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    testambiguity.out

    Output of SliceService calculations on testambiguity.xml

    The first run uses the default level of high quality (qv=30). The second explicitly sets the value to 20.

    Notice the same consensus quality values can be represented by different ambiguity codes depending on the level of high quality used.

    SliceService -q -v -c testambiguity.xml
    <Consensus>
      <Nuc>ACGT-ACGTAAACCGaRWWYD</Nuc>
      <Qualclass>9 9 9 9 21 13 13 13 13 13 13 13 13 13 13 22 22 22 22 22 22</Qualclass>
      <Qualval>45 45 45 45 45 25 25 25 25 25 25 25 25 25 25 15 15 15 15 15 3</Qualval>
    </Consensus>
    
    SliceService -q -v -c --highQuality 20 testambiguity.xml
    <Consensus>
      <Nuc>ACGT-ACGTAAACCGaRWWYD</Nuc>
      <Qualclass>9 9 9 9 21 20 20 20 20 20 20 20 20 20 20 22 22 22 22 22 22</Qualclass>
      <Qualval>45 45 45 45 45 25 25 25 25 25 25 25 25 25 25 15 15 15 15 15 3</Qualval>
    </Consensus>