Package ngs

Interface Read

    • Method Detail

      • getReadId

        java.lang.String getReadId()
                            throws ErrorMsg
        getReadId
        Returns:
        the ID-String of the Read
        Throws:
        ErrorMsg - upon an error accessing data
      • getNumFragments

        int getNumFragments()
                     throws ErrorMsg
        getNumFragments
        Returns:
        the number of biological Fragments contained in the read
        Throws:
        ErrorMsg - upon an error accessing data
      • fragmentIsAligned

        boolean fragmentIsAligned​(int fragIdx)
                           throws ErrorMsg
        fragmentIsAligned
        Parameters:
        fragIdx - is a zero-based and non-negative fragment index
        Returns:
        true if a fragment is aligned
        Throws:
        ErrorMsg - upon an error accessing data
      • getReadCategory

        int getReadCategory()
                     throws ErrorMsg
        getReadCategory
        Returns:
        the category of the read
        Throws:
        ErrorMsg - upon an error accessing data
      • getReadGroup

        java.lang.String getReadGroup()
                               throws ErrorMsg
        getReadGroup
        Returns:
        the read-group of the read
        Throws:
        ErrorMsg - upon an error accessing data
      • getReadName

        java.lang.String getReadName()
                              throws ErrorMsg
        getReadName
        Returns:
        the name of thethe read
        Throws:
        ErrorMsg - upon an error accessing data
      • getReadBases

        java.lang.String getReadBases()
                               throws ErrorMsg
        getReadBases
        Returns:
        sequence bases
        Throws:
        ErrorMsg - upon an error accessing data
      • getReadBases

        java.lang.String getReadBases​(long offset)
                               throws ErrorMsg,
                                      java.lang.IndexOutOfBoundsException
        getReadBases
        Parameters:
        offset - is zero-based and non-negative
        Returns:
        sequence bases
        Throws:
        ErrorMsg - upon an error accessing data
        java.lang.IndexOutOfBoundsException - if offset is invalid
      • getReadBases

        java.lang.String getReadBases​(long offset,
                                      long length)
                               throws ErrorMsg,
                                      java.lang.IndexOutOfBoundsException
        getReadBases
        Parameters:
        offset - is zero-based and non-negative
        length - must be ≥ 0
        Returns:
        sequence bases
        Throws:
        ErrorMsg - upon an error accessing data
        java.lang.IndexOutOfBoundsException - if offset/length are invalid
      • getReadQualities

        java.lang.String getReadQualities()
                                   throws ErrorMsg
        getReadQualities
        Returns:
        phred quality values using ASCII offset of 33
        Throws:
        ErrorMsg - upon an error accessing data
      • getReadQualities

        java.lang.String getReadQualities​(long offset)
                                   throws ErrorMsg,
                                          java.lang.IndexOutOfBoundsException
        getReadQualities
        Parameters:
        offset - is zero-based and non-negative
        Returns:
        phred quality values using ASCII offset of 33
        Throws:
        ErrorMsg - upon an error accessing data
        java.lang.IndexOutOfBoundsException - if offset is invalid
      • getReadQualities

        java.lang.String getReadQualities​(long offset,
                                          long length)
                                   throws ErrorMsg,
                                          java.lang.IndexOutOfBoundsException
        getReadQualities
        Parameters:
        offset - is zero-based and non-negative
        length - must be ≥ 0
        Returns:
        phred quality values using ASCII offset of 33
        Throws:
        ErrorMsg - upon an error accessing data
        java.lang.IndexOutOfBoundsException - if offset/length are invalid