[IGBF-4314] Rename titles and variable names for Color by and Filter of SAMtags - JIRA UNCC

Karthik Raveendran created issue - 04/Sep/25 1:47 PM

Karthik Raveendran made changes - 04/Sep/25 1:47 PM

Field	Original Value	New Value
Epic Link		IGBF-3765 [ 22984 ]

Karthik Raveendran made changes - 04/Sep/25 1:47 PM

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Karthik Raveendran made changes - 04/Sep/25 3:00 PM

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Karthik Raveendran made changes - 04/Sep/25 3:00 PM

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Karthik Raveendran [ karthik ]

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Karthik Raveendran added a comment - 04/Sep/25 3:01 PM

See commit

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Karthik Raveendran added a comment - 04/Sep/25 3:01 PM See commit

Paige Kulzer (Inactive) made changes - 11/Sep/25 10:53 AM

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Paige Kulzer [ pkulzer ]

Paige Kulzer (Inactive) made changes - 11/Sep/25 10:53 AM

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Paige Kulzer (Inactive) added a comment - 11/Sep/25 12:08 PM

I tested by fetching Karthik's branch and running it on my Mac. I'm seeing errors in the Log when I attempt to open the Color by table:

Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException: Cannot invoke "java.util.List.add(Object)" because "tags" is null
	at com.affymetrix.igb.shared.ConfigureOptionsPanel.refreshSAMTAGS(ConfigureOptionsPanel.java:199)
	at com.affymetrix.igb.shared.ConfigureOptionsPanel.init(ConfigureOptionsPanel.java:129)
	at com.affymetrix.igb.shared.ConfigureOptionsPanel.<init>(ConfigureOptionsPanel.java:99)
	at com.affymetrix.igb.util.ConfigureOptionsDialog$1.<init>(ConfigureOptionsDialog.java:65)
	at com.affymetrix.igb.util.ConfigureOptionsDialog.init(ConfigureOptionsDialog.java:65)
	at com.affymetrix.igb.util.ConfigureOptionsDialog.<init>(ConfigureOptionsDialog.java:57)
	at com.affymetrix.igb.util.ConfigureOptionsDialog.<init>(ConfigureOptionsDialog.java:44)
	at com.affymetrix.igb.action.ColorByAction.actionPerformed(ColorByAction.java:71)
	at java.desktop/javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:1972)
	at java.desktop/javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2314)
	at java.desktop/javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:407)
	at java.desktop/javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:262)
	at java.desktop/javax.swing.AbstractButton.doClick(AbstractButton.java:374)
	at java.desktop/javax.swing.plaf.basic.BasicMenuItemUI.doClick(BasicMenuItemUI.java:1029)
	at java.desktop/com.apple.laf.AquaMenuItemUI.doClick(AquaMenuItemUI.java:157)
	at java.desktop/javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(BasicMenuItemUI.java:1073)
	at java.desktop/java.awt.Component.processMouseEvent(Component.java:6621)
	at java.desktop/javax.swing.JComponent.processMouseEvent(JComponent.java:3398)
	at java.desktop/java.awt.Component.processEvent(Component.java:6386)
	at java.desktop/java.awt.Container.processEvent(Container.java:2266)
	at java.desktop/java.awt.Component.dispatchEventImpl(Component.java:4996)
	at java.desktop/java.awt.Container.dispatchEventImpl(Container.java:2324)
	at java.desktop/java.awt.Component.dispatchEvent(Component.java:4828)
	at java.desktop/java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4948)
	at java.desktop/java.awt.LightweightDispatcher.processMouseEvent(Container.java:4575)
	at java.desktop/java.awt.LightweightDispatcher.dispatchEvent(Container.java:4516)
	at java.desktop/java.awt.Container.dispatchEventImpl(Container.java:2310)
	at java.desktop/java.awt.Window.dispatchEventImpl(Window.java:2780)
	at java.desktop/java.awt.Component.dispatchEvent(Component.java:4828)
	at java.desktop/java.awt.EventQueue.dispatchEventImpl(EventQueue.java:775)
	at java.desktop/java.awt.EventQueue$4.run(EventQueue.java:720)
	at java.desktop/java.awt.EventQueue$4.run(EventQueue.java:714)
	at java.base/java.security.AccessController.doPrivileged(AccessController.java:400)
	at java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:87)
	at java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:98)
	at java.desktop/java.awt.EventQueue$5.run(EventQueue.java:747)
	at java.desktop/java.awt.EventQueue$5.run(EventQueue.java:745)
	at java.base/java.security.AccessController.doPrivileged(AccessController.java:400)
	at java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:87)
	at java.desktop/java.awt.EventQueue.dispatchEvent(EventQueue.java:744)
	at java.desktop/java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:203)
	at java.desktop/java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:124)
	at java.desktop/java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:113)
	at java.desktop/java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:109)
	at java.desktop/java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
	at java.desktop/java.awt.EventDispatchThread.run(EventDispatchThread.java:90)

