exit(1);
}
}
-
+//**********************************************************************************************************************
+string SummaryQualCommand::getOutputFileNameTag(string type, string inputName=""){
+ try {
+ string outputFileName = "";
+ map<string, vector<string> >::iterator it;
+
+ //is this a type this command creates
+ it = outputTypes.find(type);
+ if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
+ else {
+ if (type == "summary") { outputFileName = "qual.summary"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
+ }
+ return outputFileName;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SummaryQualCommand", "getOutputFileNameTag");
+ exit(1);
+ }
+}
//**********************************************************************************************************************
SummaryQualCommand::SummaryQualCommand(){
try {
//check for required parameters
qualfile = validParameter.validFile(parameters, "qfile", true);
- if (qualfile == "not open") { abort = true; }
+ if (qualfile == "not open") { qualfile = ""; abort = true; }
else if (qualfile == "not found") {
qualfile = m->getQualFile();
if (qualfile != "") { m->mothurOut("Using " + qualfile + " as input file for the qfile parameter."); m->mothurOutEndLine(); }
string temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = m->getProcessors(); }
m->setProcessors(temp);
- convert(temp, processors);
+ m->mothurConvert(temp, processors);
+
+ if (namefile == "") {
+ vector<string> files; files.push_back(qualfile);
+ parser.getNameFile(files);
+ }
}
}
catch(exception& e) {
if (namefile != "") { nameMap = m->readNames(namefile); }
vector<unsigned long long> positions;
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
positions = m->divideFile(qualfile, processors);
for (int i = 0; i < (positions.size()-1); i++) { lines.push_back(linePair(positions[i], positions[(i+1)])); }
#else
lines.push_back(linePair(0, 1000));
}else {
positions = m->setFilePosFasta(qualfile, numSeqs);
+ if (positions.size() < processors) { processors = positions.size(); }
//figure out how many sequences you have to process
int numSeqsPerProcessor = numSeqs / processors;
if (m->control_pressed) { return 0; }
//print summary file
- string summaryFile = outputDir + m->getRootName(m->getSimpleName(qualfile)) + "qual.summary";
+ string summaryFile = outputDir + m->getRootName(m->getSimpleName(qualfile)) + getOutputFileNameTag("summary");
printQual(summaryFile, position, averageQ, scores);
if (m->control_pressed) { m->mothurRemove(summaryFile); return 0; }
count += num;
}
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
unsigned long long pos = in.tellg();
if ((pos == -1) || (pos >= filePos.end)) { break; }
#else
int numSeqs = 0;
processIDS.clear();
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
//loop through and create all the processes you want
while (process != processors) {
//////////////////////////////////////////////////////////////////////////////////////////////////////
//Windows version shared memory, so be careful when passing variables through the seqSumQualData struct.
//Above fork() will clone, so memory is separate, but that's not the case with windows,
- //Taking advantage of shared memory to allow both threads to add info to vectors.
+ //Taking advantage of shared memory to pass results vectors.
//////////////////////////////////////////////////////////////////////////////////////////////////////
vector<seqSumQualData*> pDataArray;
for( int i=0; i<processors; i++ ){
// Allocate memory for thread data.
- seqSumQualData* tempSum = new seqSumQualData(&position, &averageQ, &scores, filename, m, lines[i].start, lines[i].end, namefile, nameMap);
+ seqSumQualData* tempSum = new seqSumQualData(filename, m, lines[i].start, lines[i].end, namefile, nameMap);
pDataArray.push_back(tempSum);
processIDS.push_back(i);
-
- //MySeqSumThreadFunction is in header. It must be global or static to work with the threads.
- //default security attributes, thread function name, argument to thread function, use default creation flags, returns the thread identifier
+
hThreadArray[i] = CreateThread(NULL, 0, MySeqSumQualThreadFunction, pDataArray[i], 0, &dwThreadIdArray[i]);
}
//Close all thread handles and free memory allocations.
for(int i=0; i < pDataArray.size(); i++){
numSeqs += pDataArray[i]->count;
+ int tempNum = pDataArray[i]->position.size();
+ if (position.size() < tempNum) { position.resize(tempNum, 0); }
+ if (averageQ.size() < tempNum) { averageQ.resize(tempNum, 0); }
+ if (scores.size() < tempNum) {
+ scores.resize(tempNum);
+ for (int i = 0; i < scores.size(); i++) { scores[i].resize(41, 0); }
+ }
+
+ for (int k = 0; k < tempNum; k++) { position[k] += pDataArray[i]->position[k]; }
+ for (int k = 0; k < tempNum; k++) { averageQ[k] += pDataArray[i]->averageQ[k]; }
+ for (int k = 0; k < tempNum; k++) { for (int j = 0; j < 41; j++) { scores[k][j] += pDataArray[i]->scores[k][j]; } }
+
CloseHandle(hThreadArray[i]);
delete pDataArray[i];
}