/usr/include/ngs/itf/AlignmentItf.hpp is in libngs-sdk-dev 1.3.0-2.
This file is owned by root:root, with mode 0o644.
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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.
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#ifndef _hpp_ngs_itf_alignment_
#define _hpp_ngs_itf_alignment_
#ifndef _hpp_ngs_itf_refcount
#include <ngs/itf/Refcount.hpp>
#endif
struct NGS_Alignment_v1;
namespace ngs
{
/*----------------------------------------------------------------------
* forwards
*/
class StringItf;
/*----------------------------------------------------------------------
* AlignmentItf
*/
class AlignmentItf : public Refcount < AlignmentItf, NGS_Alignment_v1 >
{
public:
StringItf * getAlignmentId () const
throw ( ErrorMsg );
StringItf * getReferenceSpec () const
throw ( ErrorMsg );
int32_t getMappingQuality () const
throw ( ErrorMsg );
StringItf * getReferenceBases () const
throw ( ErrorMsg );
StringItf * getReadGroup () const
throw ( ErrorMsg );
StringItf * getReadId () const
throw ( ErrorMsg );
StringItf * getClippedFragmentBases () const
throw ( ErrorMsg );
StringItf * getClippedFragmentQualities () const
throw ( ErrorMsg );
StringItf * getAlignedFragmentBases () const
throw ( ErrorMsg );
uint32_t getAlignmentCategory () const
throw ( ErrorMsg );
int64_t getAlignmentPosition () const
throw ( ErrorMsg );
uint64_t getReferencePositionProjectionRange ( int64_t ref_pos ) const
throw ( ErrorMsg );
uint64_t getAlignmentLength () const
throw ( ErrorMsg );
bool getIsReversedOrientation () const
throw ( ErrorMsg );
int32_t getSoftClip ( uint32_t edge ) const
throw ( ErrorMsg );
uint64_t getTemplateLength () const
throw ( ErrorMsg );
StringItf * getShortCigar ( bool clipped ) const
throw ( ErrorMsg );
StringItf * getLongCigar ( bool clipped ) const
throw ( ErrorMsg );
char getRNAOrientation () const
throw ( ErrorMsg );
bool hasMate () const
throw ();
StringItf * getMateAlignmentId () const
throw ( ErrorMsg );
AlignmentItf * getMateAlignment () const
throw ( ErrorMsg );
StringItf * getMateReferenceSpec () const
throw ( ErrorMsg );
bool getMateIsReversedOrientation () const
throw ( ErrorMsg );
bool nextAlignment ()
throw ( ErrorMsg );
};
} // namespace ngs
#endif // _hpp_ngs_itf_alignment_
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