java.lang.IndexOutOfBoundsException: Index (-1) is negative

GitHub | fac2003 | 4 years ago
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    RealignmentProcessor can visit negative genome coordinates

    GitHub | 4 years ago | fac2003
    java.lang.IndexOutOfBoundsException: Index (-1) is negative

    Root Cause Analysis

    1. java.lang.IndexOutOfBoundsException

      Index (-1) is negative

      at it.unimi.dsi.bits.AbstractBitVector.ensureRestrictedIndex()
    2. DSI Utilities
      AbstractBitVector.getBoolean
      1. it.unimi.dsi.bits.AbstractBitVector.ensureRestrictedIndex(AbstractBitVector.java:58)
      2. it.unimi.dsi.bits.LongArrayBitVector.getBoolean(LongArrayBitVector.java:366)
      3. it.unimi.dsi.bits.AbstractBitVector.getBoolean(AbstractBitVector.java:90)
      3 frames
    3. fastutil
      AbstractBooleanList.get
      1. it.unimi.dsi.fastutil.booleans.AbstractBooleanList.get(AbstractBooleanList.java:391)
      1 frame
    4. edu.cornell.med
      GobyDriver.main
      1. edu.cornell.med.icb.goby.reads.RandomAccessSequenceCache.get(RandomAccessSequenceCache.java:351)
      2. edu.cornell.med.icb.goby.alignments.processors.RealignmentProcessor.realign(RealignmentProcessor.java:328)
      3. edu.cornell.med.icb.goby.alignments.processors.RealignmentProcessor.realign(RealignmentProcessor.java:223)
      4. edu.cornell.med.icb.goby.alignments.processors.RealignmentProcessor.nextRealignedEntry(RealignmentProcessor.java:165)
      5. edu.cornell.med.icb.goby.alignments.processors.LocalSortProcessor.nextRealignedEntry(LocalSortProcessor.java:106)
      6. edu.cornell.med.icb.goby.alignments.IterateSortedAlignments.iterate(IterateSortedAlignments.java:327)
      7. edu.cornell.med.icb.goby.modes.DiscoverSequenceVariantsMode.execute(DiscoverSequenceVariantsMode.java:727)
      8. edu.cornell.med.icb.goby.modes.GenericToolsDriver.execute(GenericToolsDriver.java:219)
      9. edu.cornell.med.icb.goby.modes.GobyDriver.main(GobyDriver.java:55)
      9 frames