/usr/include/ngs/inl/ReadCollection.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.
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*/
#ifndef _hpp_ngs_itf_collection_
#define _hpp_ngs_itf_collection_
#ifndef _hpp_ngs_itf_collection_
#include <ngs/ReadCollection.hpp>
#endif
#ifndef _hpp_ngs_itf_read_collectionitf_
#include <ngs/itf/ReadCollectionItf.hpp>
#endif
namespace ngs
{
/*----------------------------------------------------------------------
* ReadCollection
*/
inline
String ReadCollection :: getName () const
throw ( ErrorMsg )
{ return StringRef ( self -> getName () ) . toString (); }
inline
ReadGroupIterator ReadCollection :: getReadGroups () const
throw ( ErrorMsg )
{ return ReadGroupIterator ( self -> getReadGroups () ); }
inline
bool ReadCollection :: hasReadGroup ( const String & spec ) const
throw ()
{ return self -> hasReadGroup ( spec . c_str () ); }
inline
ReadGroup ReadCollection :: getReadGroup ( const String & spec ) const
throw ( ErrorMsg )
{ return ReadGroup ( self -> getReadGroup ( spec . c_str () ) ); }
inline
ReferenceIterator ReadCollection :: getReferences () const
throw ( ErrorMsg )
{ return ReferenceIterator ( self -> getReferences () ); }
inline
bool ReadCollection :: hasReference ( const String & spec ) const
throw ()
{ return self -> hasReference ( spec . c_str () ); }
inline
Reference ReadCollection :: getReference ( const String & spec ) const
throw ( ErrorMsg )
{ return Reference ( self -> getReference ( spec . c_str () ) ); }
inline
Alignment ReadCollection :: getAlignment ( const String & alignmentId ) const
throw ( ErrorMsg )
{ return Alignment ( ( AlignmentRef ) self -> getAlignment ( alignmentId . c_str () ) ); }
inline
AlignmentIterator ReadCollection :: getAlignments ( Alignment :: AlignmentCategory categories ) const
throw ( ErrorMsg )
{ return AlignmentIterator ( ( AlignmentRef ) self -> getAlignments ( ( uint32_t ) categories ) ); }
inline
uint64_t ReadCollection :: getAlignmentCount () const
throw ( ErrorMsg )
{ return self -> getAlignmentCount ( ( uint32_t ) Alignment :: all ); }
inline
uint64_t ReadCollection :: getAlignmentCount ( Alignment :: AlignmentCategory categories ) const
throw ( ErrorMsg )
{ return self -> getAlignmentCount ( ( uint32_t ) categories ); }
inline
AlignmentIterator ReadCollection :: getAlignmentRange ( uint64_t first, uint64_t count ) const
throw ( ErrorMsg )
{ return AlignmentIterator ( ( AlignmentRef ) self -> getAlignmentRange ( first, count, ( uint32_t ) Alignment :: all ) ); }
inline
AlignmentIterator ReadCollection :: getAlignmentRange ( uint64_t first, uint64_t count, Alignment :: AlignmentCategory categories ) const
throw ( ErrorMsg )
{ return AlignmentIterator ( ( AlignmentRef ) self -> getAlignmentRange ( first, count, ( uint32_t ) categories ) ); }
inline
Read ReadCollection :: getRead ( const String & readId ) const
throw ( ErrorMsg )
{ return Read ( ( ReadRef ) self -> getRead ( readId . c_str () ) ); }
inline
ReadIterator ReadCollection :: getReads ( Read :: ReadCategory categories ) const
throw ( ErrorMsg )
{ return ReadIterator ( ( ReadRef ) self -> getReads ( ( uint32_t ) categories ) ); }
inline
uint64_t ReadCollection :: getReadCount () const
throw ( ErrorMsg )
{ return self -> getReadCount ( ( uint32_t ) Read :: all ); }
inline
uint64_t ReadCollection :: getReadCount ( Read :: ReadCategory categories ) const
throw ( ErrorMsg )
{ return self -> getReadCount ( ( uint32_t ) categories ); }
inline
ReadIterator ReadCollection :: getReadRange ( uint64_t first, uint64_t count ) const
throw ( ErrorMsg )
{ return ReadIterator ( ( ReadRef ) self -> getReadRange ( first, count ) ); }
inline
ReadIterator ReadCollection :: getReadRange ( uint64_t first, uint64_t count, Read :: ReadCategory categories ) const
throw ( ErrorMsg )
{ return ReadIterator ( ( ReadRef ) self -> getReadRange ( first, count, ( uint32_t ) categories ) ); }
} // namespace ngs
#endif // _hpp_ngs_itf_collection_
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