char buffer5 [2];
in.read(buffer5, 2);
header.clipQualRight = be_int2(*(unsigned short *)(&buffer5));
-
+
//read clipAdapterLeft
char buffer6 [2];
in.read(buffer6, 2);
}else{
//if you wanted the sfftxt then you already converted the bases to the right case
if (!sfftxt) {
+ int endValue = header.clipQualRight;
//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(); }
+ if(endValue == 0){ endValue = 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]); }
+ for (int i = (header.clipQualLeft-1); i < (endValue-1); i++) { seq[i] = toupper(seq[i]); }
+ for (int i = (endValue-1); i < seq.length(); i++) { seq[i] = tolower(seq[i]); }
}
}
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(); }
+ int endValue = header.clipQualRight;
+ if(endValue == 0){ endValue = 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]); }
+ for (int i = (header.clipQualLeft-1); i < (endValue-1); i++) { read.bases[i] = toupper(read.bases[i]); }
+ for (int i = (endValue-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'; }
}else{
//if you wanted the sfftxt then you already converted the bases to the right case
if (!sfftxt) {
+ int endValue = header.clipQualRight;
//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(); }
+ if(endValue == 0){ endValue = 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]); }
+ for (int i = (header.clipQualLeft-1); i < (endValue-1); i++) { seq[i] = toupper(seq[i]); }
+ for (int i = (endValue-1); i < seq.length(); i++) { seq[i] = tolower(seq[i]); }
}
}
//**********************************************************************************************************************
int SffInfoCommand::printFlowSeqData(ofstream& out, seqRead& read, Header& header) {
try {
- if (header.clipQualRight == 0) { header.clipQualRight = read.flowgram.size(); }
- if(header.clipQualRight > header.clipQualLeft){
-
- int rightIndex = 0;
- for (int i = 0; i < header.clipQualRight; i++) { rightIndex += read.flowIndex[i]; }
-
- out << header.name << ' ' << rightIndex;
- for (int i = 0; i < read.flowgram.size(); i++) { out << setprecision(2) << ' ' << (read.flowgram[i]/(float)100); }
- out << endl;
- }
+ int endValue = header.clipQualRight;
+ if (header.clipQualRight == 0) {
+ endValue = read.flowIndex.size();
+ if (m->debug) { m->mothurOut("[DEBUG]: " + header.name + " has clipQualRight=0.\n"); }
+ }
+ if(endValue > header.clipQualLeft){
+
+ int rightIndex = 0;
+ for (int i = 0; i < endValue; i++) { rightIndex += read.flowIndex[i]; }
+
+ out << header.name << ' ' << rightIndex;
+ for (int i = 0; i < read.flowgram.size(); i++) { out << setprecision(2) << ' ' << (read.flowgram[i]/(float)100); }
+ out << endl;
+ }
return 0;