/usr/include/ngs/Reference.hpp is in libngs-sdk-dev 1.3.0-2.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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*
* 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 <ngs/AlignmentIterator.hpp>
#endif
#ifndef _hpp_ngs_pileup_iterator_
#include <ngs/PileupIterator.hpp>
#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 <ngs/inl/Reference.hpp>
#endif
#endif // _hpp_ngs_reference_
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