Package ngs

Interface Reference

All Known Subinterfaces:
ReferenceIterator
public interface Reference
Represents a reference sequence

  • Method Details

    • getCommonName

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

    • getCanonicalName

      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

      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

      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

      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

      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

    • getAlignmentCount

      long getAlignmentCount(int categories) throws ErrorMsg
      Count selected Alignments within the Reference
      Parameters:
      categories - is a bitfield of AlignmentCategory
      Returns:
      count of all alignments
      Throws:
      ErrorMsg - if no AlignmentCount can be found
      See Also:

    • getAlignment

      Alignment getAlignment(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