dec/25 11:45 PM - edited PR is merged. New installers are build and deployed tp the early access section of the bioviz.org website. Ready for testing.

Nowlan Freese added a comment - 02/Dec/25 2:18 PM - edited Ann Loraine - when I try to open the early access installer for Mac I'm seeing "IGB-macos-universal-main.dmg” is damaged and can’t be opened. You should move it to the Trash." Can you rebuild and redeploy the installer? Update - I tried building installers from my branch and got the same error. I have a feeling this has to do with this warning in the build: [WARNING] Certificate issued to Developer ID Application: Ann Loraine expired on Nov 20, 2025, 7:57 PM. I created IGBF-4369 to address this issue. I will test this ticket using main branch jar.

Nowlan Freese added a comment - 02/Dec/25 4:16 PM Tested on Mac using main branch jar. Able to load GFF files with and without fasta section. No errors in log. Closing ticket.