[BUG-27] Subsequent bam file loading causes Null Pointer Exception - JIRA UNCC

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

BUG-622 File format issues

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Adam Baxter (Inactive) created issue - 21/Mar/11 7:43 AM

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Adam Baxter (Inactive) added a comment - 21/Mar/11 7:43 AM

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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Adam Baxter (Inactive) added a comment - 21/Mar/11 7:43 AM 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 Gulledge (Inactive) added a comment - 04/Apr/11 11:38 AM

I think this got assigned to Ann by mistake

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Alyssa Gulledge (Inactive) added a comment - 04/Apr/11 11:38 AM I think this got assigned to Ann by mistake

Alyssa Gulledge (Inactive) made changes - 04/Apr/11 11:38 AM

Field	Original Value	New Value
Assignee	Ann Loraine [ aloraine ]	Hiral Vora [ hiralv ]

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Hiral Vora (Inactive) added a comment - 04/Apr/11 12:50 PM

fixed.

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Hiral Vora (Inactive) added a comment - 04/Apr/11 12:50 PM fixed.

Hiral Vora (Inactive) made changes - 04/Apr/11 12:50 PM

Assignee

Hiral Vora [ hiralv ]

Alyssa Gulledge [ alyssa ]

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Alyssa Gulledge (Inactive) added a comment - 05/Apr/11 8:56 AM

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

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Alyssa Gulledge (Inactive) added a comment - 05/Apr/11 8:56 AM Adam - can you test this and see that it is fixed?

Alyssa Gulledge (Inactive) made changes - 05/Apr/11 8:56 AM

Assignee

Alyssa Gulledge [ alyssa ]

Adam Baxter [ adam ]

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Adam Baxter (Inactive) added a comment - 06/Apr/11 6:01 AM

This problem is fixed. Tested with SVN 7970.

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Adam Baxter (Inactive) added a comment - 06/Apr/11 6:01 AM This problem is fixed. Tested with SVN 7970.

Adam Baxter (Inactive) made changes - 06/Apr/11 6:01 AM

Assignee

Adam Baxter [ adam ]

Alyssa Gulledge [ alyssa ]

Alyssa Gulledge (Inactive) made changes - 06/Apr/11 6:20 AM

Status	Open [ 1 ]	Resolved [ 5 ]
Resolution		Fixed [ 1 ]

Alyssa Gulledge (Inactive) made changes - 06/Apr/11 6:20 AM

Status

Resolved [ 5 ]

Closed [ 6 ]

Alyssa Gulledge (Inactive) made changes - 08/Apr/11 10:45 AM

Project	IGB6.5 [ 10010 ]	Bug Repository [ 10030 ]
Key	~~IGB-106~~	~~BUG-27~~

Alyssa Gulledge (Inactive) made changes - 31/Aug/11 5:26 AM

Resolution	Fixed [ 1 ]
Status	Closed [ 6 ]	Reopened [ 4 ]

David Norris (Inactive) made changes - 31/Aug/11 12:49 PM

Assignee

Alyssa Gulledge [ alyssa ]

David Norris (Inactive) made changes - 31/Aug/11 12:49 PM

Status	Reopened [ 4 ]	Resolved [ 5 ]
Resolution		Fixed [ 1 ]

David Norris (Inactive) made changes - 31/Aug/11 12:49 PM

Status

Resolved [ 5 ]

Closed [ 6 ]

Alyssa Gulledge (Inactive) made changes - 10/Jan/12 8:41 AM

Resolution	Fixed [ 1 ]
Status	Closed [ 6 ]	Reopened [ 4 ]
Assignee		Katharine Kubiak [ kkubiak ]

Katharine Kubiak (Inactive) made changes - 17/Jan/12 11:07 AM

Assignee

Katharine Kubiak [ kkubiak ]

Alyssa Gulledge [ alyssa ]

Alyssa Gulledge (Inactive) made changes - 17/Jan/12 11:10 AM

Assignee

Alyssa Gulledge [ alyssa ]

Katharine Kubiak [ kkubiak ]

Alyssa Gulledge (Inactive) made changes - 17/Jan/12 11:12 AM

Description

Process:
Chose Species Arabidopsis thaliana and version A_thaliana_Jun_2009.
Load the Whole Genome of TAIR10mRNA from the Bioviz(QuickLoad) site.

(Load the files from tophat-1.1.4-new-pilot-pollen-processed)
Drag in'treatment_drought1_out.sm.bam'
Set load mode to 'Region In View' and click 'Refresh Data'
Drag in 'treatment_drought2_out.sm.bam'
Set load mode to 'Region In View' and click 'Refresh Data'

Result:
IGB does not load the drought2 file and the logs show an Null Pointer exception (in comments).

