Package ngs

Interface Fragment

    • Method Detail

      • getFragmentId

        java.lang.String getFragmentId()
                                throws ErrorMsg
        getFragmentId
        Returns:
        the unique ID of the fragment
        Throws:
        ErrorMsg - upon an error accessing data
      • getFragmentBases

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

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

        java.lang.String getFragmentBases​(long offset,
                                          long length)
                                   throws ErrorMsg,
                                          java.lang.IndexOutOfBoundsException
        getFragmentBases
        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 - upon invalid offset
      • getFragmentQualities

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

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

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

        boolean isPaired()
                  throws ErrorMsg
        isPaired
        Returns:
        true if fragment has a mate
        Throws:
        ErrorMsg - upon an error accessing data
      • isAligned

        boolean isAligned()
                   throws ErrorMsg
        check to see if Fragment has alignment data (requires interface 1.1)
        Returns:
        true if Fragment is aligned
        Throws:
        ErrorMsg - if object is invalid or implementation too old