HANDLE hThreadArray[processors-1];
//Create processor worker threads.
- for( int i=0; i<processors-1; i++){
+ for( int h=0; h<processors-1; h++){
string extension = "";
- if (i != 0) { extension = toString(i) + ".temp"; processIDS.push_back(i); }
+ if (h != 0) { extension = toString(h) + ".temp"; processIDS.push_back(h); }
vector<vector<string> > tempFASTAFileNames = fastaFileNames;
vector<vector<string> > tempPrimerQualFileNames = qualFileNames;
vector<vector<string> > tempNameFileNames = nameFileNames;
tempFASTAFileNames,
tempPrimerQualFileNames,
tempNameFileNames,
- lines[i].start, lines[i].end, qLines[i].start, qLines[i].end, m,
+ lines[h].start, lines[h].end, qLines[h].start, qLines[h].end, m,
pdiffs, bdiffs, ldiffs, sdiffs, tdiffs, primers, barcodes, revPrimer, linker, spacer,
primerNameVector, barcodeNameVector, createGroup, allFiles, keepforward, keepFirst, removeLast,
qWindowStep, qWindowSize, qWindowAverage, qtrim, qThreshold, qAverage, qRollAverage,
minLength, maxAmbig, maxHomoP, maxLength, flip, nameMap, nameCount);
pDataArray.push_back(tempTrim);
- hThreadArray[i] = CreateThread(NULL, 0, MyTrimThreadFunction, pDataArray[i], 0, &dwThreadIdArray[i]);
+ hThreadArray[h] = CreateThread(NULL, 0, MyTrimThreadFunction, pDataArray[h], 0, &dwThreadIdArray[h]);
}
//parent do my part
m->openOutputFile(trimNameFileName, temp); temp.close();
m->openOutputFile(scrapNameFileName, temp); temp.close();
}
+ vector<vector<string> > tempFASTAFileNames = fastaFileNames;
+ vector<vector<string> > tempPrimerQualFileNames = qualFileNames;
+ vector<vector<string> > tempNameFileNames = nameFileNames;
+ if(allFiles){
+ ofstream temp;
+ string extension = toString(processors-1) + ".temp";
+ for(int i=0;i<tempFASTAFileNames.size();i++){
+ for(int j=0;j<tempFASTAFileNames[i].size();j++){
+ if (tempFASTAFileNames[i][j] != "") {
+ tempFASTAFileNames[i][j] += extension;
+ m->openOutputFile(tempFASTAFileNames[i][j], temp); temp.close();
+
+ if(qFileName != ""){
+ tempPrimerQualFileNames[i][j] += extension;
+ m->openOutputFile(tempPrimerQualFileNames[i][j], temp); temp.close();
+ }
+ if(nameFile != ""){
+ tempNameFileNames[i][j] += extension;
+ m->openOutputFile(tempNameFileNames[i][j], temp); temp.close();
+ }
+ }
+ }
+ }
+ }
- driverCreateTrim(filename, qFileName, (trimFASTAFileName + toString(processors-1) + ".temp"), (scrapFASTAFileName + toString(processors-1) + ".temp"), (trimQualFileName + toString(processors-1) + ".temp"), (scrapQualFileName + toString(processors-1) + ".temp"), (trimNameFileName + toString(processors-1) + ".temp"), (scrapNameFileName + toString(processors-1) + ".temp"), (trimCountFileName + toString(processors-1) + ".temp"), (scrapCountFileName + toString(processors-1) + ".temp"), (groupFile + toString(processors-1) + ".temp"), fastaFileNames, qualFileNames, nameFileNames, lines[processors-1], qLines[processors-1]);
+ driverCreateTrim(filename, qFileName, (trimFASTAFileName + toString(processors-1) + ".temp"), (scrapFASTAFileName + toString(processors-1) + ".temp"), (trimQualFileName + toString(processors-1) + ".temp"), (scrapQualFileName + toString(processors-1) + ".temp"), (trimNameFileName + toString(processors-1) + ".temp"), (scrapNameFileName + toString(processors-1) + ".temp"), (trimCountFileName + toString(processors-1) + ".temp"), (scrapCountFileName + toString(processors-1) + ".temp"), (groupFile + toString(processors-1) + ".temp"), tempFASTAFileNames, tempPrimerQualFileNames, tempNameFileNames, lines[processors-1], qLines[processors-1]);
processIDS.push_back(processors-1);