/usr/include/ngs/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.
*
* 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_collection_
#define _hpp_ngs_read_collection_
#ifndef _hpp_ngs_read_group_iterator_
#include <ngs/ReadGroupIterator.hpp>
#endif
#ifndef _hpp_ngs_reference_iterator_
#include <ngs/ReferenceIterator.hpp>
#endif
#ifndef _hpp_ngs_alignment_iterator_
#include <ngs/AlignmentIterator.hpp>
#endif
namespace ngs
{
/*----------------------------------------------------------------------
* forwards and typedefs
*/
typedef class ReadCollectionItf * ReadCollectionRef;
/*======================================================================
* ReadCollection
* represents an NGS-capable object with a collection of Reads
*/
class ReadCollection
{
public:
/* getName
* returns the simple name of the read collection
* this name is generally extracted from the "spec"
* used to create the object, but may also be mapped
* to a canonical name if one may be determined and
* differs from that given in the spec.
*
* if the name is extracted from "spec" and contains
* well-known file extensions that do not form part of
* a canonical name (e.g. ".sra"), they will be removed.
*/
String getName () const
throw ( ErrorMsg );
/*------------------------------------------------------------------
* READ GROUPS
*/
/* getReadGroups
* returns an iterator of all ReadGroups used
*/
ReadGroupIterator getReadGroups () const
throw ( ErrorMsg );
/* hasReadGroup
* returns true if a call to "getReadGroup()" should succeed
*/
bool hasReadGroup ( const String & spec ) const
throw ();
/* getReadGroup
*/
ReadGroup getReadGroup ( const String & spec ) const
throw ( ErrorMsg );
/*------------------------------------------------------------------
* REFERENCES
*/
/* getReferences
* returns an iterator of all References used
* iterator will be empty if no Reads are aligned
*/
ReferenceIterator getReferences () const
throw ( ErrorMsg );
/* hasReference
* returns true if a call to "getReference()" should succeed
*/
bool hasReference ( const String & spec ) const
throw ();
/* getReference
*/
Reference getReference ( const String & spec ) const
throw ( ErrorMsg );
/*------------------------------------------------------------------
* ALIGNMENTS
*/
/* getAlignment
* returns an individual Alignment
* throws ErrorMsg if Alignment does not exist
*/
Alignment getAlignment ( const String & alignmentId ) const
throw ( ErrorMsg );
/* getAlignments
* returns an iterator of all Alignments from specified categories
*/
AlignmentIterator getAlignments ( Alignment :: AlignmentCategory categories ) const
throw ( ErrorMsg );
/* getAlignmentCount
* returns count of all alignments
* "categories" provides a means of filtering by AlignmentCategory
*/
uint64_t getAlignmentCount () const
throw ( ErrorMsg );
uint64_t getAlignmentCount ( Alignment :: AlignmentCategory categories ) const
throw ( ErrorMsg );
/* getAlignmentRange
* returns an iterator across a range of Alignments
* "first" is an ordinal into set
* "categories" provides a means of filtering by AlignmentCategory
*/
AlignmentIterator getAlignmentRange ( uint64_t first, uint64_t count ) const
throw ( ErrorMsg );
AlignmentIterator getAlignmentRange ( uint64_t first, uint64_t count, Alignment :: AlignmentCategory categories ) const
throw ( ErrorMsg );
/*------------------------------------------------------------------
* READS
*/
/* getRead
* returns an individual Read
* throws ErrorMsg if Read does not exist
*/
Read getRead ( const String & readId ) const
throw ( ErrorMsg );
/* getReads
* returns an iterator of all contained machine Reads
* "categories" provides a means of filtering by ReadCategory
*/
ReadIterator getReads ( Read :: ReadCategory categories ) const
throw ( ErrorMsg );
/* getReadCount
* returns the number of reads in the collection
* "categories" provides an optional means of filtering by ReadCategory
*/
uint64_t getReadCount () const
throw ( ErrorMsg );
uint64_t getReadCount ( Read :: ReadCategory categories ) const
throw ( ErrorMsg );
/* getReadRange
* returns an iterator across a range of Reads
* "first" is an ordinal into set
* "categories" provides an optional means of filtering by ReadCategory
*/
ReadIterator getReadRange ( uint64_t first, uint64_t count ) const
throw ( ErrorMsg );
ReadIterator getReadRange ( uint64_t first, uint64_t count, Read :: ReadCategory categories ) const
throw ( ErrorMsg );
public:
// C++ support
ReadCollection & operator = ( ReadCollectionRef ref )
throw ();
ReadCollection ( ReadCollectionRef ref )
throw ();
ReadCollection & operator = ( const ReadCollection & obj )
throw ();
ReadCollection ( const ReadCollection & obj )
throw ();
~ ReadCollection ()
throw ();
protected:
ReadCollectionRef self;
};
} // namespace ngs
#ifndef _inl_ngs_read_collection_
#include <ngs/inl/ReadCollection.hpp>
#endif
#endif // _hpp_ngs_read_collection_
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