libStatGen Software 1
SamSingleBaseMatchInfo Class Reference

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

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.

207 : myType(UNKNOWN),
208 myQueryIndex(0)
209{
210}

◆ ~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.

225{
226 return(myQueryIndex);
227}

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.

219{
220 return(myType);
221}

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.

237{
238 myQueryIndex = queryIndex;
239}

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.

231{
232 myType = newType;
233}

Referenced by SamQuerySeqWithRefIter::getNextMatchMismatch().


The documentation for this class was generated from the following files: