map<string, int> groupCounts;
map<string, string> groupMap;
- //map<string, int> combos;
- //map<string, int> groupToIndex;
- //vector<string> groupVector;
fastqRead readFastq(ifstream&, bool&);
- vector< vector<string> > readFastqFiles(unsigned long int&);
- bool checkReads(fastqRead&, fastqRead&);
+ vector< vector< vector<string> > > preProcessData(unsigned long int&);
+ vector< vector<string> > readFileNames(string);
+ vector< vector<string> > readFastqFiles(unsigned long int&, string, string);
+ vector< vector<string> > readFastaFiles(unsigned long int&, string, string);
+ bool checkReads(fastqRead&, fastqRead&, string, string);
int createProcesses(vector< vector<string> >, string, string, string, string, string, vector<vector<string> >, vector<vector<string> >);
int driver(vector<string>, string, string, string, string, string, vector<vector<string> >, vector<vector<string> >);
- bool getOligos(vector<vector<string> >&, vector<vector<string> >&);
+ bool getOligos(vector<vector<string> >&, vector< vector<string> >&, string);
string reverseOligo(string);
vector<pairFastqRead> getReads(bool ignoref, bool ignorer, fastqRead forward, fastqRead reverse, map<string, fastqRead>& uniques);
};
if (pDataArray->fastaFileNames[i][j] != "") {
ofstream temp;
pDataArray->m->openOutputFile(pDataArray->fastaFileNames[i][j], temp); temp.close();
- pDataArray->m->openOutputFile(pDataArray->qualFileNames[i][j], temp); temp.close();
+ if (thisfqualfile != "") { pDataArray->m->openOutputFile(pDataArray->qualFileNames[i][j], temp); temp.close(); }
}
}
}
}
ifstream inFFasta, inRFasta, inFQual, inRQual;
+ ofstream outFasta, outQual, outMisMatch, outScrapFasta, outScrapQual;
pDataArray->m->openInputFile(thisffastafile, inFFasta);
- pDataArray->m->openInputFile(thisfqualfile, inFQual);
pDataArray->m->openInputFile(thisrfastafile, inRFasta);
- pDataArray->m->openInputFile(thisrqualfile, inRQual);
-
- ofstream outFasta, outQual, outMisMatch, outScrapFasta, outScrapQual;
+ if (thisfqualfile != "") {
+ pDataArray->m->openInputFile(thisfqualfile, inFQual);
+ pDataArray->m->openInputFile(thisrqualfile, inRQual);
+ pDataArray->m->openOutputFile(pDataArray->outputQual, outQual);
+ pDataArray->m->openOutputFile(pDataArray->outputScrapQual, outScrapQual);
+ }
pDataArray->m->openOutputFile(pDataArray->outputFasta, outFasta);
- pDataArray->m->openOutputFile(pDataArray->outputQual, outQual);
pDataArray->m->openOutputFile(pDataArray->outputMisMatches, outMisMatch);
pDataArray->m->openOutputFile(pDataArray->outputScrapFasta, outScrapFasta);
- pDataArray->m->openOutputFile(pDataArray->outputScrapQual, outScrapQual);
+
outMisMatch << "Name\tLength\tMisMatches\n";
TrimOligos trimOligos(pDataArray->pdiffs, pDataArray->bdiffs, 0, 0, pDataArray->primers, pDataArray->barcodes);
- while ((!inFQual.eof()) && (!inFFasta.eof()) && (!inRFasta.eof()) && (!inRQual.eof())) {
+ while ((!inFFasta.eof()) && (!inRFasta.eof())) {
if (pDataArray->m->control_pressed) { break; }
//read seqs and quality info
Sequence fSeq(inFFasta); pDataArray->m->gobble(inFFasta);
Sequence rSeq(inRFasta); pDataArray->m->gobble(inRFasta);
- QualityScores fQual(inFQual); pDataArray->m->gobble(inFQual);
- QualityScores rQual(inRQual); pDataArray->m->gobble(inRQual);
+ QualityScores* fQual = NULL; QualityScores* rQual = NULL;
+ if (thisfqualfile != "") {
+ fQual = new QualityScores(inFQual); pDataArray->m->gobble(inFQual);
+ rQual = new QualityScores(inRQual); pDataArray->m->gobble(inRQual);
+ }
int barcodeIndex = 0;
int primerIndex = 0;
if(pDataArray->barcodes.size() != 0){
- success = trimOligos.stripBarcode(fSeq, rSeq, fQual, rQual, barcodeIndex);
+ if (thisfqualfile != "") {
+ success = trimOligos.stripBarcode(fSeq, rSeq, *fQual, *rQual, barcodeIndex);
+ }else {
+ success = trimOligos.stripBarcode(fSeq, rSeq, barcodeIndex);
+ }
if(success > pDataArray->bdiffs) { trashCode += 'b'; }
