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

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java.lang.IndexOutOfBoundsException: Index (-1) is negative
at it.unimi.dsi.bits.AbstractBitVector.ensureRestrictedIndex(AbstractBitVector.java:58)
at it.unimi.dsi.bits.LongArrayBitVector.getBoolean(LongArrayBitVector.java:366)
at it.unimi.dsi.bits.AbstractBitVector.getBoolean(AbstractBitVector.java:90)
at edu.cornell.med.icb.goby.reads.RandomAccessSequenceCache.get(RandomAccessSequenceCache.java:351)
at edu.cornell.med.icb.goby.alignments.processors.RealignmentProcessor.realign(RealignmentProcessor.java:328)
at edu.cornell.med.icb.goby.alignments.processors.RealignmentProcessor.realign(RealignmentProcessor.java:223)
at edu.cornell.med.icb.goby.alignments.processors.RealignmentProcessor.nextRealignedEntry(RealignmentProcessor.java:165)
at edu.cornell.med.icb.goby.alignments.processors.LocalSortProcessor.nextRealignedEntry(LocalSortProcessor.java:106)
at edu.cornell.med.icb.goby.alignments.IterateSortedAlignments.iterate(IterateSortedAlignments.java:327)
at edu.cornell.med.icb.goby.modes.DiscoverSequenceVariantsMode.execute(DiscoverSequenceVariantsMode.java:727)
at edu.cornell.med.icb.goby.modes.GenericToolsDriver.execute(GenericToolsDriver.java:219)
at edu.cornell.med.icb.goby.modes.GobyDriver.main(GobyDriver.java:55)

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