/usr/include/ngs/inl/Read.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_read_
#define _inl_ngs_read_
#ifndef _hpp_ngs_read_
#include <ngs/Read.hpp>
#endif
#include <ngs/itf/ReadItf.hpp>
namespace ngs
{
// the "self" member is typed as FragmentRef
// but is used here as an ReadRef
#define self reinterpret_cast < const ReadItf * > ( self )
/*----------------------------------------------------------------------
* Read
* represents an NGS machine read
* having some number of biological Fragments
*/
inline
StringRef Read :: getReadId () const
throw ( ErrorMsg )
{ return StringRef ( self -> getReadId () ); }
inline
uint32_t Read :: getNumFragments () const
throw ( ErrorMsg )
{ return self -> getNumFragments (); }
inline
bool Read :: fragmentIsAligned ( uint32_t fragIdx ) const
throw ( ErrorMsg )
{ return self -> fragmentIsAligned ( fragIdx ); }
inline
Read :: ReadCategory Read :: getReadCategory () const
throw ( ErrorMsg )
{ return ( Read :: ReadCategory ) self -> getReadCategory (); }
inline
String Read :: getReadGroup () const
throw ( ErrorMsg )
{ return StringRef ( self -> getReadGroup () ) . toString (); }
inline
StringRef Read :: getReadName () const
throw ( ErrorMsg )
{ return StringRef ( self -> getReadName () ); }
inline
StringRef Read :: getReadBases () const
throw ( ErrorMsg )
{ return StringRef ( self -> getReadBases () ); }
inline
StringRef Read :: getReadBases ( uint64_t offset ) const
throw ( ErrorMsg )
{ return StringRef ( self -> getReadBases ( offset ) ); }
inline
StringRef Read :: getReadBases ( uint64_t offset, uint64_t length ) const
throw ( ErrorMsg )
{ return StringRef ( self -> getReadBases ( offset, length ) ); }
inline
StringRef Read :: getReadQualities () const
throw ( ErrorMsg )
{ return StringRef ( self -> getReadQualities () ); }
inline
StringRef Read :: getReadQualities ( uint64_t offset ) const
throw ( ErrorMsg )
{ return StringRef ( self -> getReadQualities ( offset ) ); }
inline
StringRef Read :: getReadQualities ( uint64_t offset, uint64_t length ) const
throw ( ErrorMsg )
{ return StringRef ( self -> getReadQualities ( offset, length ) ); }
#undef self
} // namespace ngs
#endif // _inl_ngs_read_
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