else{ currentSeqsDiffs += success; }
}
if(pDataArray->primers.size() != 0){
- success = trimOligos.stripForward(fSeq, rSeq, fQual, rQual, primerIndex);
+ if (thisfqualfile != "") {
+ success = trimOligos.stripForward(fSeq, rSeq, *fQual, *rQual, primerIndex);
+ }else {
+ success = trimOligos.stripForward(fSeq, rSeq, primerIndex);
+ }
if(success > pDataArray->pdiffs) { trashCode += 'f'; }
else{ currentSeqsDiffs += success; }
}
//flip the reverse reads
rSeq.reverseComplement();
- rQual.flipQScores();
+ if (thisfqualfile != "") { rQual->flipQScores(); }
//pairwise align
alignment->align(fSeq.getUnaligned(), rSeq.getUnaligned());
int numMismatches = 0;
string seq1 = fSeq.getAligned();
string seq2 = rSeq.getAligned();
- vector<int> scores1 = fQual.getQualityScores();
- vector<int> scores2 = rQual.getQualityScores();
+ vector<int> scores1, scores2;
+ if (thisfqualfile != "") {
+ scores1 = fQual->getQualityScores();
+ scores2 = rQual->getQualityScores();
+ delete fQual; delete rQual;
+ }
int overlapStart = fSeq.getStartPos();
int seq2Start = rSeq.getStartPos();
overlapStart = seq2Start;
for (int i = 0; i < overlapStart; i++) {
contig += seq1[i];
- contigScores.push_back(scores1[ABaseMap[i]]);
+ if (thisfqualfile != "") { contigScores.push_back(scores1[ABaseMap[i]]); }
}
}else { //seq1 starts later so take from 0 to overlapStart from seq2
for (int i = 0; i < overlapStart; i++) {
contig += seq2[i];
- contigScores.push_back(scores2[BBaseMap[i]]);
+ if (thisfqualfile != "") { contigScores.push_back(scores2[BBaseMap[i]]); }
}
}
for (int i = overlapStart; i < overlapEnd; i++) {
if (seq1[i] == seq2[i]) { //match, add base and choose highest score
contig += seq1[i];
- contigScores.push_back(scores1[ABaseMap[i]]);
- if (scores1[ABaseMap[i]] < scores2[BBaseMap[i]]) { contigScores[contigScores.size()-1] = scores2[BBaseMap[i]]; }
- }else if (((seq1[i] == '.') || (seq1[i] == '-')) && ((seq2[i] != '-') && (seq2[i] != '.'))) { //seq1 is a gap and seq2 is a base, choose seq2, unless quality score for base is below threshold. In that case eliminate base
- if (scores2[BBaseMap[i]] < pDataArray->threshold) { } //
- else {
- contig += seq2[i];
- contigScores.push_back(scores2[BBaseMap[i]]);
- }
- }else if (((seq2[i] == '.') || (seq2[i] == '-')) && ((seq1[i] != '-') && (seq1[i] != '.'))) { //seq2 is a gap and seq1 is a base, choose seq1, unless quality score for base is below threshold. In that case eliminate base
- if (scores1[ABaseMap[i]] < pDataArray->threshold) { } //
- else {
- contig += seq1[i];
+ if (thisfqualfile != "") {
contigScores.push_back(scores1[ABaseMap[i]]);
+ if (scores1[ABaseMap[i]] < scores2[BBaseMap[i]]) { contigScores[contigScores.size()-1] = scores2[BBaseMap[i]]; }
}
+ }else if (((seq1[i] == '.') || (seq1[i] == '-')) && ((seq2[i] != '-') && (seq2[i] != '.'))) { //seq1 is a gap and seq2 is a base, choose seq2, unless quality score for base is below threshold. In that case eliminate base
+ if (thisfqualfile != "") {
+ if (scores2[BBaseMap[i]] < pDataArray->threshold) { } //
+ else {
+ contig += seq2[i];
+ contigScores.push_back(scores2[BBaseMap[i]]);
+ }
+ }else { contig += seq2[i]; }
+ }else if (((seq2[i] == '.') || (seq2[i] == '-')) && ((seq1[i] != '-') && (seq1[i] != '.'))) { //seq2 is a gap and seq1 is a base, choose seq1, unless quality score for base is below threshold. In that case eliminate base
+ if (thisfqualfile != "") {
+ if (scores1[ABaseMap[i]] < pDataArray->threshold) { } //
+ else {
+ contig += seq1[i];
+ contigScores.push_back(scores1[ABaseMap[i]]);
+ }
+ }else { contig += seq1[i]; }
}else if (((seq1[i] != '-') && (seq1[i] != '.')) && ((seq2[i] != '-') && (seq2[i] != '.'))) { //both bases choose one with better quality
- char c = seq1[i];
- contigScores.push_back(scores1[ABaseMap[i]]);
- if (scores1[ABaseMap[i]] < scores2[BBaseMap[i]]) { contigScores[contigScores.size()-1] = scores2[BBaseMap[i]]; c = seq2[i]; }
- contig += c;
- numMismatches++;
+ if (thisfqualfile != "") {
+ char c = seq1[i];
+ contigScores.push_back(scores1[ABaseMap[i]]);
+ if (scores1[ABaseMap[i]] < scores2[BBaseMap[i]]) { contigScores[contigScores.size()-1] = scores2[BBaseMap[i]]; c = seq2[i]; }
+ contig += c;
+ numMismatches++;
+ }else { numMismatches++; }
}else { //should never get here
pDataArray->m->mothurOut("[ERROR]: case I didn't think of seq1 = " + toString(seq1[i]) + " and seq2 = " + toString(seq2[i]) + "\n");
}
if (seq1End < seq2End) { //seq1 ends before seq2 so take from overlap to length from seq2
for (int i = overlapEnd; i < length; i++) {
contig += seq2[i];
- contigScores.push_back(scores2[BBaseMap[i]]);
+ if (thisfqualfile != "") { contigScores.push_back(scores2[BBaseMap[i]]); }
}
}else { //seq2 ends before seq1 so take from overlap to length from seq1
for (int i = overlapEnd; i < length; i++) {
contig += seq1[i];
- contigScores.push_back(scores1[ABaseMap[i]]);
+ if (thisfqualfile != "") { contigScores.push_back(scores1[ABaseMap[i]]); }
}
}
output << ">" << fSeq.getName() << endl << contig << endl;
output.close();
- pDataArray->m->openOutputFileAppend(pDataArray->qualFileNames[barcodeIndex][primerIndex], output);
- output << ">" << fSeq.getName() << endl;
- for (int i = 0; i < contigScores.size(); i++) { output << contigScores[i] << ' '; }
- output << endl;
- output.close();
+ if (thisfqualfile != "") {
+ pDataArray->m->openOutputFileAppend(pDataArray->qualFileNames[barcodeIndex][primerIndex], output);
+ output << ">" << fSeq.getName() << endl;
+ for (int i = 0; i < contigScores.size(); i++) { output << contigScores[i] << ' '; }
+ output << endl;
+ output.close();
+ }
}
//output
outFasta << ">" << fSeq.getName() << endl << contig << endl;
- outQual << ">" << fSeq.getName() << endl;
- for (int i = 0; i < contigScores.size(); i++) { outQual << contigScores[i] << ' '; }
- outQual << endl;
+ if (thisfqualfile != "") {
+ outQual << ">" << fSeq.getName() << endl;
+ for (int i = 0; i < contigScores.size(); i++) { outQual << contigScores[i] << ' '; }
+ outQual << endl;
+ }
outMisMatch << fSeq.getName() << '\t' << contig.length() << '\t' << numMismatches << endl;
}else {
//output
outScrapFasta << ">" << fSeq.getName() << " | " << trashCode << endl << contig << endl;
- outScrapQual << ">" << fSeq.getName() << " | " << trashCode << endl;
- for (int i = 0; i < contigScores.size(); i++) { outScrapQual << contigScores[i] << ' '; }
- outScrapQual << endl;
+ if (thisfqualfile != "") {
+ outScrapQual << ">" << fSeq.getName() << " | " << trashCode << endl;
+ for (int i = 0; i < contigScores.size(); i++) { outScrapQual << contigScores[i] << ' '; }
+ outScrapQual << endl;
+ }
}
num++;
if((num) % 1000 != 0){ pDataArray->m->mothurOut(toString(num)); pDataArray->m->mothurOutEndLine(); }
inFFasta.close();
- inFQual.close();
inRFasta.close();
- inRQual.close();
outFasta.close();
- outQual.close();
outMisMatch.close();
outScrapFasta.close();
- outScrapQual.close();
+ if (thisfqualfile != "") {
+ inFQual.close();
+ inRQual.close();
+ outQual.close();
+ outScrapQual.close();
+ }
delete alignment;
- if (pDataArray->m->control_pressed) { pDataArray->m->mothurRemove(pDataArray->outputQual); pDataArray->m->mothurRemove(pDataArray->outputFasta); pDataArray->m->mothurRemove(pDataArray->outputMisMatches); pDataArray->m->mothurRemove(pDataArray->outputScrapQual); pDataArray->m->mothurRemove(pDataArray->outputScrapFasta);}
+ if (pDataArray->m->control_pressed) { pDataArray->m->mothurRemove(pDataArray->outputFasta); pDataArray->m->mothurRemove(pDataArray->outputMisMatches); pDataArray->m->mothurRemove(pDataArray->outputScrapFasta); if (thisfqualfile != "") { pDataArray->m->mothurRemove(pDataArray->outputQual); pDataArray->m->mothurRemove(pDataArray->outputScrapQual); } }
return 0;
projects / mothur.git / blobdiff