java.lang.IndexOutOfBoundsException

GitHub | achevali | 3 months ago
  1. 0

    How to handle index out of bounds exception from a ByteBuffer

    Stack Overflow | 1 year ago | John E.
    java.lang.IndexOutOfBoundsException
  2. 0

    GitHub comment 1566#238864313

    GitHub | 4 months ago | slivne
    java.lang.IndexOutOfBoundsException
  3. Speed up your debug routine!

    Automated exception search integrated into your IDE

  4. 0

    ERB parsing in JRuby 1.6.6

    GitHub | 5 years ago | hartjus
    java.lang.IndexOutOfBoundsException

    Not finding the right solution?
    Take a tour to get the most out of Samebug.

    Tired of useless tips?

    Automated exception search integrated into your IDE

    Root Cause Analysis

    1. java.lang.IndexOutOfBoundsException

      No message provided

      at java.nio.ByteBuffer.wrap()
    2. Java RT
      ByteBuffer.wrap
      1. java.nio.ByteBuffer.wrap(ByteBuffer.java:375)
      1 frame
    3. HTS JDK
      BAMRecord.getCigar
      1. htsjdk.samtools.BAMRecord.getCigar(BAMRecord.java:246)
      1 frame
    4. org.seqdoop.hadoop_bam
      AnySAMInputFormat.getSplits
      1. org.seqdoop.hadoop_bam.BAMSplitGuesser.guessNextBAMRecordStart(BAMSplitGuesser.java:189)
      2. org.seqdoop.hadoop_bam.BAMInputFormat.addProbabilisticSplits(BAMInputFormat.java:244)
      3. org.seqdoop.hadoop_bam.BAMInputFormat.getSplits(BAMInputFormat.java:159)
      4. org.seqdoop.hadoop_bam.AnySAMInputFormat.getSplits(AnySAMInputFormat.java:253)
      4 frames
    5. Spark
      RDD$$anonfun$partitions$2.apply
      1. org.apache.spark.rdd.NewHadoopRDD.getPartitions(NewHadoopRDD.scala:120)
      2. org.apache.spark.rdd.RDD$$anonfun$partitions$2.apply(RDD.scala:239)
      3. org.apache.spark.rdd.RDD$$anonfun$partitions$2.apply(RDD.scala:237)
      3 frames
    6. Scala
      Option.getOrElse
      1. scala.Option.getOrElse(Option.scala:120)
      1 frame
    7. Spark
      RDD$$anonfun$partitions$2.apply
      1. org.apache.spark.rdd.RDD.partitions(RDD.scala:237)
      2. org.apache.spark.rdd.MapPartitionsRDD.getPartitions(MapPartitionsRDD.scala:35)
      3. org.apache.spark.rdd.RDD$$anonfun$partitions$2.apply(RDD.scala:239)
      4. org.apache.spark.rdd.RDD$$anonfun$partitions$2.apply(RDD.scala:237)
      4 frames
    8. Scala
      Option.getOrElse
      1. scala.Option.getOrElse(Option.scala:120)
      1 frame
    9. Spark
      RDD$$anonfun$partitions$2.apply
      1. org.apache.spark.rdd.RDD.partitions(RDD.scala:237)
      2. org.apache.spark.rdd.MapPartitionsRDD.getPartitions(MapPartitionsRDD.scala:35)
      3. org.apache.spark.rdd.RDD$$anonfun$partitions$2.apply(RDD.scala:239)
      4. org.apache.spark.rdd.RDD$$anonfun$partitions$2.apply(RDD.scala:237)
      4 frames
    10. Scala
      Option.getOrElse
      1. scala.Option.getOrElse(Option.scala:120)
      1 frame
    11. Spark
      RDD$$anonfun$partitions$2.apply
      1. org.apache.spark.rdd.RDD.partitions(RDD.scala:237)
      2. org.apache.spark.rdd.MapPartitionsRDD.getPartitions(MapPartitionsRDD.scala:35)
      3. org.apache.spark.rdd.RDD$$anonfun$partitions$2.apply(RDD.scala:239)
      4. org.apache.spark.rdd.RDD$$anonfun$partitions$2.apply(RDD.scala:237)
      4 frames
    12. Scala
      Option.getOrElse
      1. scala.Option.getOrElse(Option.scala:120)
      1 frame
    13. Spark
      RDD$$anonfun$partitions$2.apply
      1. org.apache.spark.rdd.RDD.partitions(RDD.scala:237)
      2. org.apache.spark.rdd.MapPartitionsRDD.getPartitions(MapPartitionsRDD.scala:35)
      3. org.apache.spark.rdd.RDD$$anonfun$partitions$2.apply(RDD.scala:239)
      4. org.apache.spark.rdd.RDD$$anonfun$partitions$2.apply(RDD.scala:237)
      4 frames
    14. Scala
      Option.getOrElse
      1. scala.Option.getOrElse(Option.scala:120)
      1 frame
    15. Spark
      RDD$$anonfun$partitions$2.apply
      1. org.apache.spark.rdd.RDD.partitions(RDD.scala:237)
      2. org.apache.spark.rdd.MapPartitionsRDD.getPartitions(MapPartitionsRDD.scala:35)
      3. org.apache.spark.rdd.RDD$$anonfun$partitions$2.apply(RDD.scala:239)
      4. org.apache.spark.rdd.RDD$$anonfun$partitions$2.apply(RDD.scala:237)
      4 frames
    16. Scala
