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    libSlice::ConsensusData Class Reference
    [C++ Interface]

    Detailed Description

    Stores all of the results of calculations on slices.

    Different attributes can be queried without rerunning the calculations. If a different quality threshold is desired, set a new quality threshold in the slice data, and create a new consensus data result

    Examples:

    SliceDataExample.cc.

    Definition at line 27 of file ConsensusData.hh.

    Public Member Functions

     ~ConsensusData ()
     Empty Deconstructor.

    char getConsensus () const
     Returns the consensus (which may be an ambiguity code).

    char getConsensusBase () const
     Return a single base consensus.

    char getAmbiguityCode () const
     Gets the consensus as an ambiguity code (which may be a single base).

    char getAmbiguityFlags () const
     Get the raw bit flags for which of the 5 bases are in the ambiguity code.

    int getQualityClass () const
     Gets the quality class of the slice.

    int getQualityValue () const
     Gets the consensus quality value of the slice.

    int getQualityValue (char base) const
     Gets the consensus quality value of the 5 different bases.

    long double getProbability (char base) const
     Gets the probability of error that the given base is the consensus.

    int testAmbiguityCode (char base) const
     Tests if the given base is part of the ambiguity code.


    Friends

    class SliceData
     Only SliceData can create ConsensusResult objects.

    Member Function Documentation

    long double libSlice::ConsensusData::getProbability (  char  base  )  const
     

    Gets the probability of error that the given base is the consensus.

    Parameters:
    base Base in {'A','C','G','T','-'}
    Return values:
    Error probability that the given base is the consensus

    Definition at line 137 of file ConsensusData.cc.

    int libSlice::ConsensusData::getQualityValue (  char  base  )  const
     

    Gets the consensus quality value of the 5 different bases.

    The consensus quality value of each base is a representation of the error probability that the given base is the true consensus.

    Parameters:
    base Base in {'A','C','G','T','-'}
    Return values:
    Consensus quality value of the specified base

    Definition at line 77 of file ConsensusData.cc.

    int libSlice::ConsensusData::testAmbiguityCode (  char  base  )  const
     

    Tests if the given base is part of the ambiguity code.

    This allows for tests to check the presense of any of the bases in the ambiguity code, including testing if '-' should be a part of the code in the extended ambiguity code set.

    Parameters:
    base Base in {'A','C','G','T','-'}
    Return values:
    Bool indicating if base should be included

    Definition at line 103 of file ConsensusData.cc.

    The documentation for this class was generated from the following files: