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)
This bug was fixed in the package igv - 2.4.14+dfsg-2
---------------
igv (2.4.14+dfsg-2) unstable; urgency=medium
[ Olivier Sallou ]
fix for FTBS openjdk 11, Closes: #895765
- thanks to Markus Koschany <email address hidden>
-- Olivier Sallou <email address hidden> Tue, 23 Oct 2018 14:55:18 +0200