/usr/include/ngs/inl/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 _inl_ngs_reference_
#define _inl_ngs_reference_
#ifndef _hpp_ngs_reference_
#include <ngs/Reference.hpp>
#endif
#ifndef _hpp_ngs_itf_referenceitf_
#include <ngs/itf/ReferenceItf.hpp>
#endif
namespace ngs
{
/*----------------------------------------------------------------------
* Reference
*/
inline
String Reference :: getCommonName () const
throw ( ErrorMsg )
{ return StringRef ( self -> getCommonName () ) . toString (); }
inline
String Reference :: getCanonicalName () const
throw ( ErrorMsg )
{ return StringRef ( self -> getCanonicalName () ) . toString (); }
inline
bool Reference :: getIsCircular () const
throw ( ErrorMsg )
{ return self -> getIsCircular (); }
inline
uint64_t Reference :: getLength () const
throw ( ErrorMsg )
{ return self -> getLength (); }
inline
String Reference :: getReferenceBases ( uint64_t offset ) const
throw ( ErrorMsg )
{ return StringRef ( self -> getReferenceBases ( offset ) ) . toString (); }
inline
String Reference :: getReferenceBases ( uint64_t offset, uint64_t length ) const
throw ( ErrorMsg )
{ return StringRef ( self -> getReferenceBases ( offset, length ) ) . toString (); }
inline
StringRef Reference :: getReferenceChunk ( uint64_t offset ) const
throw ( ErrorMsg )
{ return StringRef ( self -> getReferenceChunk ( offset ) ); }
inline
StringRef Reference :: getReferenceChunk ( uint64_t offset, uint64_t length ) const
throw ( ErrorMsg )
{ return StringRef ( self -> getReferenceChunk ( offset, length ) ); }
inline
uint64_t Reference :: getAlignmentCount () const
throw ( ErrorMsg )
{ return self -> getAlignmentCount (); }
inline
uint64_t Reference :: getAlignmentCount ( Alignment :: AlignmentCategory categories ) const
throw ( ErrorMsg )
{ return self -> getAlignmentCount ( ( uint32_t ) categories ); }
inline
Alignment Reference :: getAlignment ( const String & alignmentId ) const
throw ( ErrorMsg )
{ return Alignment ( ( AlignmentRef ) self -> getAlignment ( alignmentId . c_str () ) ); }
inline
AlignmentIterator Reference :: getAlignments ( Alignment :: AlignmentCategory categories ) const
throw ( ErrorMsg )
{ return AlignmentIterator ( ( AlignmentRef ) self -> getAlignments ( ( uint32_t ) categories ) ); }
inline
AlignmentIterator Reference :: getAlignmentSlice ( int64_t start, uint64_t length ) const
throw ( ErrorMsg )
{ return AlignmentIterator ( ( AlignmentRef ) self -> getAlignmentSlice ( start, length ) ); }
inline
AlignmentIterator Reference :: getAlignmentSlice ( int64_t start, uint64_t length, Alignment :: AlignmentCategory categories ) const
throw ( ErrorMsg )
{ return AlignmentIterator ( ( AlignmentRef ) self -> getAlignmentSlice ( start, length, ( uint32_t ) categories ) ); }
inline
AlignmentIterator Reference :: getFilteredAlignmentSlice ( int64_t start, uint64_t length, Alignment :: AlignmentCategory categories, Alignment :: AlignmentFilter filters, int32_t mappingQuality ) const
throw ( ErrorMsg )
{ return AlignmentIterator ( ( AlignmentRef ) self -> getFilteredAlignmentSlice ( start, length, ( uint32_t ) categories, ( uint32_t ) filters, mappingQuality ) ); }
inline
PileupIterator Reference :: getPileups ( Alignment :: AlignmentCategory categories ) const
throw ( ErrorMsg )
{ return PileupIterator ( ( PileupRef ) self -> getPileups ( ( uint32_t ) categories ) ); }
inline
PileupIterator Reference :: getFilteredPileups ( Alignment :: AlignmentCategory categories, Alignment :: AlignmentFilter filters, int32_t mappingQuality ) const
throw ( ErrorMsg )
{ return PileupIterator ( ( PileupRef ) self -> getFilteredPileups ( ( uint32_t ) categories, ( uint32_t ) filters, mappingQuality ) ); }
inline
PileupIterator Reference :: getPileupSlice ( int64_t start, uint64_t length ) const
throw ( ErrorMsg )
{ return PileupIterator ( ( PileupRef ) self -> getPileupSlice ( start, length ) ); }
inline
PileupIterator Reference :: getPileupSlice ( int64_t start, uint64_t length, Alignment :: AlignmentCategory categories ) const
throw ( ErrorMsg )
{ return PileupIterator ( ( PileupRef ) self -> getPileupSlice ( start, length, ( uint32_t ) categories ) ); }
inline
PileupIterator Reference :: getFilteredPileupSlice ( int64_t start, uint64_t length, Alignment :: AlignmentCategory categories, Alignment :: AlignmentFilter filters, int32_t mappingQuality ) const
throw ( ErrorMsg )
{ return PileupIterator ( ( PileupRef ) self -> getFilteredPileupSlice ( start, length, ( uint32_t ) categories, ( uint32_t ) filters, mappingQuality ) ); }
} // namespace ngs
#endif // _inl_ngs_reference_
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