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  1. Bug Repository
  2. BUG-27

Subsequent bam file loading causes Null Pointer Exception

          Details

          • Type: Bug
          • Status: Closed (View Workflow)
          • Priority: Major
          • Resolution: Fixed
          • Labels:
            None
          • Environment:

            OS X 10.6
            Java: "1.6.0_24"
            IGB: 7791

            Description

            Load Tair10 and zoom in to a gene.

            With the console open, Drag in 1 bam file from our data site. Drag in a second. Then load data - there should be no error.

            THEN: drag in a third, load data.

            There should be no errors.

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                Issue Links

                relates to

                Task - A task that needs to be done. BUG-622 File format issues

                • Blocker - Blocks development and/or testing work, production could not run.
                • Closed

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                  adam Adam Baxter (Inactive) added a comment -

                  Log output:

                  Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException
                  at com.affymetrix.igb.view.load.GeneralLoadUtils.checkBamLoading(GeneralLoadUtils.java:760)
                  at com.affymetrix.igb.view.load.GeneralLoadUtils.loadAndDisplaySpan(GeneralLoadUtils.java:671)
                  at com.affymetrix.igb.view.load.GeneralLoadUtils.loadAndDisplayAnnotations(GeneralLoadUtils.java:650)
                  at com.affymetrix.igb.view.load.GeneralLoadView.loadFeatures(GeneralLoadView.java:621)
                  at com.affymetrix.igb.view.load.GeneralLoadView.loadVisibleFeatures(GeneralLoadView.java:589)
                  at com.affymetrix.igb.action.RefreshDataAction.actionPerformed(RefreshDataAction.java:32)
                  at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2028)
                  at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2351)
                  at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:387)
                  at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:242)
                  at javax.swing.plaf.basic.BasicButtonListener.mouseReleased(BasicButtonListener.java:236)
                  at java.awt.AWTEventMulticaster.mouseReleased(AWTEventMulticaster.java:272)
                  at java.awt.Component.processMouseEvent(Component.java:6374)
                  at javax.swing.JComponent.processMouseEvent(JComponent.java:3267)
                  at java.awt.Component.processEvent(Component.java:6139)
                  at java.awt.Container.processEvent(Container.java:2085)
                  at java.awt.Component.dispatchEventImpl(Component.java:4736)
                  at java.awt.Container.dispatchEventImpl(Container.java:2143)
                  at java.awt.Component.dispatchEvent(Component.java:4566)
                  at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4621)
                  at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4282)
                  at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4212)
                  at java.awt.Container.dispatchEventImpl(Container.java:2129)
                  at java.awt.Window.dispatchEventImpl(Window.java:2478)
                  at java.awt.Component.dispatchEvent(Component.java:4566)
                  at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:680)
                  at java.awt.EventQueue.access$000(EventQueue.java:86)
                  at java.awt.EventQueue$1.run(EventQueue.java:639)
                  at java.awt.EventQueue$1.run(EventQueue.java:637)
                  at java.security.AccessController.doPrivileged(Native Method)
                  at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87)
                  at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:98)
                  at java.awt.EventQueue$2.run(EventQueue.java:653)
                  at java.awt.EventQueue$2.run(EventQueue.java:651)
                  at java.security.AccessController.doPrivileged(Native Method)
                  at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87)
                  at java.awt.EventQueue.dispatchEvent(EventQueue.java:650)
                  at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:296)
                  at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:211)
                  at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:201)
                  at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:196)
                  at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:188)
                  at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)

