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 -- You received this bug notification because you are a member of Ubuntu Bugs, which is subscribed to Ubuntu. https://bugs.launchpad.net/bugs/1476650 Title: IGV hangs when using hg19 To manage notifications about this bug go to: https://bugs.launchpad.net/ubuntu/+source/igv/+bug/1476650/+subscriptions -- ubuntu-bugs mailing list ubuntu-bugs@lists.ubuntu.com https://lists.ubuntu.com/mailman/listinfo/ubuntu-bugs