Public bug reported:
If you open a BAM file and select hg19 as the reference genome and then
navigate to any location, IGV hangs and you get the following stacktrace
on the command line:
ERROR [2015-07-21 14:45:01,686] [DefaultExceptionHandler.java:42]
[AWT-EventQueue-0] Unhandled exception
java.lang.NoClassDefFoundError: com/google/java/contract/util/Objects
at org.broad.igv.data.Interval.contains(Interval.java:59)
at
org.broad.igv.sam.AlignmentDataManager.getGroupedAlignmentsContaining(AlignmentDataManager.java:420)
at
org.broad.igv.sam.AlignmentTrack.getAlignmentAt(AlignmentTrack.java:758)
at
org.broad.igv.sam.AlignmentTrack.getValueStringAt(AlignmentTrack.java:747)
at
org.broad.igv.ui.panel.DataPanel.updateTooltipText(DataPanel.java:422)
at
org.broad.igv.ui.panel.DataPanel$DataPanelMouseAdapter.mouseMoved(DataPanel.java:565)
at java.awt.AWTEventMulticaster.mouseMoved(AWTEventMulticaster.java:329)
at java.awt.Component.processMouseMotionEvent(Component.java:6561)
at javax.swing.JComponent.processMouseMotionEvent(JComponent.java:3330)
at java.awt.Component.processEvent(Component.java:6285)
at java.awt.Container.processEvent(Container.java:2229)
at java.awt.Component.dispatchEventImpl(Component.java:4872)
at java.awt.Container.dispatchEventImpl(Container.java:2287)
at java.awt.Component.dispatchEvent(Component.java:4698)
at
java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4832)
at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4505)
at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4422)
at java.awt.Container.dispatchEventImpl(Container.java:2273)
at java.awt.Window.dispatchEventImpl(Window.java:2719)
at java.awt.Component.dispatchEvent(Component.java:4698)
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:747)
at java.awt.EventQueue.access$300(EventQueue.java:103)
at java.awt.EventQueue$3.run(EventQueue.java:706)
at java.awt.EventQueue$3.run(EventQueue.java:704)
at java.security.AccessController.doPrivileged(Native Method)
at
java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:76)
at
java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:87)
at java.awt.EventQueue$4.run(EventQueue.java:720)
at java.awt.EventQueue$4.run(EventQueue.java:718)
at java.security.AccessController.doPrivileged(Native Method)
at
java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:76)
at java.awt.EventQueue.dispatchEvent(EventQueue.java:717)
at
java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:242)
at
java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:161)
at
java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:150)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:146)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:138)
at java.awt.EventDispatchThread.run(EventDispatchThread.java:91)
ProblemType: Bug
DistroRelease: Ubuntu 14.04
Package: igv 2.3.14+dfsg-2
ProcVersionSignature: Ubuntu 3.13.0-57.95-generic 3.13.11-ckt21
Uname: Linux 3.13.0-57-generic x86_64
NonfreeKernelModules: nvidia
ApportVersion: 2.14.1-0ubuntu3.11
Architecture: amd64
CurrentDesktop: Unity
Date: Tue Jul 21 14:46:33 2015
InstallationDate: Installed on 2014-12-31 (202 days ago)
InstallationMedia: Ubuntu 14.04.1 LTS "Trusty Tahr" - Release amd64 (20140722.2)
PackageArchitecture: all
SourcePackage: igv
UpgradeStatus: No upgrade log present (probably fresh install)
** Affects: igv (Ubuntu)
Importance: Undecided
Status: New
** Tags: amd64 apport-bug third-party-packages trusty
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https://bugs.launchpad.net/bugs/1476650
Title:
IGV hangs when using hg19
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