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#include <pbdata/sam/SAMAlignment.hpp>
SAMAlignment::SAMAlignment()
{
score = xs = xe = as = xt = xq = nm = fi = xl = 0;
rg = optTagStr = "";
}
void SAMAlignment::PrintSAMAlignment(std::ostream& out)
{
out << qName << "\t" << flag << "\t" << rName << "\t" << pos << "\t" << mapQV << "\t" << cigar
<< "\t" << rNext << "\t" << pNext << "\t" << tLen << "\t" << seq << "\t" << qual << "\t"
<< optTagStr << std::endl;
}
size_t SAMAlignment::FindPosOfNthChar(std::string str, int n, char c)
{
if (n < 1) {
std::cout << "Nth should be a positive integer." << std::endl;
exit(EXIT_SUCCESS);
}
int count = 1;
size_t pos = str.find(c, 0);
// pos is the position of the first character c;
while (count < n and pos != std::string::npos) {
pos = str.find(c, pos + 1);
count++;
}
return pos;
}
std::string SAMAlignment::TrimStringEnd(std::string str)
{
std::string newStr = str;
while (newStr[newStr.size() - 1] == '\r' or newStr[newStr.size() - 1] == '\n') {
newStr.erase(newStr.size() - 1, 1);
}
return newStr;
}
bool SAMAlignment::StoreValues(std::string& line, int lineNumber)
{
std::stringstream strm(line);
std::vector<bool> usedFields;
usedFields.resize(S_QUAL);
std::fill(usedFields.begin(), usedFields.end(), false);
std::string kvPair;
bool parseError = false;
SAMAlignmentRequiredFields field{};
//
// Define a temporary mapqv value that gets over a GMAP bug that prints a mapqv < 0.
//
int tmpMapQV = 0;
if (!(strm >> qName)) {
parseError = true;
field = S_QNAME;
} else if (!(strm >> flag)) {
parseError = true;
field = S_FLAG;
} else if (!(strm >> rName)) {
parseError = true;
field = S_RNAME;
} else if (!(strm >> pos)) {
parseError = true;
field = S_POS;
} else if (!(strm >> tmpMapQV)) {
parseError = true;
field = S_MAPQV;
} else if (!(strm >> cigar)) {
parseError = true;
field = S_CIGAR;
}
else if (!(strm >> rNext)) {
parseError = true;
field = S_RNEXT;
}
else if (!(strm >> pNext)) {
parseError = true;
field = S_PNEXT;
} else if (!(strm >> tLen)) {
parseError = true;
field = S_TLEN;
} else if (!(strm >> seq)) {
parseError = true;
field = S_SEQ;
} else if (!(strm >> qual)) {
parseError = true;
field = S_QUAL;
}
mapQV = (unsigned char)tmpMapQV;
// Find posisition of the 11th tab.
size_t optTagsStartPos = FindPosOfNthChar(strm.str(), 11, '\t');
// Save all optional tags.
if (optTagsStartPos != std::string::npos) {
optTagStr = strm.str().substr(optTagsStartPos + 1);
optTagStr = TrimStringEnd(optTagStr);
}
//
// If not aligned, stop trying to read in elements from the sam string.
//
if (rName == "*") {
return true;
}
if (parseError) {
std::cout << "Error parsing alignment line " << lineNumber << ". Missing or error in field "
<< SAMAlignmentRequiredFieldNames[field] << std::endl;
std::exit(EXIT_FAILURE);
}
//
// Now parse optional data.
//
while (strm) {
std::string kvName, kvType, kvValue;
std::string typedKVPair;
if (!(strm >> typedKVPair)) {
break;
}
if (TypedKeywordValuePair::Separate(typedKVPair, kvName, kvType, kvValue)) {
std::stringstream strm(kvValue);
if (kvName == "RG") {
rg = kvValue;
} else if (kvName == "AS") {
strm >> as;
} else if (kvName == "XS") {
strm >> xs;
} else if (kvName == "XE") {
strm >> xe;
} else if (kvName == "XL") {
strm >> xl;
} else if (kvName == "XT") {
strm >> xt;
} else if (kvName == "NM") {
strm >> nm;
} else if (kvName == "FI") {
strm >> fi;
} else if (kvName == "XQ") {
strm >> xq;
} // Add quality values, including QualityValue?,
// InsertionQV, DeletionQV, SubstitutionQV,
// MergeQV and SubstitutionTag and DeletionTag
else if (kvName == "iq") {
strm >> iq;
} else if (kvName == "dq") {
strm >> dq;
} else if (kvName == "sq") {
strm >> sq;
} else if (kvName == "mq") {
strm >> mq;
} else if (kvName == "st") {
strm >> st;
} else if (kvName == "dt") {
strm >> dt;
}
} else {
std::cout << "ERROR. Could not parse typed keyword value " << typedKVPair << std::endl;
exit(EXIT_SUCCESS);
}
}
return true;
}
void SAMAlignment::CopyQVs(std::vector<std::string>* optionalQVs)
{
optionalQVs->clear();
optionalQVs->push_back(iq);
optionalQVs->push_back(dq);
optionalQVs->push_back(sq);
optionalQVs->push_back(mq);
optionalQVs->push_back(st);
optionalQVs->push_back(dt);
}
const char* SAMAlignment::SAMAlignmentRequiredFieldNames[] = {
"QNAME", "FLAG", "RNAME", "POS", "MAPQV", "CIGAR", "RNEXT", "PNEXT", "TLEN", "SEQ", "QUAL"};
const char* optionalQVTags[] = {"iq", "dq", "sq", "mq", "st", "dt"};
const char* optionalQVNames[] = {"InsertionQV", "DeletionQV", "SubstitutionQV",
"MergeQV", "SubstitutionTag", "DeletionTag"};
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