I'm seeing the same error when clicking the "Add" button in the Filter by table. I'm guessing there were some inconsistencies with variable names when making these changes.

Additionally, I have a few picky comments:

In ToolTipConstants.java, I think "SAMTags" should be "SAMtags" for consistency with other instances of this word in IGB.
In SAMtagsTable.java, should "SAMtools Tag Color Mapping" be "SAMtags Color Mapping"?

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Paige Kulzer (Inactive) added a comment - 11/Sep/25 12:08 PM I tested by fetching Karthik's branch and running it on my Mac. I'm seeing errors in the Log when I attempt to open the Color by table: Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException: Cannot invoke "java.util.List.add( Object )" because "tags" is null at com.affymetrix.igb.shared.ConfigureOptionsPanel.refreshSAMTAGS(ConfigureOptionsPanel.java:199) at com.affymetrix.igb.shared.ConfigureOptionsPanel.init(ConfigureOptionsPanel.java:129) at com.affymetrix.igb.shared.ConfigureOptionsPanel.<init>(ConfigureOptionsPanel.java:99) at com.affymetrix.igb.util.ConfigureOptionsDialog$1.<init>(ConfigureOptionsDialog.java:65) at com.affymetrix.igb.util.ConfigureOptionsDialog.init(ConfigureOptionsDialog.java:65) at com.affymetrix.igb.util.ConfigureOptionsDialog.<init>(ConfigureOptionsDialog.java:57) at com.affymetrix.igb.util.ConfigureOptionsDialog.<init>(ConfigureOptionsDialog.java:44) at com.affymetrix.igb.action.ColorByAction.actionPerformed(ColorByAction.java:71) at java.desktop/javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:1972) at java.desktop/javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2314) at java.desktop/javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:407) at java.desktop/javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:262) at java.desktop/javax.swing.AbstractButton.doClick(AbstractButton.java:374) at java.desktop/javax.swing.plaf.basic.BasicMenuItemUI.doClick(BasicMenuItemUI.java:1029) at java.desktop/com.apple.laf.AquaMenuItemUI.doClick(AquaMenuItemUI.java:157) at java.desktop/javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(BasicMenuItemUI.java:1073) at java.desktop/java.awt.Component.processMouseEvent(Component.java:6621) at java.desktop/javax.swing.JComponent.processMouseEvent(JComponent.java:3398) at java.desktop/java.awt.Component.processEvent(Component.java:6386) at java.desktop/java.awt.Container.processEvent(Container.java:2266) at java.desktop/java.awt.Component.dispatchEventImpl(Component.java:4996) at java.desktop/java.awt.Container.dispatchEventImpl(Container.java:2324) at java.desktop/java.awt.Component.dispatchEvent(Component.java:4828) at java.desktop/java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4948) at java.desktop/java.awt.LightweightDispatcher.processMouseEvent(Container.java:4575) at java.desktop/java.awt.LightweightDispatcher.dispatchEvent(Container.java:4516) at java.desktop/java.awt.Container.dispatchEventImpl(Container.java:2310) at java.desktop/java.awt.Window.dispatchEventImpl(Window.java:2780) at java.desktop/java.awt.Component.dispatchEvent(Component.java:4828) at java.desktop/java.awt.EventQueue.dispatchEventImpl(EventQueue.java:775) at java.desktop/java.awt.EventQueue$4.run(EventQueue.java:720) at java.desktop/java.awt.EventQueue$4.run(EventQueue.java:714) at java.base/java.security.AccessController.doPrivileged(AccessController.java:400) at java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:87) at java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:98) at java.desktop/java.awt.EventQueue$5.run(EventQueue.java:747) at java.desktop/java.awt.EventQueue$5.run(EventQueue.java:745) at java.base/java.security.AccessController.doPrivileged(AccessController.java:400) at java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:87) at java.desktop/java.awt.EventQueue.dispatchEvent(EventQueue.java:744) at java.desktop/java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:203) at java.desktop/java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:124) at java.desktop/java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:113) at java.desktop/java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:109) at java.desktop/java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.desktop/java.awt.EventDispatchThread.run(EventDispatchThread.java:90) I'm seeing the same error when clicking the "Add" button in the Filter by table. I'm guessing there were some inconsistencies with variable names when making these changes. Additionally, I have a few picky comments: In ToolTipConstants.java, I think " SAMTags " should be " SAMtags " for consistency with other instances of this word in IGB. In SAMtagsTable.java, should " SAMtools Tag Color Mapping " be " SAMtags Color Mapping "?

Paige Kulzer (Inactive) made changes - 11/Sep/25 12:08 PM

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First Level Review in Progress [ 10301 ]

To-Do [ 10305 ]

Paige Kulzer (Inactive) made changes - 11/Sep/25 12:08 PM

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Paige Kulzer [ pkulzer ]

Karthik Raveendran [ karthik ]

Ann Loraine made changes - 16/Sep/25 5:42 PM

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Fall 2, Fall 3 [ 225, 226 ]

Ann Loraine made changes - 16/Sep/25 5:42 PM

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Ann Loraine made changes - 28/Sep/25 11:52 AM

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Fall 2, Fall 3 [ 225, 226 ]

Fall 2, Fall 3, Fall 4 [ 225, 226, 227 ]

Ann Loraine made changes - 28/Sep/25 11:52 AM

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Ann Loraine made changes - 12/Oct/25 10:15 AM

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Fall 2, Fall 3, Fall 4 [ 225, 226, 227 ]

Fall 2, Fall 3, Fall 4, Fall 5 [ 225, 226, 227, 228 ]

Ann Loraine made changes - 12/Oct/25 10:15 AM

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Karthik Raveendran made changes - 14/Oct/25 10:03 AM

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Karthik Raveendran added a comment - 15/Oct/25 10:34 AM

Fix the errors mentioned above. See commit: https://bitbucket.org/KarthikRavee91/karthikfork-igb/commits/92b6b8d7f96f8803441a530c2af1c0dce0c0a071

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Karthik Raveendran added a comment - 15/Oct/25 10:34 AM Fix the errors mentioned above. See commit: https://bitbucket.org/KarthikRavee91/karthikfork-igb/commits/92b6b8d7f96f8803441a530c2af1c0dce0c0a071

Karthik Raveendran made changes - 15/Oct/25 10:34 AM

Status

In Progress [ 3 ]

Needs 1st Level Review [ 10005 ]

Karthik Raveendran made changes - 15/Oct/25 10:34 AM

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Karthik Raveendran [ karthik ]

Nowlan Freese made changes - 15/Oct/25 10:36 AM

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Paige Kulzer [ pkulzer ]

Paige Kulzer (Inactive) made changes - 15/Oct/25 10:59 AM

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First Level Review in Progress [ 10301 ]

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Paige Kulzer (Inactive) added a comment - 15/Oct/25 11:15 AM

I am no longer seeing an error when clicking the "Add" button in the Filter by table. However, I am seeing an error when working with the Color by table:

Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException: Cannot invoke "java.lang.Class.isInstance(Object)" because the return value of "java.util.Map.get(Object)" is null
	at com.affymetrix.genometry.general.Parameters.setParameterValue(Parameters.java:44)
	at com.affymetrix.genometry.general.Parameters.setParametersValue(Parameters.java:37)
	at com.affymetrix.genometry.color.ColorProvider.setParametersValue(ColorProvider.java:30)
	at com.affymetrix.igb.shared.ConfigureOptionsPanel.getReturnValue(ConfigureOptionsPanel.java:565)
	at com.affymetrix.igb.util.ConfigureOptionsDialog.showDialog(ConfigureOptionsDialog.java:124)
	at com.affymetrix.igb.action.ColorByAction.actionPerformed(ColorByAction.java:76)
	at java.desktop/javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:1972)
	at java.desktop/javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2314)
	at java.desktop/javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:407)
	at java.desktop/javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:262)
	at java.desktop/javax.swing.AbstractButton.doClick(AbstractButton.java:374)
	at java.desktop/javax.swing.plaf.basic.BasicMenuItemUI.doClick(BasicMenuItemUI.java:1029)
	at java.desktop/com.apple.laf.AquaMenuItemUI.doClick(AquaMenuItemUI.java:157)
	at java.desktop/javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(BasicMenuItemUI.java:1073)
	at java.desktop/java.awt.Component.processMouseEvent(Component.java:6621)
	at java.desktop/javax.swing.JComponent.processMouseEvent(JComponent.java:3398)
	at java.desktop/java.awt.Component.processEvent(Component.java:6386)
	at java.desktop/java.awt.Container.processEvent(Container.java:2266)
	at java.desktop/java.awt.Component.dispatchEventImpl(Component.java:4996)
	at java.desktop/java.awt.Container.dispatchEventImpl(Container.java:2324)
	at java.desktop/java.awt.Component.dispatchEvent(Component.java:4828)
	at java.desktop/java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4948)
	at java.desktop/java.awt.LightweightDispatcher.processMouseEvent(Container.java:4575)
	at java.desktop/java.awt.LightweightDispatcher.dispatchEvent(Container.java:4516)
	at java.desktop/java.awt.Container.dispatchEventImpl(Container.java:2310)
	at java.desktop/java.awt.Window.dispatchEventImpl(Window.java:2780)
	at java.desktop/java.awt.Component.dispatchEvent(Component.java:4828)
	at java.desktop/java.awt.EventQueue.dispatchEventImpl(EventQueue.java:775)
	at java.desktop/java.awt.EventQueue$4.run(EventQueue.java:720)
	at java.desktop/java.awt.EventQueue$4.run(EventQueue.java:714)
	at java.base/java.security.AccessController.doPrivileged(AccessController.java:400)
	at java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:87)
	at java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:98)
	at java.desktop/java.awt.EventQueue$5.run(EventQueue.java:747)
	at java.desktop/java.awt.EventQueue$5.run(EventQueue.java:745)
	at java.base/java.security.AccessController.doPrivileged(AccessController.java:400)
	at java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:87)
	at java.desktop/java.awt.EventQueue.dispatchEvent(EventQueue.java:744)
	at java.desktop/java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:203)
	at java.desktop/java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:124)
	at java.desktop/java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:113)
	at java.desktop/java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:109)
	at java.desktop/java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
	at java.desktop/java.awt.EventDispatchThread.run(EventDispatchThread.java:90)

To reproduce, add the 10X_PMBC3k QL and zoom to chr21:27,484,286-27,484,423. Add an entry to the SAMtools Tag Color Mapping window (e.g., TGTACTCAGA), assign it a color, and select the UB SAMtag. Then, click Save and Apply, click OK, and observe the error.

I'm also seeing an error that I believe is unrelated to these title/variable changes:

Exception in thread "AWT-EventQueue-0" java.lang.ClassCastException: class java.lang.String cannot be cast to class java.lang.Integer (java.lang.String and java.lang.Integer are in module java.base of loader 'bootstrap')
	at com.affymetrix.igb.util.ConfigureFilters.beginEditing(ConfigureFilters.java:256)
	at com.affymetrix.igb.util.ConfigureFilters.editButtonActionPerformed(ConfigureFilters.java:156)
	at java.desktop/javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:1972)
	at java.desktop/javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2314)
	at java.desktop/javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:407)
	at java.desktop/javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:262)
	at java.desktop/javax.swing.plaf.basic.BasicButtonListener.mouseReleased(BasicButtonListener.java:279)
	at java.desktop/java.awt.Component.processMouseEvent(Component.java:6621)
	at java.desktop/javax.swing.JComponent.processMouseEvent(JComponent.java:3398)
	at java.desktop/java.awt.Component.processEvent(Component.java:6386)
	at java.desktop/java.awt.Container.processEvent(Container.java:2266)
	at java.desktop/java.awt.Component.dispatchEventImpl(Component.java:4996)
	at java.desktop/java.awt.Container.dispatchEventImpl(Container.java:2324)
	at java.desktop/java.awt.Component.dispatchEvent(Component.java:4828)
	at java.desktop/java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4948)
	at java.desktop/java.awt.LightweightDispatcher.processMouseEvent(Container.java:4575)
	at java.desktop/java.awt.LightweightDispatcher.dispatchEvent(Container.java:4516)
	at java.desktop/java.awt.Container.dispatchEventImpl(Container.java:2310)
	at java.desktop/java.awt.Window.dispatchEventImpl(Window.java:2780)
	at java.desktop/java.awt.Component.dispatchEvent(Component.java:4828)
	at java.desktop/java.awt.EventQueue.dispatchEventImpl(EventQueue.java:775)
	at java.desktop/java.awt.EventQueue$4.run(EventQueue.java:720)
	at java.desktop/java.awt.EventQueue$4.run(EventQueue.java:714)
	at java.base/java.security.AccessController.doPrivileged(AccessController.java:400)
	at java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:87)
	at java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:98)
	at java.desktop/java.awt.EventQueue$5.run(EventQueue.java:747)
	at java.desktop/java.awt.EventQueue$5.run(EventQueue.java:745)
	at java.base/java.security.AccessController.doPrivileged(AccessController.java:400)
	at java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:87)
	at java.desktop/java.awt.EventQueue.dispatchEvent(EventQueue.java:744)
	at java.desktop/java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:203)
	at java.desktop/java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:124)
	at java.desktop/java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:113)
	at java.desktop/java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:109)
	at java.desktop/java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
	at java.desktop/java.awt.EventDispatchThread.run(EventDispatchThread.java:90)

