java.lang.IllegalArgumentException: Malformed CIGAR string: 71M12D-1I30M

GitHub | JoKw | 5 months ago
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  1. 0

    GitHub comment 37#246365458

    GitHub | 5 months ago | JoKw
    java.lang.IllegalArgumentException: Malformed CIGAR string: 71M12D-1I30M
  2. 0

    CIGAR string parsing issues with alignments from bwa mem 0.7.12

    GitHub | 2 years ago | chapmanb
    java.lang.IllegalArgumentException: Malformed CIGAR string: 60S-1M1I25M15S

    Root Cause Analysis

    1. java.lang.IllegalArgumentException

      Malformed CIGAR string: 71M12D-1I30M

      at htsjdk.samtools.TextCigarCodec.decode()
    2. HTS JDK
      TextCigarCodec.decode
      1. htsjdk.samtools.TextCigarCodec.decode(TextCigarCodec.java:69)
      1 frame
    3. com.astrazeneca.vardict
      Main.main
      1. com.astrazeneca.vardict.VarDict.parseSAM(VarDict.java:1550)
      2. com.astrazeneca.vardict.VarDict.toVars(VarDict.java:2552)
      3. com.astrazeneca.vardict.VarDict.somaticNotParallel(VarDict.java:353)
      4. com.astrazeneca.vardict.VarDict.nonAmpVardict(VarDict.java:249)
      5. com.astrazeneca.vardict.VarDict.start(VarDict.java:65)
      6. com.astrazeneca.vardict.Main.run(Main.java:134)
      7. com.astrazeneca.vardict.Main.main(Main.java:25)
      7 frames