Jannovar errors on vcf import

[jvlasblom]

While importing I get an error. The offending line is the 'getTranscriptModelBuilder' call below, which returns null:

private static void inputTranscriptModelDataFromRefSeq() {
        // parse GFF/GTF
        GFFparser gff = new GFFparser();
        try {
            transcriptModelList = gff.getTranscriptModelBuilder().buildTranscriptModels();

Note this object is (the transcriptbuilder) is not initialized in Jannovar until a file is parsed: https://github.com/charite/jannovar/blob/master/src/main/java/jannovar/io/GFFparser.java#L190

2014-01-16 13:53:19,733 37539 [AWT-EventQueue-0] ERROR org.ut.biolab.medsavant.client.util.notification.VisibleMedSavantWorker - FAILED java.lang.NullPointerException at org.ut.biolab.medsavant.server.db.variants.Jannovar.inputTranscriptModelDataFromRefSeq(Jannovar.java:145) at org.ut.biolab.medsavant.server.db.variants.Jannovar.downloadSerializedFile(Jannovar.java:119) at org.ut.biolab.medsavant.server.db.variants.Jannovar.initialize(Jannovar.java:95) at org.ut.biolab.medsavant.server.db.variants.Jannovar.annotateVCFFiles(Jannovar.java:56) at org.ut.biolab.medsavant.server.db.variants.VariantManager.uploadVariants(VariantManager.java:300) at org.ut.biolab.medsavant.server.db.variants.VariantManager.uploadVariants(VariantManager.java:241) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:606) at sun.rmi.server.UnicastServerRef.dispatch(UnicastServerRef.java:322) at sun.rmi.transport.Transport$1.run(Transport.java:177) at sun.rmi.transport.Transport$1.run(Transport.java:174) at java.security.AccessController.doPrivileged(Native Method) at sun.rmi.transport.Transport.serviceCall(Transport.java:173) at sun.rmi.transport.tcp.TCPTransport.handleMessages(TCPTransport.java:556) at sun.rmi.transport.tcp.TCPTransport$ConnectionHandler.run0(TCPTransport.java:811) at sun.rmi.transport.tcp.TCPTransport$ConnectionHandler.run(TCPTransport.java:670) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615) at java.lang.Thread.run(Thread.java:744) at sun.rmi.transport.StreamRemoteCall.exceptionReceivedFromServer(StreamRemoteCall.java:275) at sun.rmi.transport.StreamRemoteCall.executeCall(StreamRemoteCall.java:252) at sun.rmi.server.UnicastRef.invoke(UnicastRef.java:161) at java.rmi.server.RemoteObjectInvocationHandler.invokeRemoteMethod(RemoteObjectInvocationHandler.java:194) at java.rmi.server.RemoteObjectInvocationHandler.invoke(RemoteObjectInvocationHandler.java:148) at com.sun.proxy.$Proxy13.uploadVariants(Unknown Source) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:606) at org.ut.biolab.medsavant.client.util.ServerModificationInvocationHandler.invoke(ServerModificationInvocationHandler.java:24) at com.sun.proxy.$Proxy18.uploadVariants(Unknown Source) at org.ut.biolab.medsavant.client.variant.ImportVariantsWizardWithAnnotation$11$1$1.runInBackground(ImportVariantsWizardWithAnnotation.java:488) at org.ut.biolab.medsavant.client.variant.ImportVariantsWizardWithAnnotation$11$1$1.runInBackground(ImportVariantsWizardWithAnnotation.java:465) at org.ut.biolab.medsavant.client.util.notification.VisibleMedSavantWorker.doInBackground(VisibleMedSavantWorker.java:233) at org.ut.biolab.medsavant.client.util.MedSavantWorker$1.doInBackground(MedSavantWorker.java:67) at javax.swing.SwingWorker$1.call(SwingWorker.java:296) at java.util.concurrent.FutureTask.run(FutureTask.java:262) at javax.swing.SwingWorker.run(SwingWorker.java:335) at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471) at java.util.concurrent.FutureTask.run(FutureTask.java:262) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615) at java.lang.Thread.run(Thread.java:744)

[ronammar]

Is this using the Jannovar.java file I updated today?

[jvlasblom]

Yes, you can see the same code here, in your commit: https://github.com/compbio-UofT/medsavant/commit/dec2ab976df235e5f57b904f32c75afa4092596f

On 16/01/14 04:32 PM, ronammar wrote:

Is this using the Jannovar.java file I updated today?

— Reply to this email directly or view it on GitHub https://github.com/compbio-UofT/medsavant/issues/255#issuecomment-32549227.

[ronammar]

Ok, will debug and see if I can figure it out asap.