5 * Created by Pat Schloss on 12/22/10.
6 * Copyright 2010 Schloss Lab. All rights reserved.
10 #include "trimflowscommand.h"
11 #include "needlemanoverlap.hpp"
14 //**********************************************************************************************************************
15 vector<string> TrimFlowsCommand::setParameters(){
17 CommandParameter pflow("flow", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pflow);
18 CommandParameter poligos("oligos", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(poligos);
19 CommandParameter pmaxhomop("maxhomop", "Number", "", "9", "", "", "",false,false); parameters.push_back(pmaxhomop);
20 CommandParameter pmaxflows("maxflows", "Number", "", "450", "", "", "",false,false); parameters.push_back(pmaxflows);
21 CommandParameter pminflows("minflows", "Number", "", "450", "", "", "",false,false); parameters.push_back(pminflows);
22 CommandParameter ppdiffs("pdiffs", "Number", "", "0", "", "", "",false,false); parameters.push_back(ppdiffs);
23 CommandParameter pbdiffs("bdiffs", "Number", "", "0", "", "", "",false,false); parameters.push_back(pbdiffs);
24 CommandParameter pldiffs("ldiffs", "Number", "", "0", "", "", "",false,false); parameters.push_back(pldiffs);
25 CommandParameter psdiffs("sdiffs", "Number", "", "0", "", "", "",false,false); parameters.push_back(psdiffs);
26 CommandParameter ptdiffs("tdiffs", "Number", "", "0", "", "", "",false,false); parameters.push_back(ptdiffs);
27 CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
28 CommandParameter psignal("signal", "Number", "", "0.50", "", "", "",false,false); parameters.push_back(psignal);
29 CommandParameter pnoise("noise", "Number", "", "0.70", "", "", "",false,false); parameters.push_back(pnoise);
30 CommandParameter pallfiles("allfiles", "Boolean", "", "t", "", "", "",false,false); parameters.push_back(pallfiles);
31 CommandParameter porder("order", "String", "", "", "", "", "",false,false); parameters.push_back(porder);
32 CommandParameter pfasta("fasta", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pfasta);
33 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
34 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
36 vector<string> myArray;
37 for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
41 m->errorOut(e, "TrimFlowsCommand", "setParameters");
45 //**********************************************************************************************************************
46 string TrimFlowsCommand::getHelpString(){
48 string helpString = "";
49 helpString += "The trim.flows command reads a flowgram file and creates .....\n";
50 helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n";
51 helpString += "For more details please check out the wiki http://www.mothur.org/wiki/Trim.flows.\n";
55 m->errorOut(e, "TrimFlowsCommand", "getHelpString");
60 //**********************************************************************************************************************
62 TrimFlowsCommand::TrimFlowsCommand(){
64 abort = true; calledHelp = true;
66 vector<string> tempOutNames;
67 outputTypes["flow"] = tempOutNames;
68 outputTypes["fasta"] = tempOutNames;
71 m->errorOut(e, "TrimFlowsCommand", "TrimFlowsCommand");
75 //**********************************************************************************************************************
77 TrimFlowsCommand::TrimFlowsCommand(string option) {
80 abort = false; calledHelp = false;
83 //allow user to run help
84 if(option == "help") { help(); abort = true; calledHelp = true; }
85 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
89 vector<string> myArray = setParameters();
91 OptionParser parser(option);
92 map<string,string> parameters = parser.getParameters();
94 ValidParameters validParameter;
95 map<string,string>::iterator it;
97 //check to make sure all parameters are valid for command
98 for (it = parameters.begin(); it != parameters.end(); it++) {
99 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
102 //initialize outputTypes
103 vector<string> tempOutNames;
104 outputTypes["flow"] = tempOutNames;
105 outputTypes["fasta"] = tempOutNames;
107 //if the user changes the input directory command factory will send this info to us in the output parameter
108 string inputDir = validParameter.validFile(parameters, "inputdir", false);
109 if (inputDir == "not found"){ inputDir = ""; }
112 it = parameters.find("flow");
113 //user has given a template file
114 if(it != parameters.end()){
115 path = m->hasPath(it->second);
116 //if the user has not given a path then, add inputdir. else leave path alone.
117 if (path == "") { parameters["flow"] = inputDir + it->second; }
120 it = parameters.find("oligos");
121 //user has given a template file
122 if(it != parameters.end()){
123 path = m->hasPath(it->second);
124 //if the user has not given a path then, add inputdir. else leave path alone.
