java.lang.IllegalArgumentException: Invalid reference index -1

GitHub | dthach1 | 10 months ago
tip
Click on the to mark the solution that helps you, Samebug will learn from it.
As a community member, you’ll be rewarded for you help.
  1. 0

    Reordersam bug?

    GitHub | 10 months ago | dthach1
    java.lang.IllegalArgumentException: Invalid reference index -1

    Root Cause Analysis

    1. java.lang.IllegalArgumentException

      Invalid reference index -1

      at htsjdk.samtools.QueryInterval.<init>()
    2. HTS JDK
      SamReader$PrimitiveSamReaderToSamReaderAdapter.query
      1. htsjdk.samtools.QueryInterval.<init>(QueryInterval.java:24)
      2. htsjdk.samtools.SamReader$PrimitiveSamReaderToSamReaderAdapter.query(SamReader.java:503)
      2 frames
    3. picard.sam
      ReorderSam.doWork
      1. picard.sam.ReorderSam.doWork(ReorderSam.java:124)
      1 frame
    4. picard.cmdline
      PicardCommandLine.main
      1. picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:209)
      2. picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:95)
      3. picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:105)
      3 frames