/usr/include/ngs/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 _hpp_ngs_read_
#define _hpp_ngs_read_
#ifndef _hpp_ngs_fragment_iterator_
#include <ngs/FragmentIterator.hpp>
#endif
namespace ngs
{
/*----------------------------------------------------------------------
* forwards and typedefs
*/
typedef FragmentRef ReadRef;
/*======================================================================
* Read
* represents an NGS machine read
* having some number of biological Fragments
*/
class Read : public FragmentIterator
{
public:
/* getReadId
*/
StringRef getReadId () const
throw ( ErrorMsg );
/* getNumFragments
* the number of biological Fragments contained in the read
*/
uint32_t getNumFragments () const
throw ( ErrorMsg );
/* fragmentIsAligned
* tests a fragment for being aligned
*/
bool fragmentIsAligned ( uint32_t fragIdx ) const
throw ( ErrorMsg );
/*------------------------------------------------------------------
* read details
*/
/* ReadCategory
*/
enum ReadCategory
{
fullyAligned = 1,
partiallyAligned = 2,
aligned = fullyAligned | partiallyAligned,
unaligned = 4,
all = aligned | unaligned
};
/* getReadCategory
*/
ReadCategory getReadCategory () const
throw ( ErrorMsg );
/* getReadGroup
*/
String getReadGroup () const
throw ( ErrorMsg );
/* getReadName
*/
StringRef getReadName () const
throw ( ErrorMsg );
/* getReadBases
* return sequence bases
* "offset" is zero-based
*/
StringRef getReadBases () const
throw ( ErrorMsg );
StringRef getReadBases ( uint64_t offset ) const
throw ( ErrorMsg );
StringRef getReadBases ( uint64_t offset, uint64_t length ) const
throw ( ErrorMsg );
/* getReadQualities
* return phred quality values
* using ASCII offset of 33
* "offset" is zero-based
*/
StringRef getReadQualities () const
throw ( ErrorMsg );
StringRef getReadQualities ( uint64_t offset ) const
throw ( ErrorMsg );
StringRef getReadQualities ( uint64_t offset, uint64_t length ) const
throw ( ErrorMsg );
public:
// C++ support
Read ( ReadRef ref )
throw ();
Read & operator = ( const Read & obj )
throw ( ErrorMsg );
Read ( const Read & obj )
throw ( ErrorMsg );
~ Read ()
throw ();
private:
Read & operator = ( ReadRef ref )
throw ();
};
} // namespace ngs
// inlines
#ifndef _inl_ngs_read_
#include <ngs/inl/Read.hpp>
#endif
#endif // _hpp_ngs_read_
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