125 if (path == "") { parameters["oligos"] = inputDir + it->second; }
131 //check for required parameters
132 flowFileName = validParameter.validFile(parameters, "flow", true);
133 if (flowFileName == "not found") {
134 flowFileName = m->getFlowFile();
135 if (flowFileName != "") { m->mothurOut("Using " + flowFileName + " as input file for the flow parameter."); m->mothurOutEndLine(); }
137 m->mothurOut("No valid current flow file. You must provide a flow file."); m->mothurOutEndLine();
140 }else if (flowFileName == "not open") { flowFileName = ""; abort = true; }
142 //if the user changes the output directory command factory will send this info to us in the output parameter
143 outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){
145 outputDir += m->hasPath(flowFileName); //if user entered a file with a path then preserve it
149 //check for optional parameter and set defaults
150 // ...at some point should added some additional type checking...
153 temp = validParameter.validFile(parameters, "minflows", false); if (temp == "not found") { temp = "450"; }
154 m->mothurConvert(temp, minFlows);
156 temp = validParameter.validFile(parameters, "maxflows", false); if (temp == "not found") { temp = "450"; }
157 m->mothurConvert(temp, maxFlows);
160 temp = validParameter.validFile(parameters, "oligos", true);
161 if (temp == "not found") { oligoFileName = ""; }
162 else if(temp == "not open") { abort = true; }
163 else { oligoFileName = temp; m->setOligosFile(oligoFileName); }
165 temp = validParameter.validFile(parameters, "fasta", false); if (temp == "not found"){ fasta = 0; }
166 else if(m->isTrue(temp)) { fasta = 1; }
168 temp = validParameter.validFile(parameters, "maxhomop", false); if (temp == "not found"){ temp = "9"; }
169 m->mothurConvert(temp, maxHomoP);
171 temp = validParameter.validFile(parameters, "signal", false); if (temp == "not found"){ temp = "0.50"; }
172 m->mothurConvert(temp, signal);
174 temp = validParameter.validFile(parameters, "noise", false); if (temp == "not found"){ temp = "0.70"; }
175 m->mothurConvert(temp, noise);
177 temp = validParameter.validFile(parameters, "bdiffs", false); if (temp == "not found"){ temp = "0"; }
178 m->mothurConvert(temp, bdiffs);
180 temp = validParameter.validFile(parameters, "pdiffs", false); if (temp == "not found"){ temp = "0"; }
181 m->mothurConvert(temp, pdiffs);
183 temp = validParameter.validFile(parameters, "ldiffs", false); if (temp == "not found") { temp = "0"; }
184 m->mothurConvert(temp, ldiffs);
186 temp = validParameter.validFile(parameters, "sdiffs", false); if (temp == "not found") { temp = "0"; }
187 m->mothurConvert(temp, sdiffs);
189 temp = validParameter.validFile(parameters, "tdiffs", false); if (temp == "not found") { int tempTotal = pdiffs + bdiffs + ldiffs + sdiffs; temp = toString(tempTotal); }
190 m->mothurConvert(temp, tdiffs);
192 if(tdiffs == 0){ tdiffs = bdiffs + pdiffs + ldiffs + sdiffs; }
195 temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = m->getProcessors(); }
196 m->setProcessors(temp);
197 m->mothurConvert(temp, processors);
199 flowOrder = validParameter.validFile(parameters, "order", false);
200 if (flowOrder == "not found"){ flowOrder = "TACG"; }
201 else if(flowOrder.length() != 4){
202 m->mothurOut("The value of the order option must be four bases long\n");
205 if(oligoFileName == "") { allFiles = 0; }
206 else { allFiles = 1; }
213 catch(exception& e) {
214 m->errorOut(e, "TrimFlowsCommand", "TrimFlowsCommand");
219 //***************************************************************************************************************
221 int TrimFlowsCommand::execute(){
224 if (abort == true) { if (calledHelp) { return 0; } return 2; }
226 string trimFlowFileName = outputDir + m->getRootName(m->getSimpleName(flowFileName)) + "trim.flow";
227 outputNames.push_back(trimFlowFileName); outputTypes["flow"].push_back(trimFlowFileName);
