This class contains the match/mismatch information between the reference and a read for a single base. More...

#include <SamQuerySeqWithRefHelper.h>

Public Types
enum	Type { UNKNOWN , MATCH , MISMATCH }
	More types can be added later as needed. More...

Public Member Functions
Type	getType ()
	Get the type (match/mismatch/unknown) for this object. More...

int32_t	getQueryIndex ()
	Get the query index for this object. More...

void	setType (Type newType)
	Set the type (match/mismatch/unkown) for this object. More...

void	setQueryIndex (int32_t queryIndex)
	Set the query index for this object. More...

Detailed Description

This class contains the match/mismatch information between the reference and a read for a single base.

Definition at line 28 of file SamQuerySeqWithRefHelper.h.

Member Enumeration Documentation

◆ Type

enum SamSingleBaseMatchInfo::Type

More types can be added later as needed.

Definition at line 32 of file SamQuerySeqWithRefHelper.h.

32{UNKNOWN, MATCH, MISMATCH};

Constructor & Destructor Documentation

◆ SamSingleBaseMatchInfo()

SamSingleBaseMatchInfo::SamSingleBaseMatchInfo ( )

Definition at line 206 of file SamQuerySeqWithRefHelper.cpp.

    : myType(UNKNOWN),
      myQueryIndex(0)
{
}

◆ ~SamSingleBaseMatchInfo()

SamSingleBaseMatchInfo::~SamSingleBaseMatchInfo ( )

Definition at line 213 of file SamQuerySeqWithRefHelper.cpp.

214{

215}

Member Function Documentation

◆ getQueryIndex()

int32_t SamSingleBaseMatchInfo::getQueryIndex ( )

Get the query index for this object.

Definition at line 224 of file SamQuerySeqWithRefHelper.cpp.

{
    return(myQueryIndex);
}

Referenced by SamFilter::clipOnMismatchThreshold(), and SamFilter::sumMismatchQuality().

◆ getType()

SamSingleBaseMatchInfo::Type SamSingleBaseMatchInfo::getType ( )

Get the type (match/mismatch/unknown) for this object.

Definition at line 218 of file SamQuerySeqWithRefHelper.cpp.

{
    return(myType);
}

Referenced by SamFilter::clipOnMismatchThreshold(), and SamFilter::sumMismatchQuality().

◆ setQueryIndex()

void SamSingleBaseMatchInfo::setQueryIndex ( int32_t queryIndex )

Set the query index for this object.

Definition at line 236 of file SamQuerySeqWithRefHelper.cpp.

{
    myQueryIndex = queryIndex;
}

Referenced by SamQuerySeqWithRefIter::getNextMatchMismatch().

◆ setType()

void SamSingleBaseMatchInfo::setType ( Type newType )

Set the type (match/mismatch/unkown) for this object.

Definition at line 230 of file SamQuerySeqWithRefHelper.cpp.

{
    myType = newType;
}