exit(1);
}
}
+//**********************************************************************************************************************
+string ScreenSeqsCommand::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 == "fasta") { outputFileName = "good" + m->getExtension(inputName); }
+ else if (type == "taxonomy") { outputFileName = "good" + m->getExtension(inputName); }
+ else if (type == "name") { outputFileName = "good" + m->getExtension(inputName); }
+ else if (type == "group") { outputFileName = "good" + m->getExtension(inputName); }
+ else if (type == "accnos") { outputFileName = "bad.accnos"; }
+ else if (type == "qfile") { outputFileName = "good" + m->getExtension(inputName); }
+ else if (type == "alignreport") { outputFileName = "good.align.report"; }
+ 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, "ScreenSeqsCommand", "getOutputFileNameTag");
+ exit(1);
+ }
+}
+
//**********************************************************************************************************************
ScreenSeqsCommand::ScreenSeqsCommand(){
try {
getSummary(positions);
}
else {
- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+ #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
positions = m->divideFile(fastafile, processors);
for (int i = 0; i < (positions.size()-1); i++) { lines.push_back(linePair(positions[i], positions[(i+1)])); }
#else
else {
int numFastaSeqs = 0;
positions = m->setFilePosFasta(fastafile, numFastaSeqs);
+ if (positions.size() < processors) { processors = positions.size(); }
//figure out how many sequences you have to process
int numSeqsPerProcessor = numFastaSeqs / processors;
#endif
}
- string goodSeqFile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "good" + m->getExtension(fastafile);
- string badAccnosFile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "bad.accnos";
+ string goodSeqFile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + getOutputFileNameTag("fasta", fastafile);
+ string badAccnosFile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + getOutputFileNameTag("accnos");
int numFastaSeqs = 0;
set<string> badSeqNames;
MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
#else
-
- //#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
- if(processors == 1){
- numFastaSeqs = driver(lines[0], goodSeqFile, badAccnosFile, fastafile, badSeqNames);
- }else{
- numFastaSeqs = createProcesses(goodSeqFile, badAccnosFile, fastafile, badSeqNames);
- }
- //#else
- // numFastaSeqs = driver(lines[0], goodSeqFile, badAccnosFile, fastafile, badSeqNames);
- //#endif
- if (m->control_pressed) { m->mothurRemove(goodSeqFile); return 0; }
+ if(processors == 1){ numFastaSeqs = driver(lines[0], goodSeqFile, badAccnosFile, fastafile, badSeqNames); }
+ else{ numFastaSeqs = createProcesses(goodSeqFile, badAccnosFile, fastafile, badSeqNames); }
+
+ if (m->control_pressed) { m->mothurRemove(goodSeqFile); return 0; }
#endif
#ifdef USE_MPI
string seqName, seqList, group;
set<string>::iterator it;
- string goodNameFile = outputDir + m->getRootName(m->getSimpleName(namefile)) + "good" + m->getExtension(namefile);
+ string goodNameFile = outputDir + m->getRootName(m->getSimpleName(namefile)) + getOutputFileNameTag("name", namefile);
outputNames.push_back(goodNameFile); outputTypes["name"].push_back(goodNameFile);
ofstream goodNameOut; m->openOutputFile(goodNameFile, goodNameOut);
ifstream inputGroups;
m->openInputFile(groupfile, inputGroups);
- string goodGroupFile = outputDir + m->getRootName(m->getSimpleName(groupfile)) + "good" + m->getExtension(groupfile);
+ string goodGroupFile = outputDir + m->getRootName(m->getSimpleName(groupfile)) + getOutputFileNameTag("group", groupfile);
outputNames.push_back(goodGroupFile); outputTypes["group"].push_back(goodGroupFile);
ofstream goodGroupOut; m->openOutputFile(goodGroupFile, goodGroupOut);
vector<int> longHomoPolymer;
vector<unsigned long long> positions;
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
positions = m->divideFile(fastafile, processors);
for (int i = 0; i < (positions.size()-1); i++) { lines.push_back(linePair(positions[i], positions[(i+1)])); }
#else
else {
