/usr/include/ngs/Fragment.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.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 | /*===========================================================================
*
* 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_fragment_
#define _hpp_ngs_fragment_
#ifndef _hpp_ngs_error_msg_
#include <ngs/ErrorMsg.hpp>
#endif
#ifndef _hpp_ngs_stringref_
#include <ngs/StringRef.hpp>
#endif
#include <stdint.h>
namespace ngs
{
/*----------------------------------------------------------------------
* forwards and typedefs
*/
typedef class FragmentItf * FragmentRef;
/*======================================================================
* Fragment
* represents an NGS biological fragment
*/
class Fragment
{
public:
/* getFragmentId
* returns an unique id within the context of the ReadCollection
* representing a single biological fragment
*/
StringRef getFragmentId () const
throw ( ErrorMsg );
/*------------------------------------------------------------------
* fragment details
*/
/* getFragmentBases
* return sequence bases
* "offset" is zero-based
*/
StringRef getFragmentBases () const
throw ( ErrorMsg );
StringRef getFragmentBases ( uint64_t offset ) const
throw ( ErrorMsg );
StringRef getFragmentBases ( uint64_t offset, uint64_t length ) const
throw ( ErrorMsg );
/* getFragmentQualities
* return phred quality values
* using ASCII offset of 33
* "offset" is zero-based
*/
StringRef getFragmentQualities () const
throw ( ErrorMsg );
StringRef getFragmentQualities ( uint64_t offset ) const
throw ( ErrorMsg );
StringRef getFragmentQualities ( uint64_t offset, uint64_t length ) const
throw ( ErrorMsg );
/* isPaired
* returns true if fragment has a mate
*/
bool isPaired () const
throw ( ErrorMsg );
/* isAligned
* returns true if fragment has alignment data
*/
bool isAligned () const
throw ( ErrorMsg );
public:
// C++ support
Fragment ( FragmentRef ref )
throw ();
Fragment & operator = ( const Fragment & obj )
throw ( ErrorMsg );
Fragment ( const Fragment & obj )
throw ( ErrorMsg );
~ Fragment ()
throw ();
private:
Fragment & operator = ( FragmentRef ref )
throw ();
protected:
FragmentRef self;
};
} // namespace ngs
// inlines
#ifndef _inl_ngs_fragment_
#include <ngs/inl/Fragment.hpp>
#endif
#endif // _hpp_ngs_fragment_
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