229 string scrapFlowFileName = outputDir + m->getRootName(m->getSimpleName(flowFileName)) + "scrap.flow";
230 outputNames.push_back(scrapFlowFileName); outputTypes["flow"].push_back(scrapFlowFileName);
232 string fastaFileName = outputDir + m->getRootName(m->getSimpleName(flowFileName)) + "flow.fasta";
234 outputNames.push_back(fastaFileName); outputTypes["fasta"].push_back(fastaFileName);
237 vector<unsigned long long> flowFilePos;
238 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
239 flowFilePos = getFlowFileBreaks();
240 for (int i = 0; i < (flowFilePos.size()-1); i++) {
241 lines.push_back(new linePair(flowFilePos[i], flowFilePos[(i+1)]));
244 ifstream in; m->openInputFile(flowFileName, in); in >> numFlows; in.close();
245 ///////////////////////////////////////// until I fix multiple processors for windows //////////////////
247 ///////////////////////////////////////// until I fix multiple processors for windows //////////////////
248 if (processors == 1) {
249 lines.push_back(new linePair(0, 1000));
252 flowFilePos = m->setFilePosEachLine(flowFileName, numFlowLines);
253 flowFilePos.erase(flowFilePos.begin() + 1); numFlowLines--;
255 //figure out how many sequences you have to process
256 int numSeqsPerProcessor = numFlowLines / processors;
257 cout << numSeqsPerProcessor << '\t' << numFlowLines << endl;
258 for (int i = 0; i < processors; i++) {
259 int startIndex = i * numSeqsPerProcessor;
260 if(i == (processors - 1)){ numSeqsPerProcessor = numFlowLines - i * numSeqsPerProcessor; }
261 lines.push_back(new linePair(flowFilePos[startIndex], numSeqsPerProcessor));
262 cout << flowFilePos[startIndex] << '\t' << numSeqsPerProcessor << endl;
267 vector<vector<string> > barcodePrimerComboFileNames;
268 if(oligoFileName != ""){
269 getOligos(barcodePrimerComboFileNames);
273 driverCreateTrim(flowFileName, trimFlowFileName, scrapFlowFileName, fastaFileName, barcodePrimerComboFileNames, lines[0]);
275 createProcessesCreateTrim(flowFileName, trimFlowFileName, scrapFlowFileName, fastaFileName, barcodePrimerComboFileNames);
278 if (m->control_pressed) { return 0; }
280 string flowFilesFileName;
284 set<string> namesAlreadyProcessed;
285 flowFilesFileName = outputDir + m->getRootName(m->getSimpleName(flowFileName)) + "flow.files";
286 m->openOutputFile(flowFilesFileName, output);
288 for(int i=0;i<barcodePrimerComboFileNames.size();i++){
289 for(int j=0;j<barcodePrimerComboFileNames[0].size();j++){
290 if (namesAlreadyProcessed.count(barcodePrimerComboFileNames[i][j]) == 0) {
292 unsigned long long size;
294 //get num bytes in file
295 pFile = fopen (barcodePrimerComboFileNames[i][j].c_str(),"rb");
296 if (pFile==NULL) perror ("Error opening file");
298 fseek (pFile, 0, SEEK_END);
304 m->mothurRemove(barcodePrimerComboFileNames[i][j]);
307 output << m->getFullPathName(barcodePrimerComboFileNames[i][j]) << endl;
308 outputNames.push_back(barcodePrimerComboFileNames[i][j]);
309 outputTypes["flow"].push_back(barcodePrimerComboFileNames[i][j]);
311 namesAlreadyProcessed.insert(barcodePrimerComboFileNames[i][j]);
318 flowFilesFileName = outputDir + m->getRootName(m->getSimpleName(flowFileName)) + "flow.files";
319 m->openOutputFile(flowFilesFileName, output);
321 output << m->getFullPathName(trimFlowFileName) << endl;
325 outputTypes["flow.files"].push_back(flowFilesFileName);
326 outputNames.push_back(flowFilesFileName);
328 // set fasta file as new current fastafile
329 // string current = "";
330 // itTypes = outputTypes.find("fasta");
331 // if (itTypes != outputTypes.end()) {
332 // if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); }
335 m->mothurOutEndLine();
336 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
337 for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
338 m->mothurOutEndLine();
342 catch(exception& e) {
343 m->errorOut(e, "TrimSeqsCommand", "execute");
348 //***************************************************************************************************************
350 int TrimFlowsCommand::driverCreateTrim(string flowFileName, string trimFlowFileName, string scrapFlowFileName, string fastaFileName, vector<vector<string> > thisBarcodePrimerComboFileNames, linePair* line){
353 ofstream trimFlowFile;
354 m->openOutputFile(trimFlowFileName, trimFlowFile);
355 trimFlowFile.setf(ios::fixed, ios::floatfield); trimFlowFile.setf(ios::showpoint);
357 ofstream scrapFlowFile;
358 m->openOutputFile(scrapFlowFileName, scrapFlowFile);
359 scrapFlowFile.setf(ios::fixed, ios::floatfield); scrapFlowFile.setf(ios::showpoint);
362 if(fasta){ m->openOutputFile(fastaFileName, fastaFile); }
365 m->openInputFile(flowFileName, flowFile);
367 flowFile.seekg(line->start);
369 if(line->start == 0){
370 flowFile >> numFlows; m->gobble(flowFile);
371 scrapFlowFile << maxFlows << endl;
372 trimFlowFile << maxFlows << endl;
374 for(int i=0;i<thisBarcodePrimerComboFileNames.size();i++){
375 for(int j=0;j<thisBarcodePrimerComboFileNames[0].size();j++){
377 m->openOutputFile(thisBarcodePrimerComboFileNames[i][j], temp);
378 temp << maxFlows << endl;
385 FlowData flowData(numFlows, signal, noise, maxHomoP, flowOrder);
386 //cout << " driver flowdata address " << &flowData << &flowFile << endl;
390 TrimOligos trimOligos(pdiffs, bdiffs, primers, barcodes, revPrimer);
394 if (m->control_pressed) { break; }
397 int currentSeqDiffs = 0;
398 string trashCode = "";
400 flowData.getNext(flowFile);
401 //cout << "driver good bit " << flowFile.good() << endl;
402 flowData.capFlows(maxFlows);
404 Sequence currSeq = flowData.getSequence();
406 if(!flowData.hasMinFlows(minFlows)){ //screen to see if sequence is of a minimum number of flows
412 int barcodeIndex = 0;
415 success = trimOligos.stripLinker(currSeq);
416 if(success > ldiffs) { trashCode += 'k'; }
417 else{ currentSeqDiffs += success; }
421 if(barcodes.size() != 0){
422 success = trimOligos.stripBarcode(currSeq, barcodeIndex);
423 if(success > bdiffs) { trashCode += 'b'; }
424 else{ currentSeqDiffs += success; }
428 success = trimOligos.stripSpacer(currSeq);
429 if(success > sdiffs) { trashCode += 's'; }
430 else{ currentSeqDiffs += success; }
434 if(numFPrimers != 0){
435 success = trimOligos.stripForward(currSeq, primerIndex);
436 if(success > pdiffs) { trashCode += 'f'; }
437 else{ currentSeqDiffs += success; }
440 if (currentSeqDiffs > tdiffs) { trashCode += 't'; }
442 if(numRPrimers != 0){
443 success = trimOligos.stripReverse(currSeq);
444 if(!success) { trashCode += 'r'; }
447 if(trashCode.length() == 0){
449 flowData.printFlows(trimFlowFile);
451 if(fasta) { currSeq.printSequence(fastaFile); }
455 m->openOutputFileAppend(thisBarcodePrimerComboFileNames[barcodeIndex][primerIndex], output);
456 output.setf(ios::fixed, ios::floatfield); trimFlowFile.setf(ios::showpoint);
458 flowData.printFlows(output);
463 flowData.printFlows(scrapFlowFile, trashCode);
467 //cout << "driver" << '\t' << currSeq.getName() << endl;
469 if((count) % 10000 == 0){ m->mothurOut(toString(count)); m->mothurOutEndLine(); }
471 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
472 unsigned long long pos = flowFile.tellg();
474 if ((pos == -1) || (pos >= line->end)) { break; }
476 if (flowFile.eof()) { break; }
481 if((count) % 10000 != 0){ m->mothurOut(toString(count)); m->mothurOutEndLine(); }
483 trimFlowFile.close();
484 scrapFlowFile.close();
486 if(fasta){ fastaFile.close(); }
490 catch(exception& e) {
491 m->errorOut(e, "TrimSeqsCommand", "driverCreateTrim");
496 //***************************************************************************************************************
498 void TrimFlowsCommand::getOligos(vector<vector<string> >& outFlowFileNames){
501 m->openInputFile(oligoFileName, oligosFile);
503 string type, oligo, group;
506 int indexBarcode = 0;
508 while(!oligosFile.eof()){
510 oligosFile >> type; m->gobble(oligosFile); //get the first column value of the row - is it a comment or a feature we are interested in?
