/usr/include/ngs/inl/Alignment.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_alignment_
#define _inl_ngs_alignment_
#ifndef _hpp_ngs_alignment_
#include <ngs/Alignment.hpp>
#endif
#ifndef _hpp_ngs_itf_alignmentitf_
#include <ngs/itf/AlignmentItf.hpp>
#endif
namespace ngs
{
// the "self" member is typed as FragmentRef
// but is used here as an AlignmentRef
#define self reinterpret_cast < const AlignmentItf * > ( self )
/*----------------------------------------------------------------------
* Alignment
* inline dispatch
*/
inline
StringRef Alignment :: getAlignmentId () const
throw ( ErrorMsg )
{ return StringRef ( self -> getAlignmentId () ); }
inline
String Alignment :: getReferenceSpec () const
throw ( ErrorMsg )
{ return StringRef ( self -> getReferenceSpec () ) . toString (); }
inline
int Alignment :: getMappingQuality () const
throw ( ErrorMsg )
{ return self -> getMappingQuality (); }
inline
StringRef Alignment :: getReferenceBases () const
throw ( ErrorMsg )
{ return StringRef ( self -> getReferenceBases () ); }
inline
String Alignment :: getReadGroup () const
throw ( ErrorMsg )
{ return StringRef ( self -> getReadGroup () ) . toString (); }
inline
StringRef Alignment :: getReadId () const
throw ( ErrorMsg )
{ return StringRef ( self -> getReadId () ); }
inline
StringRef Alignment :: getClippedFragmentBases () const
throw ( ErrorMsg )
{ return StringRef ( self -> getClippedFragmentBases () ); }
inline
StringRef Alignment :: getClippedFragmentQualities () const
throw ( ErrorMsg )
{ return StringRef ( self -> getClippedFragmentQualities () ); }
inline
StringRef Alignment :: getAlignedFragmentBases () const
throw ( ErrorMsg )
{ return StringRef ( self -> getAlignedFragmentBases () ); }
inline
Alignment :: AlignmentCategory Alignment :: getAlignmentCategory () const
throw ( ErrorMsg )
{ return ( Alignment :: AlignmentCategory ) self -> getAlignmentCategory (); }
inline
int64_t Alignment :: getAlignmentPosition () const
throw ( ErrorMsg )
{ return self -> getAlignmentPosition (); }
inline
uint64_t Alignment :: getReferencePositionProjectionRange (int64_t ref_pos) const
throw ( ErrorMsg )
{ return self -> getReferencePositionProjectionRange (ref_pos); }
inline
uint64_t Alignment :: getAlignmentLength () const
throw ( ErrorMsg )
{ return self -> getAlignmentLength (); }
inline
bool Alignment :: getIsReversedOrientation () const
throw ( ErrorMsg )
{ return self -> getIsReversedOrientation (); }
inline
int Alignment :: getSoftClip ( ClipEdge edge ) const
throw ( ErrorMsg )
{ return self -> getSoftClip ( edge ); }
inline
uint64_t Alignment :: getTemplateLength () const
throw ( ErrorMsg )
{ return self -> getTemplateLength (); }
inline
StringRef Alignment :: getShortCigar ( bool clipped ) const
throw ( ErrorMsg )
{ return StringRef ( self -> getShortCigar ( clipped ) ); }
inline
StringRef Alignment :: getLongCigar ( bool clipped ) const
throw ( ErrorMsg )
{ return StringRef ( self -> getLongCigar ( clipped ) ); }
inline
char Alignment :: getRNAOrientation () const
throw ( ErrorMsg )
{ return self -> getRNAOrientation (); }
inline
bool Alignment :: hasMate () const
throw ()
{ return self -> hasMate (); }
inline
StringRef Alignment :: getMateAlignmentId () const
throw ( ErrorMsg )
{ return StringRef ( self -> getMateAlignmentId () ); }
inline
Alignment Alignment :: getMateAlignment () const
throw ( ErrorMsg )
{ return Alignment ( ( AlignmentRef ) self -> getMateAlignment () ); }
inline
String Alignment :: getMateReferenceSpec () const
throw ( ErrorMsg )
{ return StringRef ( self -> getMateReferenceSpec () ) . toString (); }
inline
bool Alignment :: getMateIsReversedOrientation () const
throw ( ErrorMsg )
{ return self -> getMateIsReversedOrientation (); }
#undef self
} // namespace ngs
#endif // _inl_ngs_alignment_
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