To reproduce, add an entry to the filter by table (SAMtags or otherwise), then click Edit. Close the Edit Filter window using the red X and observe the error. Please disregard if I've already made note of this issue and a ticket has been made to address it.

Passing back to Karthik Raveendran for another round of changes.

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Paige Kulzer (Inactive) added a comment - 15/Oct/25 11:15 AM I am no longer seeing an error when clicking the "Add" button in the Filter by table. However, I am seeing an error when working with the Color by table: Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException: Cannot invoke "java.lang. Class .isInstance( Object )" because the return value of "java.util.Map.get( Object )" is null at com.affymetrix.genometry.general.Parameters.setParameterValue(Parameters.java:44) at com.affymetrix.genometry.general.Parameters.setParametersValue(Parameters.java:37) at com.affymetrix.genometry.color.ColorProvider.setParametersValue(ColorProvider.java:30) at com.affymetrix.igb.shared.ConfigureOptionsPanel.getReturnValue(ConfigureOptionsPanel.java:565) at com.affymetrix.igb.util.ConfigureOptionsDialog.showDialog(ConfigureOptionsDialog.java:124) at com.affymetrix.igb.action.ColorByAction.actionPerformed(ColorByAction.java:76) at java.desktop/javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:1972) at java.desktop/javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2314) at java.desktop/javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:407) at java.desktop/javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:262) at java.desktop/javax.swing.AbstractButton.doClick(AbstractButton.java:374) at java.desktop/javax.swing.plaf.basic.BasicMenuItemUI.doClick(BasicMenuItemUI.java:1029) at java.desktop/com.apple.laf.AquaMenuItemUI.doClick(AquaMenuItemUI.java:157) at java.desktop/javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(BasicMenuItemUI.java:1073) at java.desktop/java.awt.Component.processMouseEvent(Component.java:6621) at java.desktop/javax.swing.JComponent.processMouseEvent(JComponent.java:3398) at java.desktop/java.awt.Component.processEvent(Component.java:6386) at java.desktop/java.awt.Container.processEvent(Container.java:2266) at java.desktop/java.awt.Component.dispatchEventImpl(Component.java:4996) at java.desktop/java.awt.Container.dispatchEventImpl(Container.java:2324) at java.desktop/java.awt.Component.dispatchEvent(Component.java:4828) at java.desktop/java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4948) at java.desktop/java.awt.LightweightDispatcher.processMouseEvent(Container.java:4575) at java.desktop/java.awt.LightweightDispatcher.dispatchEvent(Container.java:4516) at java.desktop/java.awt.Container.dispatchEventImpl(Container.java:2310) at java.desktop/java.awt.Window.dispatchEventImpl(Window.java:2780) at java.desktop/java.awt.Component.dispatchEvent(Component.java:4828) at java.desktop/java.awt.EventQueue.dispatchEventImpl(EventQueue.java:775) at java.desktop/java.awt.EventQueue$4.run(EventQueue.java:720) at java.desktop/java.awt.EventQueue$4.run(EventQueue.java:714) at java.base/java.security.AccessController.doPrivileged(AccessController.java:400) at java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:87) at java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:98) at java.desktop/java.awt.EventQueue$5.run(EventQueue.java:747) at java.desktop/java.awt.EventQueue$5.run(EventQueue.java:745) at java.base/java.security.AccessController.doPrivileged(AccessController.java:400) at java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:87) at java.desktop/java.awt.EventQueue.dispatchEvent(EventQueue.java:744) at java.desktop/java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:203) at java.desktop/java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:124) at java.desktop/java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:113) at java.desktop/java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:109) at java.desktop/java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.desktop/java.awt.EventDispatchThread.run(EventDispatchThread.java:90) To reproduce, add the 10X_PMBC3k QL and zoom to chr21:27,484,286-27,484,423. Add an entry to the SAMtools Tag Color Mapping window (e.g., TGTACTCAGA), assign it a color, and select the UB