      Option.getOrElse
      1. scala.Option.getOrElse(Option.scala:120)
      1 frame
    17. Spark
      RDD$$anonfun$partitions$2.apply
      1. org.apache.spark.rdd.RDD.partitions(RDD.scala:237)
      2. org.apache.spark.rdd.MapPartitionsRDD.getPartitions(MapPartitionsRDD.scala:35)
      3. org.apache.spark.rdd.RDD$$anonfun$partitions$2.apply(RDD.scala:239)
      4. org.apache.spark.rdd.RDD$$anonfun$partitions$2.apply(RDD.scala:237)
      4 frames
    18. Scala
      Option.getOrElse
      1. scala.Option.getOrElse(Option.scala:120)
      1 frame
    19. Spark
      RDD$$anonfun$partitions$2.apply
      1. org.apache.spark.rdd.RDD.partitions(RDD.scala:237)
      2. org.apache.spark.rdd.MapPartitionsRDD.getPartitions(MapPartitionsRDD.scala:35)
      3. org.apache.spark.rdd.RDD$$anonfun$partitions$2.apply(RDD.scala:239)
      4. org.apache.spark.rdd.RDD$$anonfun$partitions$2.apply(RDD.scala:237)
      4 frames
    20. Scala
      Option.getOrElse
      1. scala.Option.getOrElse(Option.scala:120)
      1 frame
    21. Spark
      RDD$$anonfun$partitions$2.apply
      1. org.apache.spark.rdd.RDD.partitions(RDD.scala:237)
      2. org.apache.spark.rdd.MapPartitionsRDD.getPartitions(MapPartitionsRDD.scala:35)
      3. org.apache.spark.rdd.RDD$$anonfun$partitions$2.apply(RDD.scala:239)
      4. org.apache.spark.rdd.RDD$$anonfun$partitions$2.apply(RDD.scala:237)
      4 frames
    22. Scala
      Option.getOrElse
      1. scala.Option.getOrElse(Option.scala:120)
      1 frame
    23. Spark
      AbstractJavaRDDLike.countByValue
      1. org.apache.spark.rdd.RDD.partitions(RDD.scala:237)
      2. org.apache.spark.Partitioner$.defaultPartitioner(Partitioner.scala:65)
      3. org.apache.spark.rdd.PairRDDFunctions$$anonfun$reduceByKey$3.apply(PairRDDFunctions.scala:331)
      4. org.apache.spark.rdd.PairRDDFunctions$$anonfun$reduceByKey$3.apply(PairRDDFunctions.scala:331)
      5. org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:150)
      6. org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:111)
      7. org.apache.spark.rdd.RDD.withScope(RDD.scala:316)
      8. org.apache.spark.rdd.PairRDDFunctions.reduceByKey(PairRDDFunctions.scala:330)
      9. org.apache.spark.rdd.PairRDDFunctions$$anonfun$countByKey$1.apply(PairRDDFunctions.scala:381)
      10. org.apache.spark.rdd.PairRDDFunctions$$anonfun$countByKey$1.apply(PairRDDFunctions.scala:381)
      11. org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:150)
      12. org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:111)
      13. org.apache.spark.rdd.RDD.withScope(RDD.scala:316)
      14. org.apache.spark.rdd.PairRDDFunctions.countByKey(PairRDDFunctions.scala:380)
      15. org.apache.spark.rdd.RDD$$anonfun$countByValue$1.apply(RDD.scala:1187)
      16. org.apache.spark.rdd.RDD$$anonfun$countByValue$1.apply(RDD.scala:1187)
      17. org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:150)
      18. org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:111)
      19. org.apache.spark.rdd.RDD.withScope(RDD.scala:316)
      20. org.apache.spark.rdd.RDD.countByValue(RDD.scala:1186)
      21. org.apache.spark.api.java.JavaRDDLike$class.countByValue(JavaRDDLike.scala:461)
      22. org.apache.spark.api.java.AbstractJavaRDDLike.countByValue(JavaRDDLike.scala:46)
      22 frames
    24. org.broadinstitute.hellbender
      Main.main
      1. org.broadinstitute.hellbender.tools.genome.SparkGenomeReadCounts.collectReads(SparkGenomeReadCounts.java:134)
      2. org.broadinstitute.hellbender.tools.genome.SparkGenomeReadCounts.runTool(SparkGenomeReadCounts.java:213)
      3. org.broadinstitute.hellbender.engine.spark.GATKSparkTool.runPipeline(GATKSparkTool.java:313)
      4. org.broadinstitute.hellbender.engine.spark.SparkCommandLineProgram.doWork(SparkCommandLineProgram.java:38)
      5. org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:108)
      6. org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:166)
      7. org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:185)
      8. org.broadinstitute.hellbender.Main.instanceMain(Main.java:76)
      9. org.broadinstitute.hellbender.Main.main(Main.java:92)
      9 frames