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  1. Bug Repository
  2. BUG-468

Sliced View has some significant issues with showing bam files

    Details

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

      Description

      Usually I just get 3 pages of 'stack overflow errors.

      This time, I loaded a bam track, picked a gene with a low number of reads and then went to sliced view, got this error:

      Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException
      at com.affymetrix.genoviz.bioviews.Scene.removeGlyph(Scene.java:391)
      at com.affymetrix.genoviz.widget.NeoMap.removeItem(NeoMap.java:1021)
      at com.affymetrix.igb.tiers.AffyTieredMap.removeItem(AffyTieredMap.java:277)
      at com.affymetrix.igb.tiers.AffyTieredMap.removeTier(AffyTieredMap.java:296)
      at com.affymetrix.igb.tiers.AffyLabelledTierMap.removeTier(AffyLabelledTierMap.java:251)
      at com.affymetrix.igb.view.SeqMapView.copyMapTierGlyphs(SeqMapView.java:946)
      at com.affymetrix.igb.view.SeqMapView.setAnnotatedSeq(SeqMapView.java:752)
      at com.affymetrix.igb.view.AltSpliceSeqMapView.setAnnotatedSeq(AltSpliceSeqMapView.java:327)
      at com.affymetrix.igb.view.SeqMapView.setAnnotatedSeq(SeqMapView.java:700)
      at com.affymetrix.igb.view.AltSpliceSeqMapView.setAnnotatedSeq(AltSpliceSeqMapView.java:62)
      at com.affymetrix.igb.view.SeqMapView.setAnnotatedSeq(SeqMapView.java:686)
      at com.affymetrix.igb.view.AltSpliceSeqMapView.sliceAndDiceNow(AltSpliceSeqMapView.java:295)
      at com.affymetrix.igb.view.AltSpliceSeqMapView.mapRefresh(AltSpliceSeqMapView.java:215)
      at com.affymetrix.igb.view.SeqMapView.setAnnotatedSeq(SeqMapView.java:869)
      at com.affymetrix.igb.view.SeqMapView.updatePanel(SeqMapView.java:2575)
      at com.affymetrix.igb.view.SeqMapView.updatePanel(SeqMapView.java:2583)
      at com.affymetrix.igb.trackAdjuster.TrackAdjusterTab$2.actionPerformed(TrackAdjusterTab.java:213)
      at com.jidesoft.combobox.AbstractComboBox.fireActionEvent(Unknown Source)
      at com.jidesoft.combobox.AbstractComboBox.setSelectedItem(Unknown Source)
      at com.jidesoft.combobox.ColorComboBox.setSelectedItem(Unknown Source)
      at com.jidesoft.combobox.AbstractComboBox.setSelectedItem(Unknown Source)
      at com.jidesoft.combobox.ColorComboBox.setSelectedColor(Unknown Source)
      at com.affymetrix.igb.trackAdjuster.TrackAdjusterTab.resetStylePanel(TrackAdjusterTab.java:537)
      at com.affymetrix.igb.trackAdjuster.TrackAdjusterTab.refreshSelection(TrackAdjusterTab.java:480)
      at com.affymetrix.igb.trackAdjuster.TrackAdjusterTab.symSelectionChanged(TrackAdjusterTab.java:462)
      at com.affymetrix.genometryImpl.GenometryModel.fireSymSelectionEvent(GenometryModel.java:226)
      at com.affymetrix.genometryImpl.GenometryModel.setSelectedSymmetries(GenometryModel.java:241)
      at com.affymetrix.igb.view.SeqMapView.postSelections(SeqMapView.java:1436)
      at com.affymetrix.igb.view.SeqMapViewMouseListener.processSelections(SeqMapViewMouseListener.java:335)
      at com.affymetrix.igb.view.SeqMapViewMouseListener.mouseReleased(SeqMapViewMouseListener.java:131)
      at com.affymetrix.genoviz.widget.NeoWidget.heardMouseEvent(NeoWidget.java:1279)
      at com.affymetrix.genoviz.widget.NeoMap.heardMouseEvent(NeoMap.java:1540)
      at com.affymetrix.genoviz.widget.NeoAbstractWidget.mouseReleased(NeoAbstractWidget.java:815)
      at com.affymetrix.genoviz.bioviews.View.heardMouseEvent(View.java:923)
      at com.affymetrix.genoviz.bioviews.View.mouseReleased(View.java:841)
      at java.awt.AWTEventMulticaster.mouseReleased(AWTEventMulticaster.java:272)
      at java.awt.AWTEventMulticaster.mouseReleased(AWTEventMulticaster.java:272)
      at java.awt.AWTEventMulticaster.mouseReleased(AWTEventMulticaster.java:272)
      at java.awt.Component.processMouseEvent(Component.java:6373)
      at javax.swing.JComponent.processMouseEvent(JComponent.java:3267)
      at java.awt.Component.processEvent(Component.java:6138)
      at java.awt.Container.processEvent(Container.java:2085)
      at java.awt.Component.dispatchEventImpl(Component.java:4735)
      at java.awt.Container.dispatchEventImpl(Container.java:2143)
      at java.awt.Component.dispatchEvent(Component.java:4565)
      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:4565)
      at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:679)
      at java.awt.EventQueue.access$000(EventQueue.java:85)
      at java.awt.EventQueue$1.run(EventQueue.java:638)
      at java.awt.EventQueue$1.run(EventQueue.java:636)
      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:652)
      at java.awt.EventQueue$2.run(EventQueue.java:650)
      at java.security.AccessController.doPrivileged(Native Method)
      at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87)
      at java.awt.EventQueue.dispatchEvent(EventQueue.java:649)
      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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            Hide
            hiralv Hiral Vora (Inactive) added a comment -

            Try r11894 or later.

            Show
            hiralv Hiral Vora (Inactive) added a comment - Try r11894 or later.
            Hide
            kkubiak Katharine Kubiak (Inactive) added a comment -

            No errors on Windows v12138

            Have tried loading several BAMs, zoomed in and out, selected different reads, all sorts of different things and could not get an error.

            Show
            kkubiak Katharine Kubiak (Inactive) added a comment - No errors on Windows v12138 Have tried loading several BAMs, zoomed in and out, selected different reads, all sorts of different things and could not get an error.
            Hide
            richard Richard Linchangco (Inactive) added a comment -

            Passed V.13782, Mac, Java 1.7.0_10

            This particular bug passed. Tested with 1, then 2, then 3 bam files. Colors for the tracks, ORFs, etc were all changed. 'Stack Height' was adjusted, reads were selected and the 'Sliced View' viewer was zoomed in and out without producing any errors.

            Show
            richard Richard Linchangco (Inactive) added a comment - Passed V.13782, Mac, Java 1.7.0_10 This particular bug passed. Tested with 1, then 2, then 3 bam files. Colors for the tracks, ORFs, etc were all changed. 'Stack Height' was adjusted, reads were selected and the 'Sliced View' viewer was zoomed in and out without producing any errors.

              People

              • Assignee:
                Unassigned
                Reporter:
                alyssa Alyssa Gulledge (Inactive)
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                0 Start watching this issue

                Dates

                • Created:
                  Updated:
                  Resolved: