/usr/include/ngs/itf/ReadCollectionItf.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.
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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_read_collectionitf_
#define _hpp_ngs_itf_read_collectionitf_
#ifndef _hpp_ngs_itf_refcount_
#include <ngs/itf/Refcount.hpp>
#endif
struct NGS_ReadCollection_v1;
namespace ngs
{
/*----------------------------------------------------------------------
* forwards
*/
class ReadItf;
class StringItf;
class ReadGroupItf;
class ReferenceItf;
class AlignmentItf;
/*----------------------------------------------------------------------
* ReadCollectionItf
*/
class ReadCollectionItf : public Refcount < ReadCollectionItf, NGS_ReadCollection_v1 >
{
public:
StringItf * getName () const
throw ( ErrorMsg );
ReadGroupItf * getReadGroups () const
throw ( ErrorMsg );
bool hasReadGroup ( const char * spec ) const
throw ();
ReadGroupItf * getReadGroup ( const char * spec ) const
throw ( ErrorMsg );
ReferenceItf * getReferences () const
throw ( ErrorMsg );
bool hasReference ( const char * spec ) const
throw ();
ReferenceItf * getReference ( const char * spec ) const
throw ( ErrorMsg );
AlignmentItf * getAlignment ( const char * alignmentId ) const
throw ( ErrorMsg );
AlignmentItf * getAlignments ( uint32_t categories ) const
throw ( ErrorMsg );
uint64_t getAlignmentCount ( uint32_t categories ) const
throw ( ErrorMsg );
AlignmentItf * getAlignmentRange ( uint64_t first, uint64_t count, uint32_t categories ) const
throw ( ErrorMsg );
ReadItf * getRead ( const char * readId ) const
throw ( ErrorMsg );
ReadItf * getReads ( uint32_t categories ) const
throw ( ErrorMsg );
uint64_t getReadCount ( uint32_t categories ) const
throw ( ErrorMsg );
ReadItf * getReadRange ( uint64_t first, uint64_t count ) const
throw ( ErrorMsg );
ReadItf * getReadRange ( uint64_t first, uint64_t count, uint32_t categories ) const
throw ( ErrorMsg );
};
} // namespace ngs
#endif // _hpp_ngs_itf_read_collectionitf_
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