Package ngs

Interface Alignment

  • All Superinterfaces:
    Fragment
    All Known Subinterfaces:
    AlignmentIterator

    public interface Alignment
    extends Fragment
    Represents an alignment between a Fragment and Reference sub-sequence provides a path to Read and mate Alignment
    • Method Detail

      • getAlignmentId

        java.lang.String getAlignmentId()
                                 throws ErrorMsg
        Retrieve an identifying String that can be used for later access. The id will be unique within ReadCollection.
        Returns:
        alignment id
        Throws:
        ErrorMsg - if the property cannot be retrieved
      • getReferenceSpec

        java.lang.String getReferenceSpec()
                                   throws ErrorMsg
        getReferenceSpec
        Returns:
        the name of the reference
        Throws:
        ErrorMsg - if the property cannot be retrieved
      • getMappingQuality

        int getMappingQuality()
                       throws ErrorMsg
        getMappingQuality
        Returns:
        mapping quality
        Throws:
        ErrorMsg - if the property cannot be retrieved
      • getReferenceBases

        java.lang.String getReferenceBases()
                                    throws ErrorMsg
        getReferenceBases
        Returns:
        reference bases
        Throws:
        ErrorMsg - if the property cannot be retrieved
      • getReadGroup

        java.lang.String getReadGroup()
                               throws ErrorMsg
        getReadGroup
        Returns:
        the name of the read-group
        Throws:
        ErrorMsg - if the property cannot be retrieved
      • getReadId

        java.lang.String getReadId()
                            throws ErrorMsg
        getReadId
        Returns:
        the unique name of the read
        Throws:
        ErrorMsg - if the property cannot be retrieved
      • getClippedFragmentBases

        java.lang.String getClippedFragmentBases()
                                          throws ErrorMsg
        getClippedFragmentBases
        Returns:
        clipped fragment bases
        Throws:
        ErrorMsg - if the property cannot be retrieved
      • getClippedFragmentQualities

        java.lang.String getClippedFragmentQualities()
                                              throws ErrorMsg
        getClippedFragmentQualities
        Returns:
        clipped fragment phred quality values using ASCII offset of 33
        Throws:
        ErrorMsg - if the property cannot be retrieved
      • getAlignedFragmentBases

        java.lang.String getAlignedFragmentBases()
                                          throws ErrorMsg
        getAlignedFragmentBases
        Returns:
        fragment bases in their aligned orientation
        Throws:
        ErrorMsg - if the property cannot be retrieved
      • getAlignmentCategory

        int getAlignmentCategory()
                          throws ErrorMsg
        Alignments are categorized as primary or secondary (alternate).
        Returns:
        either Alignment.primaryAlignment or Alignment.secondaryAlignment
        Throws:
        ErrorMsg - if the property cannot be retrieved
      • getAlignmentPosition

        long getAlignmentPosition()
                           throws ErrorMsg
        Retrieve the Alignment's starting position on the Reference
        Returns:
        unsigned 0-based offset from start of Reference
        Throws:
        ErrorMsg - if the property cannot be retrieved
      • getAlignmentLength

        long getAlignmentLength()
                         throws ErrorMsg
        Retrieve the projected length of an Alignment projected upon Reference.
        Returns:
        unsigned length of projection
        Throws:
        ErrorMsg - if the property cannot be retrieved
      • getIsReversedOrientation

        boolean getIsReversedOrientation()
                                  throws ErrorMsg
        Test if orientation is reversed with respect to the Reference sequence.
        Returns:
        true if reversed
        Throws:
        ErrorMsg - if the property cannot be retrieved
      • getSoftClip

        int getSoftClip​(int edge)
                 throws ErrorMsg
        getSoftClip
        Parameters:
        edge - which edge
        Returns:
        the position of the clipping
        Throws:
        ErrorMsg - if the property cannot be retrieved
      • getTemplateLength

        long getTemplateLength()
                        throws ErrorMsg
        getTemplateLength
        Returns:
        the lenght of the template
        Throws:
        ErrorMsg - if the property cannot be retrieved
      • getShortCigar

        java.lang.String getShortCigar​(boolean clipped)
                                throws ErrorMsg
        getShortCigar
        Parameters:
        clipped - selects if clipping has to be applied
        Returns:
        a text string describing alignment details
        Throws:
        ErrorMsg - if the property cannot be retrieved
      • getLongCigar

        java.lang.String getLongCigar​(boolean clipped)
                               throws ErrorMsg
        getLongCigar
        Parameters:
        clipped - selects if clipping has to be applied
        Returns:
        a text string describing alignment details
        Throws:
        ErrorMsg - if the property cannot be retrieved
      • getRNAOrientation

        char getRNAOrientation()
                        throws ErrorMsg
        getRNAOrientation
        Returns:
        '+' if positive strand is transcribed
        Throws:
        ErrorMsg - if the property cannot be retrieved
      • hasMate

        boolean hasMate()
        hasMate
        Returns:
        if the alignment has a mate
      • getMateAlignmentId

        java.lang.String getMateAlignmentId()
                                     throws ErrorMsg
        getMateAlignmentId
        Returns:
        unique ID of th alignment
        Throws:
        ErrorMsg - if the property cannot be retrieved
      • getMateAlignment

        Alignment getMateAlignment()
                            throws ErrorMsg
        getMateAlignment
        Returns:
        the mate as alignment
        Throws:
        ErrorMsg - if the property cannot be retrieved
      • getMateReferenceSpec

        java.lang.String getMateReferenceSpec()
                                       throws ErrorMsg
        getMateReferenceSpec
        Returns:
        the name of the reference the mate is aligned at
        Throws:
        ErrorMsg - if the property cannot be retrieved
      • getMateIsReversedOrientation

        boolean getMateIsReversedOrientation()
                                      throws ErrorMsg
        getMateIsReversedOrientation
        Returns:
        the orientation of the mate
        Throws:
        ErrorMsg - if the property cannot be retrieved