Package ngs

Interface Reference

  • All Known Subinterfaces:
    ReferenceIterator

    public interface Reference
    Represents a reference sequence
    • Method Detail

      • getCommonName

        java.lang.String getCommonName()
                                throws ErrorMsg
        getCommonName
        Returns:
        the common name of reference, e.g. "chr1"
        Throws:
        ErrorMsg - if no common name found
      • getCanonicalName

        java.lang.String getCanonicalName()
                                   throws ErrorMsg
        getCanonicalName
        Returns:
        the accessioned name of reference, e.g. "NC_000001.11"
        Throws:
        ErrorMsg - if no cannonical name found
      • getIsCircular

        boolean getIsCircular()
                       throws ErrorMsg
        getIsCircular
        Returns:
        true if reference is circular
        Throws:
        ErrorMsg - if cannot detect if reference is circular
      • getIsLocal

        boolean getIsLocal()
                    throws ErrorMsg
        getIsLocal
        Returns:
        true if Reference is stored locally within the ReadCollection. Unique Reference sequences are stored locally, while Publicly available Reference sequences are stored externally. An exception to this rule is when a public Reference is small, in which case the sequence will be available both locally and externally
        Throws:
        ErrorMsg - if cannot detect if reference is local
      • getLength

        long getLength()
                throws ErrorMsg
        getLength
        Returns:
        the length of the reference sequence
        Throws:
        ErrorMsg - if length cannot be detected
      • getReferenceBases

        java.lang.String getReferenceBases​(long offset)
                                    throws ErrorMsg
        getReferenceBases
        Parameters:
        offset - is zero-based and non-negative
        Returns:
        sub-sequence bases for Reference
        Throws:
        ErrorMsg - if no reference-bases found at offset
      • getReferenceBases

        java.lang.String getReferenceBases​(long offset,
                                           long length)
                                    throws ErrorMsg
        getReferenceBases
        Parameters:
        offset - is zero-based and non-negative
        length - must be ≥ 0
        Returns:
        sub-sequence bases for Reference
        Throws:
        ErrorMsg - if no reference-bases found at offset or lenght invalid
      • getReferenceChunk

        java.lang.String getReferenceChunk​(long offset)
                                    throws ErrorMsg
        getReferenceChunk
        Parameters:
        offset - is zero-based and non-negative
        Returns:
        largest contiguous chunk available of sub-sequence bases for Reference

        NB - actual returned sequence may be shorter than requested. to obtain all bases available in chunk, use a negative "size" value

        Throws:
        ErrorMsg - if no ReferenceChunk found
      • getReferenceChunk

        java.lang.String getReferenceChunk​(long offset,
                                           long length)
                                    throws ErrorMsg
        getReferenceChunk
        Parameters:
        offset - is zero-based and non-negative
        length - must be > 0
        Returns:
        largest contiguous chunk available of sub-sequence bases for Reference

        NB - actual returned sequence may be shorter than requested. to obtain all bases available in chunk, use a negative "size" value

        Throws:
        ErrorMsg - if no ReferenceChunk found
      • getAlignmentCount

        long getAlignmentCount()
                        throws ErrorMsg
        Count all Alignments within the Reference
        Returns:
        0 if there are no aligned Reads, > 0 otherwise
        Throws:
        ErrorMsg - upon an error accessing data
      • getAlignment

        Alignment getAlignment​(java.lang.String alignmentId)
                        throws ErrorMsg
        getAlignment
        Parameters:
        alignmentId - the ID of the Alignment to be returned
        Returns:
        an individual Alignment
        Throws:
        ErrorMsg - if Alignment does not exist or is not part of this Reference
      • getAlignments

        AlignmentIterator getAlignments​(int categories)
                                 throws ErrorMsg
        getAlignments
        Parameters:
        categories - the or'ed list of categories
        Returns:
        an iterator of contained alignments
        Throws:
        ErrorMsg - if no Iterator can be created
      • getAlignmentSlice

        AlignmentIterator getAlignmentSlice​(long start,
                                            long length)
                                     throws ErrorMsg
        getAlignmentSlice
        Parameters:
        start - is a signed 0-based offset from the start of the Reference
        length - is the length of the slice.
        Returns:
        an iterator across a range of Alignments
        Throws:
        ErrorMsg - if no Iterator can be created
      • getAlignmentSlice

        AlignmentIterator getAlignmentSlice​(long start,
                                            long length,
                                            int categories)
                                     throws ErrorMsg
        getAlignmentSlice
        Parameters:
        start - is a signed 0-based offset from the start of the Reference
        length - is the length of the slice.
        categories - provides a means of filtering by AlignmentCategory
        Returns:
        an iterator across a range of Alignments
        Throws:
        ErrorMsg - if no Iterator can be created
      • getFilteredAlignmentSlice

        AlignmentIterator getFilteredAlignmentSlice​(long start,
                                                    long length,
                                                    int categories,
                                                    int filters,
                                                    int mappingQuality)
                                             throws ErrorMsg
        getFilteredAlignmentSlice Behaves like "getAlignmentSlice" except that supported filters are applied to selection
        Parameters:
        start - is a signed 0-based offset from the start of the Reference
        length - is the length of the slice.
        categories - provides a means of filtering by AlignmentCategory
        filters - is a set of filter bits defined in Alignment
        mappingQuality - is a cutoff to be used according to bits in "filter"
        Returns:
        an iterator across a range of Alignments
        Throws:
        ErrorMsg - if no Iterator can be created
      • getPileups

        PileupIterator getPileups​(int categories)
                           throws ErrorMsg
        getPileups
        Parameters:
        categories - is a bitfield of AlignmentCategory
        Returns:
        an iterator of contained Pileups
        Throws:
        ErrorMsg - if no Iterator can be created
      • getFilteredPileups

        PileupIterator getFilteredPileups​(int categories,
                                          int filters,
                                          int mappingQuality)
                                   throws ErrorMsg
        getFilteredPileups Filtered according to criteria in parameters
        Parameters:
        categories - is a bitfield of AlignmentCategory
        filters - is a set of filter bits defined in Alignment
        mappingQuality - is a cutoff to be used according to bits in "filter"
        Returns:
        an iterator of contained Pileups
        Throws:
        ErrorMsg - if no Iterator can be created
      • getPileupSlice

        PileupIterator getPileupSlice​(long start,
                                      long length)
                               throws ErrorMsg
        getPileupSlice Creates a PileupIterator on a slice (window) of reference
        Parameters:
        start - is the signed starting position on reference
        length - is the unsigned number of bases in the window
        Returns:
        an iterator of contained Pileups
        Throws:
        ErrorMsg - if no Iterator can be created
      • getPileupSlice

        PileupIterator getPileupSlice​(long start,
                                      long length,
                                      int categories)
                               throws ErrorMsg
        getPileupSlice Creates a PileupIterator on a slice (window) of reference
        Parameters:
        start - is the signed starting position on reference
        length - is the unsigned number of bases in the window
        categories - provides a means of filtering by AlignmentCategory
        Returns:
        an iterator of contained Pileups
        Throws:
        ErrorMsg - if no Iterator can be created
      • getFilteredPileupSlice

        PileupIterator getFilteredPileupSlice​(long start,
                                              long length,
                                              int categories,
                                              int filters,
                                              int mappingQuality)
                                       throws ErrorMsg
        getFilteredPileupSlice Creates a PileupIterator on a slice (window) of reference filtered according to criteria in parameters
        Parameters:
        start - is the signed starting position on reference
        length - is the unsigned number of bases in the window
        categories - provides a means of filtering by AlignmentCategory
        filters - is a set of filter bits defined in Alignment
        mappingQuality - is a cutoff to be used according to bits in "filter"
        Returns:
        an iterator of contained Pileups
        Throws:
        ErrorMsg - if no Iterator can be created