18#ifndef __SAM_QUERY_SEQ_WITH_REF_HELPER_H__
19#define __SAM_QUERY_SEQ_WITH_REF_HELPER_H__
24#include "GenomeSequence.h"
32 enum Type {UNKNOWN, MATCH, MISMATCH};
71 bool reset(
bool forward =
true);
94 uint32_t myStartOfReadOnRefIndex;
116 int32_t seq0BasedPos,
118 const char* referenceName,
120 std::string& updatedSeq);
132 int32_t seq0BasedPos,
134 const char* referenceName,
136 std::string& updatedSeq);
This class represents the CIGAR without any methods to set the cigar (see CigarRoller for that).
Create/Access/Modify/Load Genome Sequences stored as binary mapped files.
Iterates through the query and compare with reference.
bool reset(bool forward=true)
Reset to start at the beginning of the record.
bool getNextMatchMismatch(SamSingleBaseMatchInfo &matchMismatchInfo)
Returns information for the next position where the query and the reference match or mismatch.
Contains methods for converting between the query sequence and reference.
static void seqWithoutEquals(const char *currentSeq, int32_t seq0BasedPos, Cigar &cigar, const char *referenceName, const GenomeSequence &refSequence, std::string &updatedSeq)
Gets the sequence converting '=' to the appropriate base using the reference.
static void seqWithEquals(const char *currentSeq, int32_t seq0BasedPos, Cigar &cigar, const char *referenceName, const GenomeSequence &refSequence, std::string &updatedSeq)
Gets the sequence with '=' in any position where the sequence matches the reference.
Class providing an easy to use interface to get/set/operate on the fields in a SAM/BAM record.
This class contains the match/mismatch information between the reference and a read for a single base...
void setQueryIndex(int32_t queryIndex)
Set the query index for this object.
void setType(Type newType)
Set the type (match/mismatch/unkown) for this object.
Type
More types can be added later as needed.
int32_t getQueryIndex()
Get the query index for this object.
Type getType()
Get the type (match/mismatch/unknown) for this object.