java.lang.ArrayIndexOutOfBoundsException: -4

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via broadinstitute.org by Unknown author, 2 years ago
java.lang.ArrayIndexOutOfBoundsException: -4
at org.broadinstitute.sting.utils.baq.BAQ.calcEpsilon(BAQ.java:158)
at org.broadinstitute.sting.utils.baq.BAQ.hmm_glocal(BAQ.java:246)
at org.broadinstitute.sting.utils.baq.BAQ.calcBAQFromHMM(BAQ.java:542)
at org.broadinstitute.sting.utils.baq.BAQ.calcBAQFromHMM(BAQ.java:595)
at org.broadinstitute.sting.utils.baq.BAQ.calcBAQFromHMM(BAQ.java:530)
at org.broadinstitute.sting.utils.baq.BAQ.baqRead(BAQ.java:663)
at org.broadinstitute.sting.gatk.walkers.bqsr.BaseRecalibrator.calculateBAQArray(BaseRecalibrator.java:428)
at org.broadinstitute.sting.gatk.walkers.bqsr.BaseRecalibrator.map(BaseRecalibrator.java:243)
at org.broadinstitute.sting.gatk.walkers.bqsr.BaseRecalibrator.map(BaseRecalibrator.java:112)
at org.broadinstitute.sting.gatk.traversals.TraverseReadsNano$TraverseReadsMap.apply(TraverseReadsNano.java:203)
at org.broadinstitute.sting.gatk.traversals.TraverseReadsNano$TraverseReadsMap.apply(TraverseReadsNano.java:191)
at org.broadinstitute.sting.utils.nanoScheduler.NanoScheduler$MapReduceJob.run(NanoScheduler.java:468)
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)
at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:334)
at java.util.concurrent.FutureTask.run(FutureTask.java:166)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1110)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:603)
at java.lang.Thread.run(Thread.java:679)

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