java.lang.IllegalArgumentException: the 'to' index must be between 'from' and the length of the data/position sequence

GitHub | asmirnov239 | 7 months ago
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  1. 0

    GenotypeCopyNumberTriStateSegments fails when when the ReadCountsCollection targets differ from input target list

    GitHub | 7 months ago | asmirnov239
    java.lang.IllegalArgumentException: the 'to' index must be between 'from' and the length of the data/position sequence

    Root Cause Analysis

    1. java.lang.IllegalArgumentException

      the 'to' index must be between 'from' and the length of the data/position sequence

      at org.broadinstitute.hellbender.utils.Utils.validateArg()
    2. org.broadinstitute.hellbender
      GenotypeCopyNumberTriStateSegments.lambda$calculateLog10GP$6
      1. org.broadinstitute.hellbender.utils.Utils.validateArg(Utils.java:609)
      2. org.broadinstitute.hellbender.utils.param.ParamUtils.inRange(ParamUtils.java:80)
      3. org.broadinstitute.hellbender.utils.hmm.ForwardBackwardAlgorithm$Result.logProbability(ForwardBackwardAlgorithm.java:141)
      4. org.broadinstitute.hellbender.tools.exome.germlinehmm.GenotypeCopyNumberTriStateSegments.lambda$calculateLog10GP$6(GenotypeCopyNumberTriStateSegments.java:197)
      4 frames
    3. Java RT
      DoublePipeline.toArray
      1. java.util.stream.ReferencePipeline$6$1.accept(ReferencePipeline.java:244)
      2. java.util.Spliterators$ArraySpliterator.forEachRemaining(Spliterators.java:948)
      3. java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:481)
      4. java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:471)
      5. java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:545)
      6. java.util.stream.AbstractPipeline.evaluateToArrayNode(AbstractPipeline.java:260)
      7. java.util.stream.DoublePipeline.toArray(DoublePipeline.java:506)
      7 frames
    4. org.broadinstitute.hellbender
      GenotypeCopyNumberTriStateSegments.lambda$composeVariantContext$0
      1. org.broadinstitute.hellbender.tools.exome.germlinehmm.GenotypeCopyNumberTriStateSegments.calculateLog10GP(GenotypeCopyNumberTriStateSegments.java:198)
      2. org.broadinstitute.hellbender.tools.exome.germlinehmm.GenotypeCopyNumberTriStateSegments.lambda$composeVariantContext$0(GenotypeCopyNumberTriStateSegments.java:125)
      2 frames
    5. Java RT
      ReferencePipeline.collect
      1. java.util.stream.IntPipeline$4$1.accept(IntPipeline.java:250)
      2. java.util.stream.Streams$RangeIntSpliterator.forEachRemaining(Streams.java:110)
      3. java.util.Spliterator$OfInt.forEachRemaining(Spliterator.java:693)
      4. java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:481)
      5. java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:471)
      6. java.util.stream.ReduceOps$ReduceOp.evaluateSequential(ReduceOps.java:708)
      7. java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234)
      8. java.util.stream.ReferencePipeline.collect(ReferencePipeline.java:499)
      8 frames
    6. org.broadinstitute.hellbender
      CommandLineProgram.instanceMain
      1. org.broadinstitute.hellbender.tools.exome.germlinehmm.GenotypeCopyNumberTriStateSegments.composeVariantContext(GenotypeCopyNumberTriStateSegments.java:141)
      2. org.broadinstitute.hellbender.tools.exome.germlinehmm.GenotypeCopyNumberTriStateSegments.makeCalls(GenotypeCopyNumberTriStateSegments.java:104)
      3. org.broadinstitute.hellbender.tools.exome.germlinehmm.CopyNumberTriStateSegmentCaller.doWork(CopyNumberTriStateSegmentCaller.java:121)
      4. org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:108)
      5. org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:166)
      6. org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:185)
      6 frames