Problem does not occur if both files are dragged in at the same time, then have their data refreshed.

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.

Katharine Kubiak (Inactive) made changes - 18/Jan/12 10:51 AM

Comment

[ Do not have files ]

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Katharine Kubiak (Inactive) added a comment - 18/Jan/12 10:51 AM

Passed v9854 Windows

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Katharine Kubiak (Inactive) added a comment - 18/Jan/12 10:51 AM Passed v9854 Windows

Katharine Kubiak (Inactive) made changes - 18/Jan/12 10:51 AM

Assignee

Katharine Kubiak [ kkubiak ]

Anuj Puram [ anuj ]

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Anuj Puram (Inactive) added a comment - 20/Jan/12 4:23 AM

Passed 6.7.0 (9891) on Mac

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Anuj Puram (Inactive) added a comment - 20/Jan/12 4:23 AM Passed 6.7.0 (9891) on Mac

Anuj Puram (Inactive) made changes - 20/Jan/12 4:23 AM

Assignee

Anuj Puram [ anuj ]

Alyssa Gulledge [ alyssa ]

Alyssa Gulledge (Inactive) made changes - 23/Jan/12 4:04 AM

Status	Reopened [ 4 ]	Resolved [ 5 ]
Resolution		Fixed [ 1 ]

Alyssa Gulledge (Inactive) made changes - 23/Jan/12 4:04 AM

Status	Resolved [ 5 ]	Closed [ 6 ]
Assignee	Alyssa Gulledge [ alyssa ]

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Fuquan Wang (Inactive) added a comment - 12/Jun/12 11:11 AM

Passed on 7.0.0 (11945) Mac.

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Fuquan Wang (Inactive) added a comment - 12/Jun/12 11:11 AM Passed on 7.0.0 (11945) Mac.

Fuquan Wang (Inactive) made changes - 12/Jun/12 11:11 AM

Resolution	Fixed [ 1 ]
Status	Closed [ 6 ]	Reopened [ 4 ]
Assignee		Fuquan Wang [ fwang4 ]

Fuquan Wang (Inactive) made changes - 12/Jun/12 11:11 AM

Status	Reopened [ 4 ]	Resolved [ 5 ]
Assignee	Fuquan Wang [ fwang4 ]
Resolution		Fixed [ 1 ]

Richard Linchangco (Inactive) made changes - 13/Nov/12 10:20 AM

Resolution	Fixed [ 1 ]
Status	Resolved [ 5 ]	Reopened [ 4 ]

Alyssa Gulledge (Inactive) made changes - 15/Nov/12 9:56 AM

Link

This issue relates to ~~BUG-622~~ [ ~~BUG-622~~ ]

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Richard Linchangco (Inactive) added a comment - 27/Nov/12 9:22 AM

Passed V.13526, Mac, Java 1.06.0_37

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Richard Linchangco (Inactive) added a comment - 27/Nov/12 9:22 AM Passed V.13526, Mac, Java 1.06.0_37

Richard Linchangco (Inactive) made changes - 27/Nov/12 9:22 AM

Status	Reopened [ 4 ]	Resolved [ 5 ]
Assignee		Alyssa Gulledge [ alyssa ]
Resolution		Fixed [ 1 ]

Alyssa Gulledge (Inactive) made changes - 28/Nov/12 11:01 AM

Resolution	Fixed [ 1 ]
Status	Resolved [ 5 ]	Reopened [ 4 ]
Assignee	Alyssa Gulledge [ alyssa ]

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Richard Linchangco (Inactive) added a comment - 04/Dec/12 7:04 AM

Passed V.13655, Mac, Java 1.06.0_37

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Richard Linchangco (Inactive) added a comment - 04/Dec/12 7:04 AM Passed V.13655, Mac, Java 1.06.0_37

Richard Linchangco (Inactive) made changes - 04/Dec/12 7:04 AM

Status	Reopened [ 4 ]	Resolved [ 5 ]
Assignee		Alyssa Gulledge [ alyssa ]
Resolution		Fixed [ 1 ]

Alyssa Gulledge (Inactive) made changes - 04/Dec/12 8:26 AM

Assignee

Alyssa Gulledge [ alyssa ]

Alyssa Gulledge (Inactive) made changes - 04/Dec/12 8:28 AM

Status

Resolved [ 5 ]

Closed [ 6 ]

People

Assignee:

Unassigned

Reporter:

Adam Baxter (Inactive)

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Dates

Created:

21/Mar/11 7:43 AM

Updated:

04/Dec/12 8:28 AM

Resolved:

04/Dec/12 7:04 AM