/usr/include/ngs/adapter/PileupEventItf.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.
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*
* Although all reasonable efforts have been taken to ensure the accuracy
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* warranties of performance, merchantability or fitness for any particular
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*/
#ifndef _hpp_ngs_adapt_pileup_eventitf_
#define _hpp_ngs_adapt_pileup_eventitf_
#ifndef _hpp_ngs_adapt_refcount_
#include <ngs/adapter/Refcount.hpp>
#endif
#ifndef _hpp_ngs_itf_pileup_eventitf_
#include <ngs/itf/PileupEventItf.h>
#endif
namespace ngs_adapt
{
/*----------------------------------------------------------------------
* forwards
*/
class StringItf;
/*----------------------------------------------------------------------
* PileupEventItf
*/
class PileupEventItf : public Refcount < PileupEventItf, NGS_PileupEvent_v1 >
{
public:
virtual int32_t getMappingQuality () const = 0;
virtual StringItf * getAlignmentId () const = 0;
virtual int64_t getAlignmentPosition () const = 0;
virtual int64_t getFirstAlignmentPosition () const = 0;
virtual int64_t getLastAlignmentPosition () const = 0;
virtual uint32_t getEventType () const = 0;
virtual char getAlignmentBase () const = 0;
virtual char getAlignmentQuality () const = 0;
virtual StringItf * getInsertionBases () const = 0;
virtual StringItf * getInsertionQualities () const = 0;
virtual uint32_t getEventRepeatCount () const = 0;
virtual uint32_t getEventIndelType () const = 0;
virtual bool nextPileupEvent () = 0;
virtual void resetPileupEvent () = 0;
protected:
PileupEventItf ( const NGS_VTable * vt );
static struct NGS_PileupEvent_v1_vt ivt;
private:
static int32_t CC get_map_qual ( const NGS_PileupEvent_v1 * self, NGS_ErrBlock_v1 * err );
static NGS_String_v1 * CC get_align_id ( const NGS_PileupEvent_v1 * self, NGS_ErrBlock_v1 * err );
static int64_t CC get_align_pos ( const NGS_PileupEvent_v1 * self, NGS_ErrBlock_v1 * err );
static int64_t CC get_first_align_pos ( const NGS_PileupEvent_v1 * self, NGS_ErrBlock_v1 * err );
static int64_t CC get_last_align_pos ( const NGS_PileupEvent_v1 * self, NGS_ErrBlock_v1 * err );
static uint32_t CC get_event_type ( const NGS_PileupEvent_v1 * self, NGS_ErrBlock_v1 * err );
static char CC get_align_base ( const NGS_PileupEvent_v1 * self, NGS_ErrBlock_v1 * err );
static char CC get_align_qual ( const NGS_PileupEvent_v1 * self, NGS_ErrBlock_v1 * err );
static NGS_String_v1 * CC get_ins_bases ( const NGS_PileupEvent_v1 * self, NGS_ErrBlock_v1 * err );
static NGS_String_v1 * CC get_ins_quals ( const NGS_PileupEvent_v1 * self, NGS_ErrBlock_v1 * err );
static uint32_t CC get_rpt_count ( const NGS_PileupEvent_v1 * self, NGS_ErrBlock_v1 * err );
static uint32_t CC get_indel_type ( const NGS_PileupEvent_v1 * self, NGS_ErrBlock_v1 * err );
static bool CC next ( NGS_PileupEvent_v1 * self, NGS_ErrBlock_v1 * err );
static void CC reset ( NGS_PileupEvent_v1 * self, NGS_ErrBlock_v1 * err );
};
} // namespace ngs_adapt
#endif // _hpp_ngs_adapt_pileup_eventitf_
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