/usr/include/ngs/itf/ReferenceItf.hpp is in libngs-sdk-dev 1.3.0-2.
This file is owned by root:root, with mode 0o644.
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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
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* warranties of performance, merchantability or fitness for any particular
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*/
#ifndef _hpp_ngs_itf_referenceitf_
#define _hpp_ngs_itf_referenceitf_
#ifndef _hpp_ngs_itf_refcount_
#include <ngs/itf/Refcount.hpp>
#endif
struct NGS_Reference_v1;
namespace ngs
{
/*----------------------------------------------------------------------
* forwards
*/
class StringItf;
class PileupItf;
class AlignmentItf;
/*----------------------------------------------------------------------
* Reference
*/
class ReferenceItf : public Refcount < ReferenceItf, NGS_Reference_v1 >
{
public:
StringItf * getCommonName () const
throw ( ErrorMsg );
StringItf * getCanonicalName () const
throw ( ErrorMsg );
bool getIsCircular () const
throw ( ErrorMsg );
uint64_t getLength () const
throw ( ErrorMsg );
StringItf * getReferenceBases ( uint64_t offset ) const
throw ( ErrorMsg );
StringItf * getReferenceBases ( uint64_t offset, uint64_t length ) const
throw ( ErrorMsg );
StringItf * getReferenceChunk ( uint64_t offset ) const
throw ( ErrorMsg );
StringItf * getReferenceChunk ( uint64_t offset, uint64_t length ) const
throw ( ErrorMsg );
uint64_t getAlignmentCount () const
throw ( ErrorMsg );
uint64_t getAlignmentCount ( uint32_t categories ) const
throw ( ErrorMsg );
AlignmentItf * getAlignment ( const char * alignmentId ) const
throw ( ErrorMsg );
AlignmentItf * getAlignments ( uint32_t categories ) const
throw ( ErrorMsg );
AlignmentItf * getAlignmentSlice ( int64_t start, uint64_t length ) const
throw ( ErrorMsg );
AlignmentItf * getAlignmentSlice ( int64_t start, uint64_t length, uint32_t categories ) const
throw ( ErrorMsg );
AlignmentItf * getFilteredAlignmentSlice ( int64_t start, uint64_t length, uint32_t categories, uint32_t filters, int32_t mappingQuality ) const
throw ( ErrorMsg );
PileupItf * getPileups ( uint32_t categories ) const
throw ( ErrorMsg );
PileupItf * getFilteredPileups ( uint32_t categories, uint32_t filters, int32_t mappingQuality ) const
throw ( ErrorMsg );
PileupItf * getPileupSlice ( int64_t start, uint64_t length ) const
throw ( ErrorMsg );
PileupItf * getPileupSlice ( int64_t start, uint64_t length, uint32_t categories ) const
throw ( ErrorMsg );
PileupItf * getFilteredPileupSlice ( int64_t start, uint64_t length, uint32_t categories, uint32_t filters, int32_t mappingQuality ) const
throw ( ErrorMsg );
bool nextReference ()
throw ( ErrorMsg );
};
} // namespace ngs
#endif // _hpp_ngs_itf_referenceitf_
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