512 if(type[0] == '#'){ //igore the line because there's a comment
513 while (!oligosFile.eof()) { char c = oligosFile.get(); if (c == 10 || c == 13){ break; } } // get rest of line if there's any crap there
515 else{ //there's a feature we're interested in
517 for(int i=0;i<type.length();i++){ type[i] = toupper(type[i]); } //make type case insensitive
519 oligosFile >> oligo; //get the DNA sequence for the feature
521 for(int i=0;i<oligo.length();i++){ //make type case insensitive and change any U's to T's
522 oligo[i] = toupper(oligo[i]);
523 if(oligo[i] == 'U') { oligo[i] = 'T'; }
526 if(type == "FORWARD"){ //if the feature is a forward primer...
529 while (!oligosFile.eof()) { // get rest of line in case there is a primer name = will have the name of the primer
530 char c = oligosFile.get();
531 if (c == 10 || c == 13){ break; }
532 else if (c == 32 || c == 9){;} //space or tab
536 //have we seen this primer already?
537 map<string, int>::iterator itPrimer = primers.find(oligo);
538 if (itPrimer != primers.end()) { m->mothurOut("primer " + oligo + " is in your oligos file already."); m->mothurOutEndLine(); }
540 primers[oligo]=indexPrimer; indexPrimer++;
541 primerNameVector.push_back(group);
544 else if(type == "REVERSE"){
545 Sequence oligoRC("reverse", oligo);
546 oligoRC.reverseComplement();
547 revPrimer.push_back(oligoRC.getUnaligned());
549 else if(type == "BARCODE"){
552 //check for repeat barcodes
553 map<string, int>::iterator itBar = barcodes.find(oligo);
554 if (itBar != barcodes.end()) { m->mothurOut("barcode " + oligo + " is in your oligos file already."); m->mothurOutEndLine(); }
556 barcodes[oligo]=indexBarcode; indexBarcode++;
557 barcodeNameVector.push_back(group);
558 }else if(type == "LINKER"){
559 linker.push_back(oligo);
560 }else if(type == "SPACER"){
561 spacer.push_back(oligo);
564 m->mothurOut(type + " is not recognized as a valid type. Choices are forward, reverse, and barcode. Ignoring " + oligo + "."); m->mothurOutEndLine();
568 m->gobble(oligosFile);
572 if(barcodeNameVector.size() == 0 && primerNameVector[0] == ""){ allFiles = 0; }
574 //add in potential combos
575 if(barcodeNameVector.size() == 0){
577 barcodeNameVector.push_back("");
580 if(primerNameVector.size() == 0){
582 primerNameVector.push_back("");
586 outFlowFileNames.resize(barcodeNameVector.size());
587 for(int i=0;i<outFlowFileNames.size();i++){
588 outFlowFileNames[i].assign(primerNameVector.size(), "");
593 for(map<string, int>::iterator itBar = barcodes.begin();itBar != barcodes.end();itBar++){
594 for(map<string, int>::iterator itPrimer = primers.begin();itPrimer != primers.end(); itPrimer++){
596 string primerName = primerNameVector[itPrimer->second];
597 string barcodeName = barcodeNameVector[itBar->second];
599 string comboGroupName = "";
600 string fileName = "";
602 if(primerName == ""){
603 comboGroupName = barcodeNameVector[itBar->second];
604 fileName = outputDir + m->getRootName(m->getSimpleName(flowFileName)) + comboGroupName + ".flow";
607 if(barcodeName == ""){
608 comboGroupName = primerNameVector[itPrimer->second];
611 comboGroupName = barcodeNameVector[itBar->second] + "." + primerNameVector[itPrimer->second];
613 fileName = outputDir + m->getRootName(m->getSimpleName(flowFileName)) + comboGroupName + ".flow";
616 outFlowFileNames[itBar->second][itPrimer->second] = fileName;
619 m->openOutputFile(fileName, temp);
625 numFPrimers = primers.size();
626 numRPrimers = revPrimer.size();
627 numLinkers = linker.size();
628 numSpacers = spacer.size();
631 catch(exception& e) {
632 m->errorOut(e, "TrimSeqsCommand", "getOligos");
636 /**************************************************************************************************/
637 vector<unsigned long long> TrimFlowsCommand::getFlowFileBreaks() {
