/* int loadSeqs(FILE*)
* Loads the primers from the given file.
*/
int loadSeqs(FILE* prim) {
Primer* prev = NULL;
int count = 0;
while (fgets(line, MAX_SIZE, prim) != NULL) {
if (line[0] == '#')
continue;
// load name and sequence
char* name = strtok(line, CSV);
char* seq = strtok(NULL, CSV);
char* rev = strtok(NULL, DEL);
if (name == NULL || seq == NULL || rev == NULL) {
error("", ERRPRIM);
continue;
}
// check for duplicate
for (Primer* pc = primo; pc != NULL; pc = pc->next)
if (!strcmp(pc->name, name))
exit(error(name, ERRPREP));
// create primer
Primer* p = (Primer*) memalloc(sizeof(Primer));
p->name = (char*) memalloc(1 + strlen(name));
p->fwd = (char*) memalloc(1 + strlen(seq));
p->rev = (char*) memalloc(1 + strlen(rev));
strcpy(p->name, name);
strcpy(p->fwd, seq);
strcpy(p->rev, rev);
// save sequence rc's
p->frc = revComp(p->fwd);
p->rrc = revComp(p->rev);
p->fcount = p->rcount = p->fcountr = p->rcountr = 0;
p->next = NULL;
if (primo == NULL)
primo = p;
else
prev->next = p;
prev = p;
p->len = 0;
p->fpos = -1;
count++;
}
return count;
}
void SimpleAligner::align(dagcon::Alignment& aln) {
// This alignment type defined in blasr code base
blasr::Alignment initialAln, refinedAln;
FASTQSequence query;
query.seq = (Nucleotide*)aln.qstr.c_str();
query.length = aln.qstr.length();
DNASequence target;
target.seq = (Nucleotide*)aln.tstr.c_str();
target.length = aln.tstr.length();
SDPAlign(query, target, distScoreFn_, tupleMetrics_.tupleSize,
config_.sdpIndel, config_.sdpIndel, config_.indelRate*2,
initialAln, Local);
GuidedAlign(query, target, initialAln, distScoreFn_,
config_.bandSize, refinedAln);
std::string queryStr, alignStr, targetStr;
//StickPrintAlignment(initialAln, query, target, std::cout);
//StickPrintAlignment(refinedAln, query, target, std::cout);
CreateAlignmentStrings(refinedAln, query.seq, target.seq,
targetStr, alignStr, queryStr, query.length, target.length);
// alignment coordinates may change, update alignment object
aln.start += refinedAln.GenomicTBegin();
aln.end = aln.start + refinedAln.GenomicTEnd();
if (aln.strand == '-') {
aln.start = aln.tlen - aln.end;
aln.qstr = revComp(queryStr);
aln.tstr = revComp(targetStr);
} else {
aln.qstr = queryStr;
aln.tstr = targetStr;
}
aln.start++;
}
void SimpleAligner::align(dagcon::Alignment& aln) {
// This alignment type defined in blasr code base
blasr::Alignment initialAln, refinedAln;
FASTQSequence query;
query.seq = (Nucleotide*)aln.qstr.c_str();
query.length = aln.qstr.length();
query.AllocateRichQualityValues(query.length);
query.qual.Allocate(query.length);
DNASequence target;
target.seq = (Nucleotide*)aln.tstr.c_str();
target.length = aln.tstr.length();
SDPAlign(query, target, distScoreFn_, tupleMetrics_.tupleSize,
config_.sdpIndel, config_.sdpIndel, config_.indelRate*2,
initialAln, Local);
GuidedAlign(query, target, initialAln, distScoreFn_,
config_.bandSize, refinedAln);
//StickPrintAlignment(initialAln, query, target, std::cout);
//StickPrintAlignment(refinedAln, query, target, std::cout);
std::string queryStr, alignStr, targetStr;
CreateAlignmentStrings(refinedAln, query.seq, target.seq,
targetStr, alignStr, queryStr, query.length, target.length);
if (aln.strand == '-') {
aln.start = aln.len - (aln.end + refinedAln.tPos);
aln.qstr = revComp(queryStr);
aln.tstr = revComp(targetStr);
} else {
aln.start += refinedAln.tPos;
aln.qstr = queryStr;
aln.tstr = targetStr;
}
aln.start++;
}