SAMtag. Then, click Save and Apply, click OK, and observe the error. I'm also seeing an error that I believe is unrelated to these title/variable changes: Exception in thread "AWT-EventQueue-0" java.lang.ClassCastException: class java.lang. String cannot be cast to class java.lang. Integer (java.lang. String and java.lang. Integer are in module java.base of loader 'bootstrap') at com.affymetrix.igb.util.ConfigureFilters.beginEditing(ConfigureFilters.java:256) at com.affymetrix.igb.util.ConfigureFilters.editButtonActionPerformed(ConfigureFilters.java:156) at java.desktop/javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:1972) at java.desktop/javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2314) at java.desktop/javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:407) at java.desktop/javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:262) at java.desktop/javax.swing.plaf.basic.BasicButtonListener.mouseReleased(BasicButtonListener.java:279) at java.desktop/java.awt.Component.processMouseEvent(Component.java:6621) at java.desktop/javax.swing.JComponent.processMouseEvent(JComponent.java:3398) at java.desktop/java.awt.Component.processEvent(Component.java:6386) at java.desktop/java.awt.Container.processEvent(Container.java:2266) at java.desktop/java.awt.Component.dispatchEventImpl(Component.java:4996) at java.desktop/java.awt.Container.dispatchEventImpl(Container.java:2324) at java.desktop/java.awt.Component.dispatchEvent(Component.java:4828) at java.desktop/java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4948) at java.desktop/java.awt.LightweightDispatcher.processMouseEvent(Container.java:4575) at java.desktop/java.awt.LightweightDispatcher.dispatchEvent(Container.java:4516) at java.desktop/java.awt.Container.dispatchEventImpl(Container.java:2310) at java.desktop/java.awt.Window.dispatchEventImpl(Window.java:2780) at java.desktop/java.awt.Component.dispatchEvent(Component.java:4828) at java.desktop/java.awt.EventQueue.dispatchEventImpl(EventQueue.java:775) at java.desktop/java.awt.EventQueue$4.run(EventQueue.java:720) at java.desktop/java.awt.EventQueue$4.run(EventQueue.java:714) at java.base/java.security.AccessController.doPrivileged(AccessController.java:400) at java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:87) at java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:98) at java.desktop/java.awt.EventQueue$5.run(EventQueue.java:747) at java.desktop/java.awt.EventQueue$5.run(EventQueue.java:745) at java.base/java.security.AccessController.doPrivileged(AccessController.java:400) at java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:87) at java.desktop/java.awt.EventQueue.dispatchEvent(EventQueue.java:744) at java.desktop/java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:203) at java.desktop/java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:124) at java.desktop/java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:113) at java.desktop/java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:109) at java.desktop/java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.desktop/java.awt.EventDispatchThread.run(EventDispatchThread.java:90) To reproduce, add an entry to the filter by table (SAMtags or otherwise), then click Edit. Close the Edit Filter window using the red X and observe the error. Please disregard if I've already made note of this issue and a ticket has been made to address it. Passing back to Karthik Raveendran for another round of changes.

Paige Kulzer (Inactive) made changes - 15/Oct/25 11:15 AM

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Paige Kulzer (Inactive) made changes - 15/Oct/25 11:15 AM

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Paige Kulzer [ pkulzer ]

Karthik Raveendran [ karthik ]

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Karthik Raveendran added a comment - 21/Oct/25 6:46 PM

One of the labels was still SAMtools which through the error above. Bug fixed in https://bitbucket.org/KarthikRavee91/karthikfork-igb/commits/9c89f86158058bd6677818624ff16ddbc2ad3e2d

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Karthik Raveendran added a comment - 21/Oct/25 6:46 PM One of the labels was still SAMtools which through the error above. Bug fixed in https://bitbucket.org/KarthikRavee91/karthikfork-igb/commits/9c89f86158058bd6677818624ff16ddbc2ad3e2d

Karthik Raveendran made changes - 21/Oct/25 6:46 PM

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Karthik Raveendran made changes - 21/Oct/25 6:46 PM

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Karthik Raveendran made changes - 21/Oct/25 6:46 PM

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Karthik Raveendran [ karthik ]

Paige Kulzer (Inactive) made changes - 22/Oct/25 10:20 AM

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Paige Kulzer [ pkulzer ]

Paige Kulzer (Inactive) made changes - 22/Oct/25 10:20 AM

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First Level Review in Progress [ 10301 ]

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Paige Kulzer (Inactive) added a comment - 22/Oct/25 10:28 AM

I refetched this branch and tested for the above errors. All reported errors have been fixed and I am unable to find any new ones while using the Color and Filter by features. Looks good, ready for PR!

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Paige Kulzer (Inactive) added a comment - 22/Oct/25 10:28 AM I refetched this branch and tested for the above errors. All reported errors have been fixed and I am unable to find any new ones while using the Color and Filter by features. Looks good, ready for PR!

Paige Kulzer (Inactive) made changes - 22/Oct/25 10:28 AM

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First Level Review in Progress [ 10301 ]

Ready for Pull Request [ 10304 ]

Paige Kulzer (Inactive) made changes - 22/Oct/25 10:28 AM

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Paige Kulzer [ pkulzer ]

Karthik Raveendran [ karthik ]

Karthik Raveendran made changes - 24/Oct/25 3:29 PM

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Pull Request Submitted [ 10101 ]

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Karthik Raveendran added a comment - 24/Oct/25 4:29 PM

PR Submitted https://bitbucket.org/lorainelab/integrated-genome-browser/pull-requests/1083

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Karthik Raveendran added a comment - 24/Oct/25 4:29 PM PR Submitted https://bitbucket.org/lorainelab/integrated-genome-browser/pull-requests/1083

Nowlan Freese made changes - 27/Oct/25 4:22 PM

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Fall 2, Fall 3, Fall 4, Fall 5 [ 225, 226, 227, 228 ]

Fall 2, Fall 3, Fall 4, Fall 5, Fall 6 [ 225, 226, 227, 228, 229 ]

Nowlan Freese made changes - 27/Oct/25 4:22 PM

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Ranked higher

Ann Loraine made changes - 29/Oct/25 10:03 AM

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Pull Request Submitted [ 10101 ]

Reviewing Pull Request [ 10303 ]

Ann Loraine made changes - 29/Oct/25 10:03 AM

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Reviewing Pull Request [ 10303 ]

Merged Needs Testing [ 10002 ]

Nowlan Freese made changes - 29/Oct/25 10:04 AM

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Karthik Raveendran [ karthik ]

Paige Kulzer [ pkulzer ]

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Ann Loraine added a comment - 29/Oct/25 10:04 AM

PR is merged, new installers are built and deployed to bioviz.org.
Read for final testing.

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Ann Loraine added a comment - 29/Oct/25 10:04 AM PR is merged, new installers are built and deployed to bioviz.org. Read for final testing.

Paige Kulzer (Inactive) made changes - 29/Oct/25 11:48 AM

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Post-merge Testing In Progress [ 10003 ]

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Paige Kulzer (Inactive) added a comment - 29/Oct/25 12:22 PM

Downloaded the early access release from bioviz.org and tested for any remaining issues related to variable names. I'm unable to find any errors, color and filter by functionality is working as expected.

Closing ticket.

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Paige Kulzer (Inactive) added a comment - 29/Oct/25 12:22 PM Downloaded the early access release from bioviz.org and tested for any remaining issues related to variable names. I'm unable to find any errors, color and filter by functionality is working as expected. Closing ticket.

Paige Kulzer (Inactive) made changes - 29/Oct/25 12:22 PM

Resolution		Done [ 10000 ]
Status	Post-merge Testing In Progress [ 10003 ]	Closed [ 6 ]

Paige Kulzer (Inactive) made changes - 29/Oct/25 12:22 PM

Assignee

Paige Kulzer [ pkulzer ]

Karthik Raveendran [ karthik ]

Paige Kulzer (Inactive) made changes - 02/Dec/25 10:31 AM

Fix Version/s

10.2.0 [ 11100 ]

Rename titles and variable names for Color by and Filter of SAMtags

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