18 #ifndef __SAM_QUERY_SEQ_WITH_REF_HELPER_H__ 19 #define __SAM_QUERY_SEQ_WITH_REF_HELPER_H__ 23 #include "SamRecord.h" 24 #include "GenomeSequence.h" 32 enum Type {UNKNOWN, MATCH, MISMATCH};
71 bool reset(
bool forward =
true);
94 uint32_t myStartOfReadOnRefIndex;
115 static void seqWithEquals(
const char* currentSeq,
116 int32_t seq0BasedPos,
118 const char* referenceName,
120 std::string& updatedSeq);
131 static void seqWithoutEquals(
const char* currentSeq,
132 int32_t seq0BasedPos,
134 const char* referenceName,
136 std::string& updatedSeq);
Contains methods for converting between the query sequence and reference.
void setType(Type newType)
Set the type (match/mismatch/unkown) for this object.
void setQueryIndex(int32_t queryIndex)
Set the query index for this object.
Type getType()
Get the type (match/mismatch/unknown) for this object.
This class represents the CIGAR without any methods to set the cigar (see CigarRoller for that)...
Iterates through the query and compare with reference.
int32_t getQueryIndex()
Get the query index for this object.
Type
More types can be added later as needed.
Create/Access/Modify/Load Genome Sequences stored as binary mapped files.
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...