/*=========================================================================== * * PUBLIC DOMAIN NOTICE * National Center for Biotechnology Information * * This software/database is a "United States Government Work" under the * terms of the United States Copyright Act. It was written as part of * the author's official duties as a United States Government employee and * thus cannot be copyrighted. This software/database is freely available * to the public for use. The National Library of Medicine and the U.S. * Government have not placed any restriction on its use or reproduction. * * Although all reasonable efforts have been taken to ensure the accuracy * and reliability of the software and data, the NLM and the U.S. * Government do not and cannot warrant the performance or results that * may be obtained by using this software or data. The NLM and the U.S. * Government disclaim all warranties, express or implied, including * warranties of performance, merchantability or fitness for any particular * purpose. * * Please cite the author in any work or product based on this material. * * =========================================================================== * */ #ifndef _hpp_ngs_reference_ #define _hpp_ngs_reference_ #ifndef _hpp_ngs_alignment_iterator_ #include #endif #ifndef _hpp_ngs_pileup_iterator_ #include #endif namespace ngs { /*---------------------------------------------------------------------- * forwards and typedefs */ typedef class ReferenceItf * ReferenceRef; /*====================================================================== * Reference * represents a reference sequence */ class Reference { public: /* getCommonName * returns the common name of reference, e.g. "chr1" */ String getCommonName () const throw ( ErrorMsg ); /* getCanonicalName * returns the accessioned name of reference, e.g. "NC_000001.11" */ String getCanonicalName () const throw ( ErrorMsg ); /* getIsCircular * returns true if reference is circular */ bool getIsCircular () const throw ( ErrorMsg ); /* getLength * returns the length of the reference sequence */ uint64_t getLength () const throw ( ErrorMsg ); /* getReferenceBases * return sub-sequence bases for Reference * "offset" is zero-based */ String getReferenceBases ( uint64_t offset ) const throw ( ErrorMsg ); String getReferenceBases ( uint64_t offset, uint64_t length ) const throw ( ErrorMsg ); /* getReferenceChunk * return largest contiguous chunk available of * sub-sequence bases for Reference * "offset" is zero-based * * NB - actual returned sequence may be shorter * than requested. */ StringRef getReferenceChunk ( uint64_t offset ) const throw ( ErrorMsg ); StringRef getReferenceChunk ( uint64_t offset, uint64_t length ) const throw ( ErrorMsg ); /*------------------------------------------------------------------ * ALIGNMENTS */ /* getAlignmentCount * returns count of all alignments * "categories" provides a means of filtering by AlignmentCategory */ uint64_t getAlignmentCount () const throw ( ErrorMsg ); uint64_t getAlignmentCount ( Alignment :: AlignmentCategory categories ) const throw ( ErrorMsg ); /* getAlignment * returns an individual Alignment * throws ErrorMsg if Alignment does not exist * or is not part of this Reference */ Alignment getAlignment ( const String & alignmentId ) const throw ( ErrorMsg ); /* getAlignments * returns an iterator of contained alignments */ AlignmentIterator getAlignments ( Alignment :: AlignmentCategory categories ) const throw ( ErrorMsg ); /* getAlignmentSlice * returns an iterator across a slice of the Reference * * "start" is a 0-based signed offset from the start of the Reference * * "length" is the length of the slice. * will be truncated to the right edge of a non-circular Reference * or to the total length of a circular Reference. * * "categories" provides a means of filtering by AlignmentCategory */ AlignmentIterator getAlignmentSlice ( int64_t start, uint64_t length ) const throw ( ErrorMsg ); AlignmentIterator getAlignmentSlice ( int64_t start, uint64_t length, Alignment :: AlignmentCategory categories ) const throw ( ErrorMsg ); /* getFilteredAlignmentSlice * returns a filtered iterator across a slice of the Reference * behaves like "getAlignmentSlice" except that supported filters are applied to selection * "filters" is a set of filter bits defined in Alignment * "mappingQuality" is a cutoff to be used according to bits in "filters" */ AlignmentIterator getFilteredAlignmentSlice ( int64_t start, uint64_t length, Alignment :: AlignmentCategory categories, Alignment :: AlignmentFilter filters, int32_t mappingQuality ) const throw ( ErrorMsg ); /*------------------------------------------------------------------ * PILEUP */ /* getPileups * returns an iterator of contained Pileups * Alignments are filtered by rejecting failures and duplicates * No mapping qualities are taken into account. */ PileupIterator getPileups ( Alignment :: AlignmentCategory categories ) const throw ( ErrorMsg ); /* getFilteredPileups * returns an iterator of contained Pileups * filtered according to criteria in parameters * "filters" is a set of filter bits defined in Alignment * "mappingQuality" is a cutoff to be used according to bits in "filter" */ PileupIterator getFilteredPileups ( Alignment :: AlignmentCategory categories, Alignment :: AlignmentFilter filters, int32_t mappingQuality ) const throw ( ErrorMsg ); /* getPileupSlice * creates a PileupIterator on a slice (window) of reference * "start" is the signed starting position on reference * "length" is the number of bases in the window * "categories" provides a means of filtering by AlignmentCategory */ PileupIterator getPileupSlice ( int64_t start, uint64_t length ) const throw ( ErrorMsg ); PileupIterator getPileupSlice ( int64_t start, uint64_t length, Alignment :: AlignmentCategory categories ) const throw ( ErrorMsg ); /* getFilteredPileupSlice * creates a PileupIterator on a slice (window) of reference * filtered according to criteria in parameters * "filters" is a set of filter bits defined in Alignment * "mappingQuality" is a cutoff to be used according to bits in "filters" */ PileupIterator getFilteredPileupSlice ( int64_t start, uint64_t length, Alignment :: AlignmentCategory categories, Alignment :: AlignmentFilter filters, int32_t mappingQuality ) const throw ( ErrorMsg ); public: // C++ support Reference & operator = ( ReferenceRef ref ) throw (); Reference ( ReferenceRef ref ) throw (); Reference & operator = ( const Reference & obj ) throw ( ErrorMsg ); Reference ( const Reference & obj ) throw ( ErrorMsg ); ~ Reference () throw (); protected: ReferenceRef self; }; } // namespace ngs #ifndef _inl_ngs_reference_ #include #endif #endif // _hpp_ngs_reference_