/usr/include/ngs/adapter/FragmentItf.hpp is in libngs-sdk-dev 1.3.0-2.
This file is owned by root:root, with mode 0o644.
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*
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* National Center for Biotechnology Information
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#ifndef _hpp_ngs_adapt_fragmentitf_
#define _hpp_ngs_adapt_fragmentitf_
#ifndef _hpp_ngs_adapt_refcount_
#include <ngs/adapter/Refcount.hpp>
#endif
#ifndef _h_ngs_itf_fragmentitf_
#include <ngs/itf/FragmentItf.h>
#endif
namespace ngs_adapt
{
/*----------------------------------------------------------------------
* forwards
*/
class StringItf;
/*----------------------------------------------------------------------
* FragmentItf
*/
class FragmentItf : public Refcount < FragmentItf, NGS_Fragment_v1 >
{
public:
virtual StringItf * getFragmentId () const = 0;
virtual StringItf * getFragmentBases ( uint64_t offset, uint64_t length ) const = 0;
virtual StringItf * getFragmentQualities ( uint64_t offset, uint64_t length ) const = 0;
virtual bool nextFragment () = 0;
protected:
// support for C vtable
FragmentItf ( const NGS_VTable * vt );
static NGS_Fragment_v1_vt ivt;
private:
static NGS_String_v1 * CC get_id ( const NGS_Fragment_v1 * self, NGS_ErrBlock_v1 * err );
static NGS_String_v1 * CC get_bases ( const NGS_Fragment_v1 * self, NGS_ErrBlock_v1 * err,
uint64_t offset, uint64_t length );
static NGS_String_v1 * CC get_quals ( const NGS_Fragment_v1 * self, NGS_ErrBlock_v1 * err,
uint64_t offset, uint64_t length );
static bool next ( NGS_Fragment_v1 * self, NGS_ErrBlock_v1 * err );
};
} // namespace ngs_adapt
#endif // _hpp_ngs_adapt_fragmentitf_
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