char buffer3 [4];
in.read(buffer3, 4);
header.indexLength = be_int4(*(unsigned int *)(&buffer3));
-
+
//read num reads
char buffer4 [4];
in.read(buffer4, 4);
in.read(mybuffer,8);
for (int i = 0; i < filehandlesHeaders.size(); i++) {
for (int j = 0; j < filehandlesHeaders[i].size(); j++) {
+ unsigned long long offset = 0;
+ char* thisbuffer = new char[8];
+ thisbuffer[0] = (offset >> 56) & 0xFF;
+ thisbuffer[1] = (offset >> 48) & 0xFF;
+ thisbuffer[2] = (offset >> 40) & 0xFF;
+ thisbuffer[3] = (offset >> 32) & 0xFF;
+ thisbuffer[4] = (offset >> 24) & 0xFF;
+ thisbuffer[5] = (offset >> 16) & 0xFF;
+ thisbuffer[6] = (offset >> 8) & 0xFF;
+ thisbuffer[7] = offset & 0xFF;
ofstream out;
m->openOutputFileAppend(filehandlesHeaders[i][j], out);
- out.write(mybuffer, in.gcount());
+ out.write(thisbuffer, 8);
out.close();
}
}
for (int j = 0; j < filehandlesHeaders[i].size(); j++) {
ofstream out;
m->openOutputFileAppend(filehandlesHeaders[i][j], out);
- out.write(mybuffer, in.gcount());
+ int offset = 0;
+ char* thisbuffer = new char[4];
+ thisbuffer[0] = (offset >> 24) & 0xFF;
+ thisbuffer[1] = (offset >> 16) & 0xFF;
+ thisbuffer[2] = (offset >> 8) & 0xFF;
+ thisbuffer[3] = offset & 0xFF;
+ out.write(thisbuffer, 4);
out.close();
}
}
for (int i = 0; i < filehandlesHeaders.size(); i++) {
for (int j = 0; j < filehandlesHeaders[i].size(); j++) {
ofstream out;
- m->openOutputFileAppend(filehandlesHeaders[i][j], out);
+ m->openOutputFileBinaryAppend(filehandlesHeaders[i][j], out);
out.write(mybuffer, spot-spotInFile);
out.close();
}
char buffer5 [2];
in.read(buffer5, 2);
header.clipQualRight = be_int2(*(unsigned short *)(&buffer5));
-
+
//read clipAdapterLeft
char buffer6 [2];
in.read(buffer6, 2);
char * mybuffer;
mybuffer = new char [spot-startSpotInFile];
ifstream in2;
- m->openInputFile(currentFileName, in2);
+ in2.open(currentFileName.c_str(), ios::binary);
in2.seekg(startSpotInFile);
in2.read(mybuffer,spot-startSpotInFile);
in2.close();
if(trashCodeLength == 0){
ofstream out;
- m->openOutputFileAppend(filehandles[barcodeIndex][primerIndex], out);
+ m->openOutputFileBinaryAppend(filehandles[barcodeIndex][primerIndex], out);
out.write(mybuffer, in2.gcount());
out.close();
delete[] mybuffer;
}
else{
ofstream out;
- m->openOutputFileAppend(noMatchFile, out);
+ m->openOutputFileBinaryAppend(noMatchFile, out);
out.write(mybuffer, in2.gcount());
out.close();
delete[] mybuffer;
if (trim) {
if(header.clipQualRight < header.clipQualLeft){
- seq = "NNNN";
+ if (header.clipQualRight == 0) { //don't trim right
+ seq = seq.substr(header.clipQualLeft-1);
+ }else {
+ seq = "NNNN";
+ }
}
else if((header.clipQualRight != 0) && ((header.clipQualRight-header.clipQualLeft) >= 0)){
seq = seq.substr((header.clipQualLeft-1), (header.clipQualRight-header.clipQualLeft));
}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'; }
if (trim) {
if(header.clipQualRight < header.clipQualLeft){
- seq = "NNNN";
+ if (header.clipQualRight == 0) { //don't trim right
+ seq = seq.substr(header.clipQualLeft-1);
+ }else {
+ seq = "NNNN";
+ }
}
else if((header.clipQualRight != 0) && ((header.clipQualRight-header.clipQualLeft) >= 0)){
seq = seq.substr((header.clipQualLeft-1), (header.clipQualRight-header.clipQualLeft));
}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]); }
}
}
if (trim) {
if(header.clipQualRight < header.clipQualLeft){
- out << ">" << header.name << " xy=" << header.xy << endl;
- out << "0\t0\t0\t0";
+ if (header.clipQualRight == 0) { //don't trim right
+ out << ">" << header.name << " xy=" << header.xy << " length=" << (read.qualScores.size()-header.clipQualLeft) << endl;
+ for (int i = (header.clipQualLeft-1); i < read.qualScores.size(); i++) { out << read.qualScores[i] << '\t'; }
+ }else {
+ out << ">" << header.name << " xy=" << header.xy << endl;
+ out << "0\t0\t0\t0";
+ }
}
else if((header.clipQualRight != 0) && ((header.clipQualRight-header.clipQualLeft) >= 0)){
out << ">" << header.name << " xy=" << header.xy << " length=" << (header.clipQualRight-header.clipQualLeft) << endl;
//**********************************************************************************************************************
int SffInfoCommand::printFlowSeqData(ofstream& out, seqRead& read, Header& header) {
try {
- 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;
// get rest of line in case there is a primer name
while (!inOligos.eof()) {
char c = inOligos.get();
- if (c == 10 || c == 13){ break; }
+ if (c == 10 || c == 13 || c == -1){ break; }
else if (c == 32 || c == 9){;} //space or tab
else { group += c; }
}