if (m->control_pressed) { count = 0; break; }
if (count >= header.numReads) { break; }
+ //if (count >= 100) { break; }
}
//report progress
char buffer3 [4];
in.read(buffer3, 4);
header.indexLength = be_int4(*(unsigned int *)(&buffer3));
-
+
//read num reads
char buffer4 [4];
in.read(buffer4, 4);
header.numReads = be_int4(*(unsigned int *)(&buffer4));
+
+ if (m->debug) { m->mothurOut("[DEBUG]: numReads = " + toString(header.numReads) + "\n"); }
//read header length
char buffer5 [2];
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, in.gcount());
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, in.gcount());
out.close();
}
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());
+ m->openOutputFileBinaryAppend(filehandlesHeaders[i][j], out);
+ out.write(thisbuffer, 8);
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);
- out.write(mybuffer, in.gcount());
+ m->openOutputFileBinaryAppend(filehandlesHeaders[i][j], out);
+ unsigned 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);
//convert number of reads to 4 byte char*
char* thisbuffer = new char[4];
- thisbuffer[0] = (numSplitReads[i][j] >> 24) & 0xFF;
- thisbuffer[1] = (numSplitReads[i][j] >> 16) & 0xFF;
- thisbuffer[2] = (numSplitReads[i][j] >> 8) & 0xFF;
- thisbuffer[3] = numSplitReads[i][j] & 0xFF;
+ if ((m->findEdianness()) == "BIG_ENDIAN") {
+ thisbuffer[0] = (numSplitReads[i][j] >> 24) & 0xFF;
+ thisbuffer[1] = (numSplitReads[i][j] >> 16) & 0xFF;
+ thisbuffer[2] = (numSplitReads[i][j] >> 8) & 0xFF;
+ thisbuffer[3] = numSplitReads[i][j] & 0xFF;
+ }else {
+ thisbuffer[0] = numSplitReads[i][j] & 0xFF;
+ thisbuffer[1] = (numSplitReads[i][j] >> 8) & 0xFF;
+ thisbuffer[2] = (numSplitReads[i][j] >> 16) & 0xFF;
+ thisbuffer[3] = (numSplitReads[i][j] >> 24) & 0xFF;
+ }
out.write(thisbuffer, 4);
out.close();
delete[] thisbuffer;
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, in.gcount());
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, in.gcount());
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, in.gcount());
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, in.gcount());
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, in.gcount());
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, in.gcount());
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();
}
//read header length
char buffer [2];
- in.read(buffer, 2);
+ in.read(buffer, 2);
header.headerLength = be_int2(*(unsigned short *)(&buffer));
//read name length
char buffer3 [4];
in.read(buffer3, 4);
header.numBases = be_int4(*(unsigned int *)(&buffer3));
+
//read clip qual left
char buffer4 [2];
in.read(buffer4, 2);
header.clipQualLeft = be_int2(*(unsigned short *)(&buffer4));
- header.clipQualLeft = 5;
+ header.clipQualLeft = 5;
+
//read clip qual right
char buffer5 [2];
in.read(buffer5, 2);
header.clipQualRight = be_int2(*(unsigned short *)(&buffer5));
-
+
+
//read clipAdapterLeft
char buffer6 [2];
in.read(buffer6, 2);
header.clipAdapterLeft = be_int2(*(unsigned short *)(&buffer6));
+
//read clipAdapterRight
char buffer7 [2];
in.read(buffer7, 2);
header.clipAdapterRight = be_int2(*(unsigned short *)(&buffer7));
+
//read name
char* tempBuffer = new char[header.nameLength];
in.read(&(*tempBuffer), header.nameLength);
header.name = tempBuffer;
if (header.name.length() > header.nameLength) { header.name = header.name.substr(0, header.nameLength); }
+
delete[] tempBuffer;
//extract info from name
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();
int trashCodeLength = findGroup(header, read, barcodeIndex, primerIndex);
if(trashCodeLength == 0){
+ //cout << header.name << " length = " << spot << '\t' << startSpotInFile << '\t' << in2.gcount() << endl;
+
ofstream out;
- m->openOutputFileAppend(filehandles[barcodeIndex][primerIndex], out);
+ m->openOutputFileBinaryAppend(filehandles[barcodeIndex][primerIndex], out);
out.write(mybuffer, in2.gcount());
out.close();
- delete[] mybuffer;
numSplitReads[barcodeIndex][primerIndex]++;
}
else{
ofstream out;
- m->openOutputFileAppend(noMatchFile, out);
+ m->openOutputFileBinaryAppend(noMatchFile, out);
out.write(mybuffer, in2.gcount());
out.close();
- delete[] mybuffer;
}
-
+ delete[] mybuffer;
}
}else{
m->mothurOut("Error reading."); m->mothurOutEndLine();
}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;
}
filehandles[itBar->second][itPrimer->second] = thisFilename;
- m->openOutputFile(thisFilename, temp); temp.close();
+ temp.open(thisFilename.c_str(), ios::binary); temp.close();
}
}
}
projects / mothur.git / blobdiff