java.lang.IndexOutOfBoundsException

tip

Thrown to indicate that an index of some sort (such as to an array, to a string, or to a vector) is out of range. Applications can subclass this class to indicate similar exceptions.


rafael

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    • java.lang.IndexOutOfBoundsException: Index: 32, Size: 32 at java.util.ArrayList.rangeCheck(ArrayList.java:635) at java.util.ArrayList.get(ArrayList.java:411) at org.broadinstitute.gatk.tools.walkers.haplotypecaller.readthreading.DanglingChainMergingGraph.mergeDanglingTail(DanglingChainMergingGraph.java:272) at org.broadinstitute.gatk.tools.walkers.haplotypecaller.readthreading.DanglingChainMergingGraph.recoverDanglingTail(DanglingChainMergingGraph.java:184) at org.broadinstitute.gatk.tools.walkers.haplotypecaller.readthreading.DanglingChainMergingGraph.recoverDanglingTails(DanglingChainMergingGraph.java:131) at org.broadinstitute.gatk.tools.walkers.haplotypecaller.readthreading.ReadThreadingAssembler.createGraph(ReadThreadingAssembler.java:202) at org.broadinstitute.gatk.tools.walkers.haplotypecaller.readthreading.ReadThreadingAssembler.assemble(ReadThreadingAssembler.java:114) at org.broadinstitute.gatk.tools.walkers.haplotypecaller.LocalAssemblyEngine.runLocalAssembly(LocalAssemblyEngine.java:164) at org.broadinstitute.gatk.tools.walkers.haplotypecaller.HaplotypeCaller.assembleReads(HaplotypeCaller.java:1022) at org.broadinstitute.gatk.tools.walkers.haplotypecaller.HaplotypeCaller.map(HaplotypeCaller.java:882) at org.broadinstitute.gatk.tools.walkers.haplotypecaller.HaplotypeCaller.map(HaplotypeCaller.java:218) at org.broadinstitute.gatk.engine.traversals.TraverseActiveRegions$TraverseActiveRegionMap.apply(TraverseActiveRegions.java:708) at org.broadinstitute.gatk.engine.traversals.TraverseActiveRegions$TraverseActiveRegionMap.apply(TraverseActiveRegions.java:704) at org.broadinstitute.gatk.utils.nanoScheduler.NanoScheduler$ReadMapReduceJob.run(NanoScheduler.java:471) at java.util.concurrent.Executors$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:745)

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