libStatGen Software 1
|
Contains methods for converting between the query sequence and reference. More...
#include <SamQuerySeqWithRefHelper.h>
Static Public Member Functions | |
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. More... | |
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. More... | |
Contains methods for converting between the query sequence and reference.
Definition at line 101 of file SamQuerySeqWithRefHelper.h.
|
static |
Gets the sequence with '=' in any position where the sequence matches the reference.
NOTE: 'N' in both the sequence and the reference is not considered a match.
currentSeq | sequence that should be converted |
seq0BasedPos | 0 based start position of currentSeq on the reference. |
cigar | cigar string for currentSeq (used for determining how the sequence aligns to the reference) |
referenceName | reference name associated with this sequence |
refSequence | reference sequence object |
updatedSeq | return parameter that this method sets to the current sequence, replacing any matches to the reference with '='. |
Definition at line 243 of file SamQuerySeqWithRefHelper.cpp.
References BaseUtilities::areEqual(), GenomeSequence::getGenomePosition(), Cigar::getRefOffset(), Cigar::INDEX_NA, and BaseUtilities::isAmbiguous().
Referenced by SamRecord::getSequence().
|
static |
Gets the sequence converting '=' to the appropriate base using the reference.
currentSeq | sequence that should be converted |
seq0BasedPos | 0 based start position of currentSeq on the reference. |
cigar | cigar string for currentSeq (used for determining how the sequence aligns to the reference) |
referenceName | reference name associated with this sequence |
refSequence | reference sequence object |
updatedSeq | return parameter that this method sets to the current sequence, replacing any '=' with the base from the reference. |
Definition at line 296 of file SamQuerySeqWithRefHelper.cpp.
References BaseUtilities::areEqual(), GenomeSequence::getGenomePosition(), Cigar::getRefOffset(), and Cigar::INDEX_NA.
Referenced by SamRecord::getSequence().