                  Show
                  adam Adam Baxter (Inactive) added a comment - Log output: Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException at com.affymetrix.igb.view.load.GeneralLoadUtils.checkBamLoading(GeneralLoadUtils.java:760) at com.affymetrix.igb.view.load.GeneralLoadUtils.loadAndDisplaySpan(GeneralLoadUtils.java:671) at com.affymetrix.igb.view.load.GeneralLoadUtils.loadAndDisplayAnnotations(GeneralLoadUtils.java:650) at com.affymetrix.igb.view.load.GeneralLoadView.loadFeatures(GeneralLoadView.java:621) at com.affymetrix.igb.view.load.GeneralLoadView.loadVisibleFeatures(GeneralLoadView.java:589) at com.affymetrix.igb.action.RefreshDataAction.actionPerformed(RefreshDataAction.java:32) at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2028) at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2351) at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:387) at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:242) at javax.swing.plaf.basic.BasicButtonListener.mouseReleased(BasicButtonListener.java:236) at java.awt.AWTEventMulticaster.mouseReleased(AWTEventMulticaster.java:272) at java.awt.Component.processMouseEvent(Component.java:6374) at javax.swing.JComponent.processMouseEvent(JComponent.java:3267) at java.awt.Component.processEvent(Component.java:6139) at java.awt.Container.processEvent(Container.java:2085) at java.awt.Component.dispatchEventImpl(Component.java:4736) at java.awt.Container.dispatchEventImpl(Container.java:2143) at java.awt.Component.dispatchEvent(Component.java:4566) at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4621) at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4282) at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4212) at java.awt.Container.dispatchEventImpl(Container.java:2129) at java.awt.Window.dispatchEventImpl(Window.java:2478) at java.awt.Component.dispatchEvent(Component.java:4566) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:680) at java.awt.EventQueue.access$000(EventQueue.java:86) at java.awt.EventQueue$1.run(EventQueue.java:639) at java.awt.EventQueue$1.run(EventQueue.java:637) at java.security.AccessController.doPrivileged(Native Method) at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87) at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:98) at java.awt.EventQueue$2.run(EventQueue.java:653) at java.awt.EventQueue$2.run(EventQueue.java:651) at java.security.AccessController.doPrivileged(Native Method) at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87) at java.awt.EventQueue.dispatchEvent(EventQueue.java:650) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:296) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:211) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:196) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:188) at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)
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                  alyssa Alyssa Gulledge (Inactive) added a comment -

                  I think this got assigned to Ann by mistake

                  Show
                  alyssa Alyssa Gulledge (Inactive) added a comment - I think this got assigned to Ann by mistake
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                  hiralv Hiral Vora (Inactive) added a comment -

                  fixed.

                  Show
                  hiralv Hiral Vora (Inactive) added a comment - fixed.
                  Hide
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                  alyssa Alyssa Gulledge (Inactive) added a comment -

                  Adam - can you test this and see that it is fixed?

                  Show
                  alyssa Alyssa Gulledge (Inactive) added a comment - Adam - can you test this and see that it is fixed?
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                  adam Adam Baxter (Inactive) added a comment -

                  This problem is fixed. Tested with SVN 7970.

                  Show
                  adam Adam Baxter (Inactive) added a comment - This problem is fixed. Tested with SVN 7970.
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                  kkubiak Katharine Kubiak (Inactive) added a comment -

                  Passed v9854 Windows

                  Show
                  kkubiak Katharine Kubiak (Inactive) added a comment - Passed v9854 Windows
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                  anuj Anuj Puram (Inactive) added a comment -

                  Passed 6.7.0 (9891) on Mac

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                  anuj Anuj Puram (Inactive) added a comment - Passed 6.7.0 (9891) on Mac
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                  fwang4 Fuquan Wang (Inactive) added a comment -

                  Passed on 7.0.0 (11945) Mac.

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                  fwang4 Fuquan Wang (Inactive) added a comment - Passed on 7.0.0 (11945) Mac.
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                  richard Richard Linchangco (Inactive) added a comment -

                  Passed V.13526, Mac, Java 1.06.0_37

                  Show
                  richard Richard Linchangco (Inactive) added a comment - Passed V.13526, Mac, Java 1.06.0_37
                  Hide
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                  richard Richard Linchangco (Inactive) added a comment -

                  Passed V.13655, Mac, Java 1.06.0_37

                  Show
                  richard Richard Linchangco (Inactive) added a comment - Passed V.13655, Mac, Java 1.06.0_37

                    People

                    • Assignee:
                      Unassigned
                      Reporter:
                      adam Adam Baxter (Inactive)
                    • Votes:
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                      Dates

                      • Created:
                        Updated:
                        Resolved: