/usr/include/ngs/adapter/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.
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* Government disclaim all warranties, express or implied, including
* warranties of performance, merchantability or fitness for any particular
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* Please cite the author in any work or product based on this material.
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* ===========================================================================
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*/
#ifndef _hpp_ngs_adapt_referenceitf_
#define _hpp_ngs_adapt_referenceitf_
#ifndef _hpp_ngs_adapt_refcount_
#include <ngs/adapter/Refcount.hpp>
#endif
#ifndef _h_ngs_itf_referenceitf_
#include <ngs/itf/ReferenceItf.h>
#endif
namespace ngs_adapt
{
/*----------------------------------------------------------------------
* forwards
*/
class StringItf;
class PileupItf;
class AlignmentItf;
/*----------------------------------------------------------------------
* Reference
*/
class ReferenceItf : public Refcount < ReferenceItf, NGS_Reference_v1 >
{
public:
virtual StringItf * getCommonName () const = 0;
virtual StringItf * getCanonicalName () const = 0;
virtual bool getIsCircular () const = 0;
virtual uint64_t getLength () const = 0;
virtual StringItf * getReferenceBases ( uint64_t offset, uint64_t length ) const = 0;
virtual StringItf * getReferenceChunk ( uint64_t offset, uint64_t length ) const = 0;
virtual uint64_t getAlignmentCount ( bool wants_primary, bool wants_secondary ) const = 0;
virtual AlignmentItf * getAlignment ( const char * alignmentId ) const = 0;
virtual AlignmentItf * getAlignments ( bool wants_primary, bool wants_secondary ) const = 0;
virtual AlignmentItf * getAlignmentSlice ( int64_t start, uint64_t length, bool wants_primary, bool wants_secondary ) const = 0;
virtual PileupItf * getPileups ( bool wants_primary, bool wants_secondary ) const = 0;
virtual PileupItf * getFilteredPileups ( uint32_t flags, int32_t map_qual ) const = 0;
virtual PileupItf * getPileupSlice ( int64_t start, uint64_t length, bool wants_primary, bool wants_secondary ) const = 0;
virtual PileupItf * getFilteredPileupSlice ( int64_t start, uint64_t length, uint32_t flags, int32_t map_qual ) const = 0;
virtual bool nextReference () = 0;
protected:
ReferenceItf ();
static NGS_Reference_v1_vt ivt;
private:
static NGS_String_v1 * CC get_cmn_name ( const NGS_Reference_v1 * self, NGS_ErrBlock_v1 * err );
static NGS_String_v1 * CC get_canon_name ( const NGS_Reference_v1 * self, NGS_ErrBlock_v1 * err );
static bool CC is_circular ( const NGS_Reference_v1 * self, NGS_ErrBlock_v1 * err );
static uint64_t CC get_length ( const NGS_Reference_v1 * self, NGS_ErrBlock_v1 * err );
static NGS_String_v1 * CC get_ref_bases ( const NGS_Reference_v1 * self, NGS_ErrBlock_v1 * err,
uint64_t offset, uint64_t length );
static NGS_String_v1 * CC get_ref_chunk ( const NGS_Reference_v1 * self, NGS_ErrBlock_v1 * err,
uint64_t offset, uint64_t length );
static uint64_t CC get_alignment_count ( const NGS_Reference_v1 * self, NGS_ErrBlock_v1 * err,
bool wants_primary, bool wants_secondary );
static NGS_Alignment_v1 * CC get_alignment ( const NGS_Reference_v1 * self, NGS_ErrBlock_v1 * err,
const char * alignmentId );
static NGS_Alignment_v1 * CC get_alignments ( const NGS_Reference_v1 * self, NGS_ErrBlock_v1 * err,
bool wants_primary, bool wants_secondary );
static NGS_Alignment_v1 * CC get_align_slice ( const NGS_Reference_v1 * self, NGS_ErrBlock_v1 * err,
int64_t start, uint64_t length, bool wants_primary, bool wants_secondary );
static NGS_Pileup_v1 * CC get_pileups ( const NGS_Reference_v1 * self, NGS_ErrBlock_v1 * err,
bool wants_primary, bool wants_secondary );
static NGS_Pileup_v1 * CC get_filtered_pileups ( const NGS_Reference_v1 * self, NGS_ErrBlock_v1 * err,
uint32_t flags, int32_t map_qual );
static NGS_Pileup_v1 * CC get_pileup_slice ( const NGS_Reference_v1 * self, NGS_ErrBlock_v1 * err,
int64_t start, uint64_t length, bool wants_primary, bool wants_secondary );
static NGS_Pileup_v1 * CC get_filtered_pileup_slice ( const NGS_Reference_v1 * self, NGS_ErrBlock_v1 * err,
int64_t start, uint64_t length, uint32_t flags, int32_t map_qual );
static bool CC next ( NGS_Reference_v1 * self, NGS_ErrBlock_v1 * err );
};
} // namespace ngs_adapt
#endif // _hpp_ngs_adapt_referenceitf_
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