/usr/include/ngs/PileupEvent.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_pileup_event_
#define _hpp_ngs_pileup_event_
#ifndef _hpp_ngs_error_msg_
#include <ngs/ErrorMsg.hpp>
#endif
#ifndef _hpp_ngs_stringref_
#include <ngs/StringRef.hpp>
#endif
#include <stdint.h>
namespace ngs
{
/*----------------------------------------------------------------------
* forwards and typedefs
*/
typedef class PileupEventItf * PileupEventRef;
/*======================================================================
* PileupEvent
* represents a single cell of a sparse 2D matrix
* with Reference coordinates on one axis
* and stacked Alignments on the other axis
*/
class PileupEvent
{
public:
/*------------------------------------------------------------------
* Reference
*/
/* getMappingQuality
*/
int getMappingQuality () const
throw ( ErrorMsg );
/*------------------------------------------------------------------
* Alignment
*/
/* getAlignmentId
* unique within ReadCollection
*/
StringRef getAlignmentId () const
throw ( ErrorMsg );
/* getAlignmentPosition
* gives position of event on sequence
*/
int64_t getAlignmentPosition () const
throw ( ErrorMsg );
/* getFirstAlignmentPosition
* returns the position of this Alignment's first event
* in Reference coordinates
*/
int64_t getFirstAlignmentPosition () const
throw ( ErrorMsg );
/* getLastAlignmentPosition
* returns the position of this Alignment's last event
* in INCLUSIVE Reference coordinates
*/
int64_t getLastAlignmentPosition () const
throw ( ErrorMsg );
/*------------------------------------------------------------------
* event details
*/
/* EventType
*/
enum PileupEventType
{
// event types representable in reference coordinate space
match = 0,
mismatch = 1,
deletion = 2,
// an insertion cannot be represented in reference coordinate
// space ( so no insertion event can be directly represented ),
// but it can occur before a match or mismatch event.
// insertion is represented as a bit
insertion = 0x08,
// insertions into the reference
insertion_before_match = insertion | match,
insertion_before_mismatch = insertion | mismatch,
// simultaneous insertion and deletion,
// a.k.a. a replacement
insertion_before_deletion = insertion | deletion,
replacement = insertion_before_deletion,
// additional modifier bits - may be added to any event above
alignment_start = 0x80,
alignment_stop = 0x40,
alignment_minus_strand = 0x20
};
/* getEventType
* the type of event being represented
*
* a match event indicates that the aligned sequence base
* exactly matches the corresponding base in the reference.
*
* a mismatch event indicates that the sequence and
* references bases do not match even though they are
* considered aligned. The actual sequence base and its
* quality value may be retrieved with
* "getAlignmentBase()" and "getAlignmentQuality()"
*
* a deletion event indicates a base that is present in
* the reference but missing in the sequence.
*
* an insertion cannot be represented in reference coordinate
* space ( so no insertion event can be directly represented ),
* but it can occur before a match, mismatch or deletion event.
* insertion is represented as a modifier bit. If this bit
* is set, then the event was preceded by an insertion.
* The inserted bases and qualities can be retrieved by
* "getInsertionBases()" and "getInsertionQualities()"
*
*/
PileupEventType getEventType () const
throw ( ErrorMsg );
/* getAlignmentBase
* retrieves base aligned at current Reference position
* returns '-' for deletion events
*/
char getAlignmentBase () const
throw ( ErrorMsg );
/* getAlignmentQuality
* retrieves quality aligned at current Reference position
* returns '!' for deletion events
* quality is ascii-encoded phred score
*/
char getAlignmentQuality () const
throw ( ErrorMsg );
/* getInsertionBases
* returns bases corresponding to insertion event
* returns empty string for all non-insertion events
*/
StringRef getInsertionBases () const
throw ( ErrorMsg );
/* getInsertionQualities
* returns qualities corresponding to insertion event
*/
StringRef getInsertionQualities () const
throw ( ErrorMsg );
/* getEventRepeatCount
* returns the number of times this event repeats
* i.e. the distance to the first reference position
* yielding a different event for this alignment.
*/
uint32_t getEventRepeatCount () const
throw ( ErrorMsg );
/* EventIndelType
*/
enum EventIndelType
{
normal_indel = 0,
// introns behave like deletions
// (i.e. can retrieve deletion count),
// "_plus" and "_minus" signify direction
// of transcription if known
intron_plus = 1,
intron_minus = 2,
intron_unknown = 3,
// overlap is reported as an insertion,
// but is actually an overlap in the read
// inherent in technology like Complete Genomics
read_overlap = 4,
// gap is reported as a deletion,
// but is actually a gap in the read
// inherent in technology like Complete Genomics
read_gap = 5
};
/* getEventIndelType
* returns detail about the type of indel
* when event type is an insertion or deletion
*/
EventIndelType getEventIndelType () const
throw ( ErrorMsg );
public:
// C++ support
PileupEvent & operator = ( PileupEventRef ref )
throw ();
PileupEvent ( PileupEventRef ref )
throw ();
PileupEvent & operator = ( const PileupEvent & obj )
throw ( ErrorMsg );
PileupEvent ( const PileupEvent & obj )
throw ( ErrorMsg );
~ PileupEvent ()
throw ();
protected:
PileupEventRef self;
};
} // namespace ngs
#ifndef _inl_ngs_pileup_event_
#include <ngs/inl/PileupEvent.hpp>
#endif
#endif // _hpp_ngs_pileup_event_
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