641 vector<unsigned long long> filePos;
642 filePos.push_back(0);
645 unsigned long long size;
647 //get num bytes in file
648 pFile = fopen (flowFileName.c_str(),"rb");
649 if (pFile==NULL) perror ("Error opening file");
651 fseek (pFile, 0, SEEK_END);
656 //estimate file breaks
657 unsigned long long chunkSize = 0;
658 chunkSize = size / processors;
660 //file too small to divide by processors
661 if (chunkSize == 0) { processors = 1; filePos.push_back(size); return filePos; }
663 //for each process seekg to closest file break and search for next '>' char. make that the filebreak
664 for (int i = 0; i < processors; i++) {
665 unsigned long long spot = (i+1) * chunkSize;
668 m->openInputFile(flowFileName, in);
671 string dummy = m->getline(in);
673 //there was not another sequence before the end of the file
674 unsigned long long sanityPos = in.tellg();
676 // if (sanityPos == -1) { break; }
677 // else { filePos.push_back(newSpot); }
678 if (sanityPos == -1) { break; }
679 else { filePos.push_back(sanityPos); }
685 filePos.push_back(size);
687 //sanity check filePos
688 for (int i = 0; i < (filePos.size()-1); i++) {
689 if (filePos[(i+1)] <= filePos[i]) { filePos.erase(filePos.begin()+(i+1)); i--; }
693 m->openInputFile(flowFileName, in);
696 //unsigned long long spot = in.tellg();
700 processors = (filePos.size() - 1);
704 catch(exception& e) {
705 m->errorOut(e, "TrimSeqsCommand", "getFlowFileBreaks");
710 /**************************************************************************************************/
712 int TrimFlowsCommand::createProcessesCreateTrim(string flowFileName, string trimFlowFileName, string scrapFlowFileName, string fastaFileName, vector<vector<string> > barcodePrimerComboFileNames){
718 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
721 //loop through and create all the processes you want
722 while (process != processors) {
726 processIDS.push_back(pid); //create map from line number to pid so you can append files in correct order later
730 vector<vector<string> > tempBarcodePrimerComboFileNames = barcodePrimerComboFileNames;
732 for(int i=0;i<tempBarcodePrimerComboFileNames.size();i++){
733 for(int j=0;j<tempBarcodePrimerComboFileNames[0].size();j++){
734 tempBarcodePrimerComboFileNames[i][j] += toString(getpid()) + ".temp";
736 m->openOutputFile(tempBarcodePrimerComboFileNames[i][j], temp);
742 driverCreateTrim(flowFileName,
743 (trimFlowFileName + toString(getpid()) + ".temp"),
744 (scrapFlowFileName + toString(getpid()) + ".temp"),
745 (fastaFileName + toString(getpid()) + ".temp"),
746 tempBarcodePrimerComboFileNames, lines[process]);
750 m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
751 for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
758 m->openOutputFile(trimFlowFileName, temp);
761 m->openOutputFile(scrapFlowFileName, temp);
765 m->openOutputFile(fastaFileName, temp);
769 driverCreateTrim(flowFileName, trimFlowFileName, scrapFlowFileName, fastaFileName, barcodePrimerComboFileNames, lines[0]);
771 //force parent to wait until all the processes are done
772 for (int i=0;i<processIDS.size();i++) {
773 int temp = processIDS[i];
777 //////////////////////////////////////////////////////////////////////////////////////////////////////
778 //Windows version shared memory, so be careful when passing variables through the trimFlowData struct.
779 //Above fork() will clone, so memory is separate, but that's not the case with windows,
780 //////////////////////////////////////////////////////////////////////////////////////////////////////
782 vector<trimFlowData*> pDataArray;
783 DWORD dwThreadIdArray[processors-1];
784 HANDLE hThreadArray[processors-1];
786 //Create processor worker threads.
787 for( int i=0; i<processors-1; i++ ){
788 // Allocate memory for thread data.