int numFastaSeqs = 0;
positions = m->setFilePosFasta(fastafile, numFastaSeqs);
+ if (positions.size() < processors) { processors = positions.size(); }
//figure out how many sequences you have to process
int numSeqsPerProcessor = numFastaSeqs / processors;
driverCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, fastafile, lines[0]);
#else
int numSeqs = 0;
- //#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+ //#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
if(processors == 1){
numSeqs = driverCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, fastafile, lines[0]);
}else{
count++;
}
//if((count) % 100 == 0){ m->mothurOut("Optimizing sequence: " + toString(count)); m->mothurOutEndLine(); }
- #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 num = 0;
vector<int> processIDS;
-#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) {
string seqName, group;
set<string>::iterator it;
- string goodGroupFile = outputDir + m->getRootName(m->getSimpleName(groupfile)) + "good" + m->getExtension(groupfile);
- outputNames.push_back(goodGroupFile); outputTypes["group"].push_back(goodGroupFile);
+ string goodGroupFile = outputDir + m->getRootName(m->getSimpleName(groupfile)) + getOutputFileNameTag("group", groupfile);
+ outputNames.push_back(goodGroupFile); outputTypes["group"].push_back(goodGroupFile);
ofstream goodGroupOut; m->openOutputFile(goodGroupFile, goodGroupOut);
while(!inputGroups.eof()){
string seqName, group;
set<string>::iterator it;
- string goodAlignReportFile = outputDir + m->getRootName(m->getSimpleName(alignreport)) + "good" + m->getExtension(alignreport);
+ string goodAlignReportFile = outputDir + m->getRootName(m->getSimpleName(alignreport)) + getOutputFileNameTag("alignreport");
outputNames.push_back(goodAlignReportFile); outputTypes["alignreport"].push_back(goodAlignReportFile);
ofstream goodAlignReportOut; m->openOutputFile(goodAlignReportFile, goodAlignReportOut);
string seqName, tax;
set<string>::iterator it;
- string goodTaxFile = outputDir + m->getRootName(m->getSimpleName(taxonomy)) + "good" + m->getExtension(taxonomy);
+ string goodTaxFile = outputDir + m->getRootName(m->getSimpleName(taxonomy)) + getOutputFileNameTag("taxonomy", taxonomy);
outputNames.push_back(goodTaxFile); outputTypes["taxonomy"].push_back(goodTaxFile);
ofstream goodTaxOut; m->openOutputFile(goodTaxFile, goodTaxOut);
m->openInputFile(qualfile, in);
set<string>::iterator it;
- string goodQualFile = outputDir + m->getRootName(m->getSimpleName(qualfile)) + "good" + m->getExtension(qualfile);
+ string goodQualFile = outputDir + m->getRootName(m->getSimpleName(qualfile)) + getOutputFileNameTag("qfile", qualfile);
outputNames.push_back(goodQualFile); outputTypes["qfile"].push_back(goodQualFile);
ofstream goodQual; m->openOutputFile(goodQualFile, goodQual);
count++;
}
- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+ #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
unsigned long long pos = inFASTA.tellg();
if ((pos == -1) || (pos >= filePos.end)) { break; }
#else
int process = 1;
int num = 0;
-#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) {
if (i!=0) {extension += toString(i) + ".temp"; processIDS.push_back(i); }
// Allocate memory for thread data.
- sumScreenData* tempSum = new sumScreenData(startPos, endPos, maxAmbig, maxHomoP, minLength, maxLength, filename, m, lines[i].start, lines[i].end,goodFileName+extension, badAccnos+extension, &badSeqNames);
+ sumScreenData* tempSum = new sumScreenData(startPos, endPos, maxAmbig, maxHomoP, minLength, maxLength, filename, m, lines[i].start, lines[i].end,goodFileName+extension, badAccnos+extension);
pDataArray.push_back(tempSum);
//default security attributes, thread function name, argument to thread function, use default creation flags, returns the thread identifier
//Close all thread handles and free memory allocations.
for(int i=0; i < pDataArray.size(); i++){
num += pDataArray[i]->count;
+ for (set<string>::iterator it = pDataArray[i]->badSeqNames.begin(); it != pDataArray[i]->badSeqNames.end(); it++) { badSeqNames.insert(*it); }
CloseHandle(hThreadArray[i]);
delete pDataArray[i];
}