/usr/include/ngs/itf/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.
* 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
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* Please cite the author in any work or product based on this material.
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* ===========================================================================
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*/
#ifndef _hpp_ngs_itf_readitf_
#define _hpp_ngs_itf_readitf_
#ifndef _hpp_ngs_itf_refcount_
#include <ngs/itf/Refcount.hpp>
#endif
struct NGS_Read_v1;
namespace ngs
{
/*----------------------------------------------------------------------
* forwards
*/
class StringItf;
/*----------------------------------------------------------------------
* ReadItf
*/
class ReadItf : public Refcount < ReadItf, NGS_Read_v1 >
{
public:
StringItf * getReadId () const
throw ( ErrorMsg );
uint32_t getNumFragments () const
throw ( ErrorMsg );
bool fragmentIsAligned ( uint32_t fragIdx ) const
throw ( ErrorMsg );
uint32_t getReadCategory () const
throw ( ErrorMsg );
StringItf * getReadGroup () const
throw ( ErrorMsg );
StringItf * getReadName () const
throw ( ErrorMsg );
StringItf * getReadBases () const
throw ( ErrorMsg );
StringItf * getReadBases ( uint64_t offset ) const
throw ( ErrorMsg );
StringItf * getReadBases ( uint64_t offset, uint64_t length ) const
throw ( ErrorMsg );
StringItf * getReadQualities () const
throw ( ErrorMsg );
StringItf * getReadQualities ( uint64_t offset ) const
throw ( ErrorMsg );
StringItf * getReadQualities ( uint64_t offset, uint64_t length ) const
throw ( ErrorMsg );
bool nextRead ()
throw ( ErrorMsg );
};
} // namespace ngs
#endif // _hpp_ngs_itf_readitf_
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