789 string extension = "";
790 if (i != 0) { extension = toString(i) + ".temp"; processIDS.push_back(i); }
792 vector<vector<string> > tempBarcodePrimerComboFileNames = barcodePrimerComboFileNames;
794 for(int i=0;i<tempBarcodePrimerComboFileNames.size();i++){
795 for(int j=0;j<tempBarcodePrimerComboFileNames[0].size();j++){
796 tempBarcodePrimerComboFileNames[i][j] += extension;
798 m->openOutputFile(tempBarcodePrimerComboFileNames[i][j], temp);
805 trimFlowData* tempflow = new trimFlowData(flowFileName, (trimFlowFileName + extension), (scrapFlowFileName + extension), fastaFileName, flowOrder, tempBarcodePrimerComboFileNames, barcodes, primers, revPrimer, fasta, allFiles, lines[i]->start, lines[i]->end, m, signal, noise, numFlows, maxFlows, minFlows, maxHomoP, tdiffs, bdiffs, pdiffs, i);
806 pDataArray.push_back(tempflow);
808 //MyTrimFlowThreadFunction is in header. It must be global or static to work with the threads.
809 //default security attributes, thread function name, argument to thread function, use default creation flags, returns the thread identifier
810 hThreadArray[i] = CreateThread(NULL, 0, MyTrimFlowThreadFunction, pDataArray[i], 0, &dwThreadIdArray[i]);
813 //using the main process as a worker saves time and memory
815 m->openOutputFile(trimFlowFileName, temp);
818 m->openOutputFile(scrapFlowFileName, temp);
822 m->openOutputFile(fastaFileName, temp);
826 vector<vector<string> > tempBarcodePrimerComboFileNames = barcodePrimerComboFileNames;
828 for(int i=0;i<tempBarcodePrimerComboFileNames.size();i++){
829 for(int j=0;j<tempBarcodePrimerComboFileNames[0].size();j++){
830 tempBarcodePrimerComboFileNames[i][j] += toString(processors-1) + ".temp";
832 m->openOutputFile(tempBarcodePrimerComboFileNames[i][j], temp);
839 //do my part - do last piece because windows is looking for eof
840 int num = driverCreateTrim(flowFileName, (trimFlowFileName + toString(processors-1) + ".temp"), (scrapFlowFileName + toString(processors-1) + ".temp"), (fastaFileName + toString(processors-1) + ".temp"), tempBarcodePrimerComboFileNames, lines[processors-1]);
841 processIDS.push_back((processors-1));
843 //Wait until all threads have terminated.
844 WaitForMultipleObjects(processors-1, hThreadArray, TRUE, INFINITE);
846 //Close all thread handles and free memory allocations.
847 for(int i=0; i < pDataArray.size(); i++){
848 num += pDataArray[i]->count;
849 CloseHandle(hThreadArray[i]);
850 delete pDataArray[i];
856 m->mothurOutEndLine();
857 for(int i=0;i<processIDS.size();i++){
859 m->mothurOut("Appending files from process " + toString(processIDS[i])); m->mothurOutEndLine();
861 m->appendFiles((trimFlowFileName + toString(processIDS[i]) + ".temp"), trimFlowFileName);
862 m->mothurRemove((trimFlowFileName + toString(processIDS[i]) + ".temp"));
863 // m->mothurOut("\tDone with trim.flow file"); m->mothurOutEndLine();
865 m->appendFiles((scrapFlowFileName + toString(processIDS[i]) + ".temp"), scrapFlowFileName);
866 m->mothurRemove((scrapFlowFileName + toString(processIDS[i]) + ".temp"));
867 // m->mothurOut("\tDone with scrap.flow file"); m->mothurOutEndLine();
870 m->appendFiles((fastaFileName + toString(processIDS[i]) + ".temp"), fastaFileName);
871 m->mothurRemove((fastaFileName + toString(processIDS[i]) + ".temp"));
872 // m->mothurOut("\tDone with flow.fasta file"); m->mothurOutEndLine();
875 for (int j = 0; j < barcodePrimerComboFileNames.size(); j++) {
876 for (int k = 0; k < barcodePrimerComboFileNames[0].size(); k++) {
877 m->appendFiles((barcodePrimerComboFileNames[j][k] + toString(processIDS[i]) + ".temp"), barcodePrimerComboFileNames[j][k]);
878 m->mothurRemove((barcodePrimerComboFileNames[j][k] + toString(processIDS[i]) + ".temp"));
887 catch(exception& e) {
888 m->errorOut(e, "TrimFlowsCommand", "createProcessesCreateTrim");
893 //***************************************************************************************************************