java.lang.ClassCastException: java.lang.Character cannot be cast to java.lang.String

biostars.org | 8 months ago
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  1. 0

    picard: error reading BAM file

    biostars.org | 8 months ago
    java.lang.ClassCastException: java.lang.Character cannot be cast to java.lang.String

    Root Cause Analysis

    1. java.lang.ClassCastException

      java.lang.Character cannot be cast to java.lang.String

      at htsjdk.samtools.SAMRecord.isValid()
    2. HTS JDK
      SamFileValidator.validateSamFileSummary
      1. htsjdk.samtools.SAMRecord.isValid(SAMRecord.java:2000)
      2. htsjdk.samtools.SAMRecord.isValid(SAMRecord.java:1854)
      3. htsjdk.samtools.SamFileValidator.validateSamRecordsAndQualityFormat(SamFileValidator.java:274)
      4. htsjdk.samtools.SamFileValidator.validateSamFile(SamFileValidator.java:200)
      5. htsjdk.samtools.SamFileValidator.validateSamFileSummary(SamFileValidator.java:128)
      5 frames
    3. picard.sam
      ValidateSamFile.doWork
      1. picard.sam.ValidateSamFile.doWork(ValidateSamFile.java:187)
      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