+int SffInfoCommand::printSffTxtSeqData(ofstream& out, seqRead& read, Header& header) {
+ try {
+
+ out << "Flowgram: ";
+ for (int i = 0; i < read.flowgram.size(); i++) { out << setprecision(2) << (read.flowgram[i]/(float)100) << '\t'; }
+
+ out << endl << "Flow Indexes: ";
+ int sum = 0;
+ for (int i = 0; i < read.flowIndex.size(); i++) { sum += read.flowIndex[i]; out << sum << '\t'; }
+
+ //make the bases you want to clip lowercase and the bases you want to keep upper case
+ if(header.clipQualRight == 0){ header.clipQualRight = read.bases.length(); }
+ for (int i = 0; i < (header.clipQualLeft-1); i++) { read.bases[i] = tolower(read.bases[i]); }
+ for (int i = (header.clipQualLeft-1); i < (header.clipQualRight-1); i++) { read.bases[i] = toupper(read.bases[i]); }
+ for (int i = (header.clipQualRight-1); i < read.bases.length(); i++) { read.bases[i] = tolower(read.bases[i]); }
+
+ out << endl << "Bases: " << read.bases << endl << "Quality Scores: ";
+ for (int i = 0; i < read.qualScores.size(); i++) { out << read.qualScores[i] << '\t'; }
+
+
+ out << endl << endl;
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SffInfoCommand", "printSffTxtSeqData");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+int SffInfoCommand::printFastaSeqData(ofstream& out, seqRead& read, Header& header) {
+ try {
+
+ string seq = read.bases;
+
+ if (trim) {
+ if(header.clipQualRight < header.clipQualLeft){
+ seq = "NNNN";
+ }
+ else if((header.clipQualRight != 0) && ((header.clipQualRight-header.clipQualLeft) >= 0)){
+ seq = seq.substr((header.clipQualLeft-1), (header.clipQualRight-header.clipQualLeft));
+ }
+ else {
+ seq = seq.substr(header.clipQualLeft-1);
+ }
+ }else{
+ //if you wanted the sfftxt then you already converted the bases to the right case
+ if (!sfftxt) {
+ //make the bases you want to clip lowercase and the bases you want to keep upper case
+ if(header.clipQualRight == 0){ header.clipQualRight = seq.length(); }
+ for (int i = 0; i < (header.clipQualLeft-1); i++) { seq[i] = tolower(seq[i]); }
+ for (int i = (header.clipQualLeft-1); i < (header.clipQualRight-1); i++) { seq[i] = toupper(seq[i]); }
+ for (int i = (header.clipQualRight-1); i < seq.length(); i++) { seq[i] = tolower(seq[i]); }
+ }
+ }
+
+ out << ">" << header.name << endl;
+ out << seq << endl;
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SffInfoCommand", "printFastaSeqData");
+ exit(1);
+ }
+}
+
+//**********************************************************************************************************************
+int SffInfoCommand::printQualSeqData(ofstream& out, seqRead& read, Header& header) {