/usr/include/ngs/adapter/PileupItf.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.
*
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*/
#ifndef _hpp_ngs_adapt_pileupitf_
#define _hpp_ngs_adapt_pileupitf_
#ifndef _hpp_ngs_adapt_pileup_eventitf_
#include <ngs/adapter/PileupEventItf.hpp>
#endif
#ifndef _h_ngs_itf_pileupitf_
#include <ngs/itf/PileupItf.h>
#endif
namespace ngs_adapt
{
/*----------------------------------------------------------------------
* forwards
*/
class StringItf;
class PileupEventItf;
/*----------------------------------------------------------------------
* PileupItf
*/
class PileupItf : public PileupEventItf
{
public:
virtual StringItf * getReferenceSpec () const = 0;
virtual int64_t getReferencePosition () const = 0;
virtual char getReferenceBase () const = 0;
virtual uint32_t getPileupDepth () const = 0;
virtual bool nextPileup () = 0;
inline NGS_Pileup_v1 * Cast ()
{ return static_cast < NGS_Pileup_v1* > ( OpaqueRefcount :: offset_this () ); }
inline const NGS_Pileup_v1 * Cast () const
{ return static_cast < const NGS_Pileup_v1* > ( OpaqueRefcount :: offset_this () ); }
// assistance for C objects
static inline PileupItf * Self ( NGS_Pileup_v1 * obj )
{ return static_cast < PileupItf* > ( OpaqueRefcount :: offset_cobj ( obj ) ); }
static inline const PileupItf * Self ( const NGS_Pileup_v1 * obj )
{ return static_cast < const PileupItf* > ( OpaqueRefcount :: offset_cobj ( obj ) ); }
protected:
PileupItf ();
static NGS_Pileup_v1_vt ivt;
private:
static NGS_String_v1 * CC get_ref_spec ( const NGS_Pileup_v1 * self, NGS_ErrBlock_v1 * err );
static int64_t CC get_ref_pos ( const NGS_Pileup_v1 * self, NGS_ErrBlock_v1 * err );
static char CC get_ref_base ( const NGS_Pileup_v1 * self, NGS_ErrBlock_v1 * err );
static uint32_t CC get_pileup_depth ( const NGS_Pileup_v1 * self, NGS_ErrBlock_v1 * err );
static bool CC next ( NGS_Pileup_v1 * self, NGS_ErrBlock_v1 * err );
};
} // namespace ngs_adapt
#endif // _hpp_ngs_adapt_pileupitf_
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