/usr/include/ngs/adapter/ReadItf.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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* Although all reasonable efforts have been taken to ensure the accuracy
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*/
#ifndef _hpp_ngs_adapt_readitf_
#define _hpp_ngs_adapt_readitf_
#ifndef _hpp_ngs_adapt_fragmentitf_
#include <ngs/adapter/FragmentItf.hpp>
#endif
#ifndef _h_ngs_itf_readitf_
#include <ngs/itf/ReadItf.h>
#endif
namespace ngs_adapt
{
/*----------------------------------------------------------------------
* forwards
*/
class StringItf;
/*----------------------------------------------------------------------
* ReadItf
*/
class ReadItf : public FragmentItf
{
public:
virtual StringItf * getReadId () const = 0;
virtual uint32_t getNumFragments () const = 0;
virtual uint32_t getReadCategory () const = 0;
virtual StringItf * getReadGroup () const = 0;
virtual StringItf * getReadName () const = 0;
virtual StringItf * getReadBases ( uint64_t offset, uint64_t length ) const = 0;
virtual StringItf * getReadQualities ( uint64_t offset, uint64_t length ) const = 0;
virtual bool nextRead () = 0;
inline NGS_Read_v1 * Cast ()
{ return static_cast < NGS_Read_v1* > ( OpaqueRefcount :: offset_this () ); }
inline const NGS_Read_v1 * Cast () const
{ return static_cast < const NGS_Read_v1* > ( OpaqueRefcount :: offset_this () ); }
// assistance for C objects
static inline ReadItf * Self ( NGS_Read_v1 * obj )
{ return static_cast < ReadItf* > ( OpaqueRefcount :: offset_cobj ( obj ) ); }
static inline const ReadItf * Self ( const NGS_Read_v1 * obj )
{ return static_cast < const ReadItf* > ( OpaqueRefcount :: offset_cobj ( obj ) ); }
protected:
ReadItf ();
static NGS_Read_v1_vt ivt;
private:
static NGS_String_v1 * CC get_id ( const NGS_Read_v1 * self, NGS_ErrBlock_v1 * err );
static uint32_t CC get_num_frags ( const NGS_Read_v1 * self, NGS_ErrBlock_v1 * err );
static uint32_t CC get_category ( const NGS_Read_v1 * self, NGS_ErrBlock_v1 * err );
static NGS_String_v1 * CC get_read_group ( const NGS_Read_v1 * self, NGS_ErrBlock_v1 * err );
static NGS_String_v1 * CC get_name ( const NGS_Read_v1 * self, NGS_ErrBlock_v1 * err );
static NGS_String_v1 * CC get_bases ( const NGS_Read_v1 * self, NGS_ErrBlock_v1 * err, uint64_t offset, uint64_t length );
static NGS_String_v1 * CC get_quals ( const NGS_Read_v1 * self, NGS_ErrBlock_v1 * err, uint64_t offset, uint64_t length );
static bool CC next ( NGS_Read_v1 * self, NGS_ErrBlock_v1 * err );
};
} // namespace ngs_adapt
#endif // _hpp_ngs_adapt_readitf_
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