Uses of Class artificialFastqGenerator.Read
Date: 2014-10-01

## Uses of Class
artificialFastqGenerator.Read

- - ### Uses of Read in artificialFastqGenerator

    Methods in artificialFastqGenerator that return Read
    Modifier and Type | Method and Description
    --- | ---
    `Read` | Read.`getPairedEndRead()` Get the read with which this read object forms a pair.

    Methods in artificialFastqGenerator that return types with arguments of type Read
    Modifier and Type | Method and Description
    --- | ---
    `java.util.ArrayList<Read>` | Nucleobase.`getCoveringReads()` Get the list of covering reads - the reads which include this nucleobase.

    Methods in artificialFastqGenerator with parameters of type Read
    Modifier and Type | Method and Description
    --- | ---
    `void` | Nucleobase.`addCoveringRead(Read read)` Add a read to the list of reads which cover this nucleobase.
    `void` | Read.`setPairedEndRead(Read pairedEndRead)` Set the read with which this read object forms a pair.
    `void` | Read.`updateNucleobaseCoverage(Read read)` For each of the reference genome nucleobases in this read, add the read into the nucleobase's covering reads ArrayList.

    Constructors in artificialFastqGenerator with parameters of type Read
    Constructor and Description
    `Read(java.util.ArrayList<Nucleobase> sequence, long uniqueID, Read pairedEndRead, boolean leftPEAndNeedsWriting, char[] encodedQualityScores, char[] genotypesThatAreRead, int xCoordinate, int yCoordinate)` Initialise a new Read object.