trimflowscommand.cpp

   1 /*
   2  *  trimflowscommand.cpp
   3  *  Mothur
   4  *
   5  *  Created by Pat Schloss on 12/22/10.
   6  *  Copyright 2010 Schloss Lab. All rights reserved.
   7  *
   8  */
   9
  10 #include "trimflowscommand.h"
  11 #include "needlemanoverlap.hpp"
  12
  13
  14 //**********************************************************************************************************************
  15 vector<string> TrimFlowsCommand::setParameters(){
  16         try {
  17                 CommandParameter pflow("flow", "InputTypes", "", "", "none", "none", "none","flow-file",false,true,true); parameters.push_back(pflow);
  18                 CommandParameter poligos("oligos", "InputTypes", "", "", "none", "none", "none","",false,false,true); 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,true); parameters.push_back(ppdiffs);
  23                 CommandParameter pbdiffs("bdiffs", "Number", "", "0", "", "", "","",false,false,true); 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,true); 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", "Multiple", "A-B", "A", "", "", "","",false,false, true); 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);
  35
  36                 vector<string> myArray;
  37                 for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
  38                 return myArray;
  39         }
  40         catch(exception& e) {
  41                 m->errorOut(e, "TrimFlowsCommand", "setParameters");
  42                 exit(1);
  43         }
  44 }
  45 //**********************************************************************************************************************
  46 string TrimFlowsCommand::getHelpString(){
  47         try {
  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";
  52                 return helpString;
  53         }
  54         catch(exception& e) {
  55                 m->errorOut(e, "TrimFlowsCommand", "getHelpString");
  56                 exit(1);
  57         }
  58 }
  59 //**********************************************************************************************************************
  60 string TrimFlowsCommand::getOutputPattern(string type) {
  61     try {
  62         string pattern = "";
  63
  64         if (type == "flow") {  pattern = "[filename],[tag],flow"; }
  65         else if (type == "fasta") {  pattern = "[filename],flow.fasta"; }
  66         else if (type == "file") {  pattern = "[filename],flow.files"; }
  67         else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true;  }
  68
  69         return pattern;
  70     }
  71     catch(exception& e) {
  72         m->errorOut(e, "TrimFlowsCommand", "getOutputPattern");
  73         exit(1);
  74     }
  75 }
  76 //**********************************************************************************************************************
  77
  78 TrimFlowsCommand::TrimFlowsCommand(){
  79         try {
  80                 abort = true; calledHelp = true;
  81                 setParameters();
  82                 vector<string> tempOutNames;
  83                 outputTypes["flow"] = tempOutNames;
  84                 outputTypes["fasta"] = tempOutNames;
  85         outputTypes["file"] = tempOutNames;
  86         }
  87         catch(exception& e) {
  88                 m->errorOut(e, "TrimFlowsCommand", "TrimFlowsCommand");
  89                 exit(1);
  90         }
  91 }
  92 //**********************************************************************************************************************
  93
  94 TrimFlowsCommand::TrimFlowsCommand(string option)  {
  95         try {
  96
  97                 abort = false; calledHelp = false;
  98                 comboStarts = 0;
  99
 100                 //allow user to run help
 101                 if(option == "help") { help(); abort = true; calledHelp = true; }
 102                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
 103
 104                 else {
 105
 106                         vector<string> myArray = setParameters();
 107
 108                         OptionParser parser(option);
 109                         map<string,string> parameters = parser.getParameters();
 110
 111                         ValidParameters validParameter;
 112                         map<string,string>::iterator it;
 113
 114                         //check to make sure all parameters are valid for command
 115                         for (it = parameters.begin(); it != parameters.end(); it++) {
 116                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 117                         }
 118
 119                         //initialize outputTypes
 120                         vector<string> tempOutNames;
 121                         outputTypes["flow"] = tempOutNames;
 122                         outputTypes["fasta"] = tempOutNames;
 123             outputTypes["file"] = tempOutNames;
 124
 125                         //if the user changes the input directory command factory will send this info to us in the output parameter
 126                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 127                         if (inputDir == "not found"){   inputDir = "";          }
 128                         else {
 129                                 string path;
 130                                 it = parameters.find("flow");
 131                                 //user has given a template file
 132                                 if(it != parameters.end()){
 133                                         path = m->hasPath(it->second);
 134                                         //if the user has not given a path then, add inputdir. else leave path alone.
 135                                         if (path == "") {       parameters["flow"] = inputDir + it->second;             }
 136                                 }
 137
 138                                 it = parameters.find("oligos");
 139                                 //user has given a template file
 140                                 if(it != parameters.end()){
 141                                         path = m->hasPath(it->second);
 142                                         //if the user has not given a path then, add inputdir. else leave path alone.
 143                                         if (path == "") {       parameters["oligos"] = inputDir + it->second;           }
 144                                 }
 145
 146                         }
 147
 148
 149                         //check for required parameters
 150                         flowFileName = validParameter.validFile(parameters, "flow", true);
 151                         if (flowFileName == "not found") {
 152                                 flowFileName = m->getFlowFile();
 153                                 if (flowFileName != "") {  m->mothurOut("Using " + flowFileName + " as input file for the flow parameter."); m->mothurOutEndLine(); }
 154                                 else {
 155                                         m->mothurOut("No valid current flow file. You must provide a flow file."); m->mothurOutEndLine();
 156                                         abort = true;
 157                                 }
 158                         }else if (flowFileName == "not open") { flowFileName = ""; abort = true; }
 159
 160                         //if the user changes the output directory command factory will send this info to us in the output parameter
 161                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){
 162                                 outputDir = "";
 163                                 outputDir += m->hasPath(flowFileName); //if user entered a file with a path then preserve it
 164                         }
 165
 166
 167                         //check for optional parameter and set defaults
 168                         // ...at some point should added some additional type checking...
 169
 170                         string temp;
 171                         temp = validParameter.validFile(parameters, "minflows", false); if (temp == "not found") { temp = "450"; }
 172                         m->mothurConvert(temp, minFlows);
 173
 174                         temp = validParameter.validFile(parameters, "maxflows", false); if (temp == "not found") { temp = "450"; }
 175                         m->mothurConvert(temp, maxFlows);
 176
 177
 178                         temp = validParameter.validFile(parameters, "oligos", true);
 179                         if (temp == "not found")        {       oligoFileName = "";             }
 180                         else if(temp == "not open")     {       abort = true;                   }
 181                         else                                            {       oligoFileName = temp;   m->setOligosFile(oligoFileName); }
 182
 183                         temp = validParameter.validFile(parameters, "fasta", false);            if (temp == "not found"){       fasta = 0;              }
 184                         else if(m->isTrue(temp))        {       fasta = 1;      }
 185
 186                         temp = validParameter.validFile(parameters, "maxhomop", false);         if (temp == "not found"){       temp = "9";             }
 187                         m->mothurConvert(temp, maxHomoP);
 188
 189                         temp = validParameter.validFile(parameters, "signal", false);           if (temp == "not found"){       temp = "0.50";  }
 190                         m->mothurConvert(temp, signal);
 191
 192                         temp = validParameter.validFile(parameters, "noise", false);            if (temp == "not found"){       temp = "0.70";  }
 193                         m->mothurConvert(temp, noise);
 194
 195                         temp = validParameter.validFile(parameters, "bdiffs", false);           if (temp == "not found"){       temp = "0";             }
 196                         m->mothurConvert(temp, bdiffs);
 197
 198                         temp = validParameter.validFile(parameters, "pdiffs", false);           if (temp == "not found"){       temp = "0";             }
 199                         m->mothurConvert(temp, pdiffs);
 200
 201             temp = validParameter.validFile(parameters, "ldiffs", false);               if (temp == "not found") { temp = "0"; }
 202                         m->mothurConvert(temp, ldiffs);
 203
 204             temp = validParameter.validFile(parameters, "sdiffs", false);               if (temp == "not found") { temp = "0"; }
 205                         m->mothurConvert(temp, sdiffs);
 206
 207                         temp = validParameter.validFile(parameters, "tdiffs", false);           if (temp == "not found") { int tempTotal = pdiffs + bdiffs + ldiffs + sdiffs;  temp = toString(tempTotal); }
 208                         m->mothurConvert(temp, tdiffs);
 209
 210                         if(tdiffs == 0){        tdiffs = bdiffs + pdiffs + ldiffs + sdiffs;     }
 211
 212
 213                         temp = validParameter.validFile(parameters, "processors", false);       if (temp == "not found"){       temp = m->getProcessors();      }
 214                         m->setProcessors(temp);
 215                         m->mothurConvert(temp, processors);
 216
 217                         temp = validParameter.validFile(parameters, "order", false);  if (temp == "not found"){         temp = "A";     }
 218             if (temp.length() > 1) {  m->mothurOut("[ERROR]: " + temp + " is not a valid option for order. order options are A or B. A = TACG and B = TACGTACGTACGATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATAGATCGCATGACGATCGCATATCGTCAGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATAGATCGCATGACGATCGCATATCGTCAGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATAGATCGCATGACGATCGCATATCGTCAGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGATCTCAGTCAGCAGC.\n");  abort=true;
 219             }
 220             else {
 221                 if (toupper(temp[0]) == 'A') {  flowOrder = "TACG";   }
 222                 else if(toupper(temp[0]) == 'B'){
 223                     flowOrder = "TACGTACGTACGATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATAGATCGCATGACGATCGCATATCGTCAGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATAGATCGCATGACGATCGCATATCGTCAGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATAGATCGCATGACGATCGCATATCGTCAGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGATCTCAGTCAGCAGC";   }
 224                 else {
 225                     m->mothurOut("[ERROR]: " + temp + " is not a valid option for order. order options are A or B. A = TACG and B = TACGTACGTACGATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATAGATCGCATGACGATCGCATATCGTCAGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATAGATCGCATGACGATCGCATATCGTCAGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATAGATCGCATGACGATCGCATATCGTCAGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGATCTCAGTCAGCAGC.\n");  abort=true;
 226                 }
 227             }
 228
 229                         if(oligoFileName == "") {       allFiles = 0;           }
 230                         else                                    {       allFiles = 1;           }
 231
 232                         numFPrimers = 0;
 233                         numRPrimers = 0;
 234             numLinkers = 0;
 235             numSpacers = 0;
 236                 }
 237         }
 238         catch(exception& e) {
 239                 m->errorOut(e, "TrimFlowsCommand", "TrimFlowsCommand");
 240                 exit(1);
 241         }
 242 }
 243
 244 //***************************************************************************************************************
 245
 246 int TrimFlowsCommand::execute(){
 247         try{
 248
 249                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 250
 251         map<string, string> variables;
 252                 variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(flowFileName));
 253         string fastaFileName = getOutputFileName("fasta",variables);
 254                 if(fasta){ outputNames.push_back(fastaFileName); outputTypes["fasta"].push_back(fastaFileName); }
 255
 256         variables["[tag]"] = "trim";
 257                 string trimFlowFileName = getOutputFileName("flow",variables);
 258                 outputNames.push_back(trimFlowFileName); outputTypes["flow"].push_back(trimFlowFileName);
 259
 260         variables["[tag]"] = "scrap";
 261                 string scrapFlowFileName = getOutputFileName("flow",variables);
 262                 outputNames.push_back(scrapFlowFileName); outputTypes["flow"].push_back(scrapFlowFileName);
 263
 264
 265
 266                 vector<unsigned long long> flowFilePos;
 267         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 268                 flowFilePos = getFlowFileBreaks();
 269                 for (int i = 0; i < (flowFilePos.size()-1); i++) {
 270                         lines.push_back(new linePair(flowFilePos[i], flowFilePos[(i+1)]));
 271                 }
 272         #else
 273                 ifstream in; m->openInputFile(flowFileName, in); in >> numFlows; in.close();
 274         ///////////////////////////////////////// until I fix multiple processors for windows //////////////////
 275                 processors = 1;
 276         ///////////////////////////////////////// until I fix multiple processors for windows //////////////////
 277                 if (processors == 1) {
 278                         lines.push_back(new linePair(0, 1000));
 279                 }else {
 280                         int numFlowLines;
 281                         flowFilePos = m->setFilePosEachLine(flowFileName, numFlowLines);
 282                         flowFilePos.erase(flowFilePos.begin() + 1); numFlowLines--;
 283
 284                         //figure out how many sequences you have to process
 285                         int numSeqsPerProcessor = numFlowLines / processors;
 286                         cout << numSeqsPerProcessor << '\t' << numFlowLines << endl;
 287                         for (int i = 0; i < processors; i++) {
 288                                 int startIndex =  i * numSeqsPerProcessor;
 289                                 if(i == (processors - 1)){      numSeqsPerProcessor = numFlowLines - i * numSeqsPerProcessor;   }
 290                                 lines.push_back(new linePair(flowFilePos[startIndex], numSeqsPerProcessor));
 291                                 cout << flowFilePos[startIndex] << '\t' << numSeqsPerProcessor << endl;
 292                         }
 293                 }
 294         #endif
 295
 296                 vector<vector<string> > barcodePrimerComboFileNames;
 297                 if(oligoFileName != ""){
 298                         getOligos(barcodePrimerComboFileNames);
 299                 }
 300
 301                 if(processors == 1){
 302                         driverCreateTrim(flowFileName, trimFlowFileName, scrapFlowFileName, fastaFileName, barcodePrimerComboFileNames, lines[0]);
 303                 }else{
 304                         createProcessesCreateTrim(flowFileName, trimFlowFileName, scrapFlowFileName, fastaFileName, barcodePrimerComboFileNames);
 305                 }
 306
 307                 if (m->control_pressed) {  return 0; }
 308
 309                 string flowFilesFileName;
 310                 ofstream output;
 311
 312                 if(allFiles){
 313                         set<string> namesAlreadyProcessed;
 314                         flowFilesFileName = getOutputFileName("file",variables);
 315                         m->openOutputFile(flowFilesFileName, output);
 316
 317                         for(int i=0;i<barcodePrimerComboFileNames.size();i++){
 318                                 for(int j=0;j<barcodePrimerComboFileNames[0].size();j++){
 319                                         if (namesAlreadyProcessed.count(barcodePrimerComboFileNames[i][j]) == 0) {
 320                         if (barcodePrimerComboFileNames[i][j] != "") {
 321                             FILE * pFile;
 322                             unsigned long long size;
 323
 324                             //get num bytes in file
 325                             pFile = fopen (barcodePrimerComboFileNames[i][j].c_str(),"rb");
 326                             if (pFile==NULL) perror ("Error opening file");
 327                             else{
 328                                 fseek (pFile, 0, SEEK_END);
 329                                 size=ftell(pFile);
 330                                 fclose (pFile);
 331                             }
 332
 333                             if(size < 10){
 334                                 m->mothurRemove(barcodePrimerComboFileNames[i][j]);
 335                             }
 336                             else{
 337                                 output << m->getFullPathName(barcodePrimerComboFileNames[i][j]) << endl;
 338                                 outputNames.push_back(barcodePrimerComboFileNames[i][j]);
 339                                 outputTypes["flow"].push_back(barcodePrimerComboFileNames[i][j]);
 340                             }
 341                             namesAlreadyProcessed.insert(barcodePrimerComboFileNames[i][j]);
 342                         }
 343                                         }
 344                                 }
 345                         }
 346                         output.close();
 347                 }
 348                 else{
 349                         flowFilesFileName = getOutputFileName("file",variables);
 350                         m->openOutputFile(flowFilesFileName, output);
 351
 352                         output << m->getFullPathName(trimFlowFileName) << endl;
 353
 354                         output.close();
 355                 }
 356                 outputTypes["file"].push_back(flowFilesFileName);
 357                 outputNames.push_back(flowFilesFileName);
 358
 359                 m->mothurOutEndLine();
 360                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 361                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 362                 m->mothurOutEndLine();
 363
 364                 return 0;
 365         }
 366         catch(exception& e) {
 367                 m->errorOut(e, "TrimSeqsCommand", "execute");
 368                 exit(1);
 369         }
 370 }
 371
 372 //***************************************************************************************************************
 373
 374 int TrimFlowsCommand::driverCreateTrim(string flowFileName, string trimFlowFileName, string scrapFlowFileName, string fastaFileName, vector<vector<string> > thisBarcodePrimerComboFileNames, linePair* line){
 375
 376         try {
 377                 ofstream trimFlowFile;
 378                 m->openOutputFile(trimFlowFileName, trimFlowFile);
 379                 trimFlowFile.setf(ios::fixed, ios::floatfield); trimFlowFile.setf(ios::showpoint);
 380
 381                 ofstream scrapFlowFile;
 382                 m->openOutputFile(scrapFlowFileName, scrapFlowFile);
 383                 scrapFlowFile.setf(ios::fixed, ios::floatfield); scrapFlowFile.setf(ios::showpoint);
 384
 385                 ofstream fastaFile;
 386                 if(fasta){      m->openOutputFile(fastaFileName, fastaFile);    }
 387
 388                 ifstream flowFile;
 389                 m->openInputFile(flowFileName, flowFile);
 390
 391                 flowFile.seekg(line->start);
 392
 393                 if(line->start == 0){
 394                         flowFile >> numFlows; m->gobble(flowFile);
 395                         scrapFlowFile << maxFlows << endl;
 396                         trimFlowFile << maxFlows << endl;
 397                         if(allFiles){
 398                                 for(int i=0;i<thisBarcodePrimerComboFileNames.size();i++){
 399                                         for(int j=0;j<thisBarcodePrimerComboFileNames[0].size();j++){
 400                         if (thisBarcodePrimerComboFileNames[i][j] != "") {
 401                             ofstream temp;
 402                             m->openOutputFile(thisBarcodePrimerComboFileNames[i][j], temp);
 403                             temp << maxFlows << endl;
 404                             temp.close();
 405                         }
 406                                         }
 407                                 }
 408                         }
 409                 }
 410
 411                 FlowData flowData(numFlows, signal, noise, maxHomoP, flowOrder);
 412                 //cout << " driver flowdata address " <<  &flowData  << &flowFile << endl;
 413                 int count = 0;
 414                 bool moreSeqs = 1;
 415
 416                 TrimOligos trimOligos(pdiffs, bdiffs, ldiffs, sdiffs, primers, barcodes, revPrimer, linker, spacer);
 417
 418                 while(moreSeqs) {
 419
 420                         if (m->control_pressed) { break; }
 421
 422                         int success = 1;
 423                         int currentSeqDiffs = 0;
 424                         string trashCode = "";
 425
 426                         flowData.getNext(flowFile);
 427                         flowData.capFlows(maxFlows);
 428
 429                         Sequence currSeq = flowData.getSequence();
 430                         if(!flowData.hasMinFlows(minFlows)){    //screen to see if sequence is of a minimum number of flows
 431                                 success = 0;
 432                                 trashCode += 'l';
 433                         }
 434
 435                         int primerIndex = 0;
 436                         int barcodeIndex = 0;
 437
 438             if(numLinkers != 0){
 439                 success = trimOligos.stripLinker(currSeq);
 440                 if(success > ldiffs)            {       trashCode += 'k';       }
 441                 else{ currentSeqDiffs += success;  }
 442
 443             }
 444
 445             if (m->debug) { m->mothurOut("[DEBUG]: " + currSeq.getName() + " " + currSeq.getUnaligned() + "\n"); }
 446
 447                         if(barcodes.size() != 0){
 448                                 success = trimOligos.stripBarcode(currSeq, barcodeIndex);
 449                                 if(success > bdiffs)            {       trashCode += 'b';       }
 450                                 else{ currentSeqDiffs += success;  }
 451                         }
 452
 453             if(numSpacers != 0){
 454                 success = trimOligos.stripSpacer(currSeq);
 455                 if(success > sdiffs)            {       trashCode += 's';       }
 456                 else{ currentSeqDiffs += success;  }
 457
 458             }
 459
 460                         if(numFPrimers != 0){
 461                                 success = trimOligos.stripForward(currSeq, primerIndex);
 462                                 if(success > pdiffs)            {       trashCode += 'f';       }
 463                                 else{ currentSeqDiffs += success;  }
 464                         }
 465
 466                         if (currentSeqDiffs > tdiffs)   {       trashCode += 't';   }
 467
 468                         if(numRPrimers != 0){
 469                                 success = trimOligos.stripReverse(currSeq);
 470                                 if(!success)                            {       trashCode += 'r';       }
 471                         }
 472
 473                         if(trashCode.length() == 0){
 474                 string thisGroup = "";
 475                 if(barcodes.size() != 0){
 476                     thisGroup = barcodeNameVector[barcodeIndex];
 477                     if (primers.size() != 0) {
 478                         if (primerNameVector[primerIndex] != "") {
 479                             if(thisGroup != "") {
 480                                 thisGroup += "." + primerNameVector[primerIndex];
 481                             }else {
 482                                 thisGroup = primerNameVector[primerIndex];
 483                             }
 484                         }
 485                     }
 486                 }
 487
 488                 int pos = thisGroup.find("ignore");
 489                 if (pos == string::npos) {
 490                     flowData.printFlows(trimFlowFile);
 491
 492                     if(fasta)   {       currSeq.printSequence(fastaFile);       }
 493
 494                     if(allFiles){
 495                         ofstream output;
 496                         m->openOutputFileAppend(thisBarcodePrimerComboFileNames[barcodeIndex][primerIndex], output);
 497                         output.setf(ios::fixed, ios::floatfield); trimFlowFile.setf(ios::showpoint);
 498
 499                         flowData.printFlows(output);
 500                         output.close();
 501                     }
 502                 }
 503                         }
 504                         else{
 505                                 flowData.printFlows(scrapFlowFile, trashCode);
 506                         }
 507
 508                         count++;
 509                         //cout << "driver" << '\t' << currSeq.getName() << endl;
 510                         //report progress
 511                         if((count) % 10000 == 0){       m->mothurOut(toString(count)); m->mothurOutEndLine();           }
 512
 513 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 514                         unsigned long long pos = flowFile.tellg();
 515
 516                         if ((pos == -1) || (pos >= line->end)) { break; }
 517 #else
 518                         if (flowFile.eof()) { break; }
 519 #endif
 520
 521                 }
 522                 //report progress
 523                 if((count) % 10000 != 0){       m->mothurOut(toString(count)); m->mothurOutEndLine();           }
 524
 525                 trimFlowFile.close();
 526                 scrapFlowFile.close();
 527                 flowFile.close();
 528                 if(fasta){      fastaFile.close();      }
 529
 530                 return count;
 531         }
 532         catch(exception& e) {
 533                 m->errorOut(e, "TrimSeqsCommand", "driverCreateTrim");
 534                 exit(1);
 535         }
 536 }
 537
 538 //***************************************************************************************************************
 539
 540 void TrimFlowsCommand::getOligos(vector<vector<string> >& outFlowFileNames){
 541         try {
 542                 ifstream oligosFile;
 543                 m->openInputFile(oligoFileName, oligosFile);
 544
 545                 string type, oligo, group;
 546
 547                 int indexPrimer = 0;
 548                 int indexBarcode = 0;
 549
 550                 while(!oligosFile.eof()){
 551
 552                         oligosFile >> type; m->gobble(oligosFile);      //get the first column value of the row - is it a comment or a feature we are interested in?
 553
 554                         if(type[0] == '#'){     //igore the line because there's a comment
 555                                 while (!oligosFile.eof())       {       char c = oligosFile.get(); if (c == 10 || c == 13){     break;  }       } // get rest of line if there's any crap there
 556                         }
 557                         else{                           //there's a feature we're interested in
 558
 559                                 for(int i=0;i<type.length();i++){       type[i] = toupper(type[i]);  }                                  //make type case insensitive
 560
 561                                 oligosFile >> oligo;    //get the DNA sequence for the feature
 562
 563                                 for(int i=0;i<oligo.length();i++){      //make type case insensitive and change any U's to T's
 564                                         oligo[i] = toupper(oligo[i]);
 565                                         if(oligo[i] == 'U')     {       oligo[i] = 'T'; }
 566                                 }
 567
 568                                 if(type == "FORWARD"){  //if the feature is a forward primer...
 569                                         group = "";
 570
 571                                         while (!oligosFile.eof())       {       // get rest of line in case there is a primer name = will have the name of the primer
 572                                                 char c = oligosFile.get();
 573                                                 if (c == 10 || c == 13){        break;  }
 574                                                 else if (c == 32 || c == 9){;} //space or tab
 575                                                 else {  group += c;  }
 576                                         }
 577
 578                                         //have we seen this primer already?
 579                                         map<string, int>::iterator itPrimer = primers.find(oligo);
 580                                         if (itPrimer != primers.end()) { m->mothurOut("primer " + oligo + " is in your oligos file already."); m->mothurOutEndLine();  }
 581
 582                                         primers[oligo]=indexPrimer; indexPrimer++;
 583                                         primerNameVector.push_back(group);
 584
 585                                 }
 586                                 else if(type == "REVERSE"){
 587                                         string oligoRC = reverseOligo(oligo);
 588                                         revPrimer.push_back(oligoRC);
 589                                 }
 590                                 else if(type == "BARCODE"){
 591                                         oligosFile >> group;
 592
 593                                         //check for repeat barcodes
 594                                         map<string, int>::iterator itBar = barcodes.find(oligo);
 595                                         if (itBar != barcodes.end()) { m->mothurOut("barcode " + oligo + " is in your oligos file already."); m->mothurOutEndLine();  }
 596
 597                                         barcodes[oligo]=indexBarcode; indexBarcode++;
 598                                         barcodeNameVector.push_back(group);
 599                                 }else if(type == "LINKER"){
 600                                         linker.push_back(oligo);
 601                                 }else if(type == "SPACER"){
 602                                         spacer.push_back(oligo);
 603                                 }
 604                                 else{
 605                                         m->mothurOut(type + " is not recognized as a valid type. Choices are forward, reverse, and barcode. Ignoring " + oligo + "."); m->mothurOutEndLine();
 606                                 }
 607                         }
 608
 609                         m->gobble(oligosFile);
 610                 }
 611                 oligosFile.close();
 612
 613                 if(barcodeNameVector.size() == 0 && primerNameVector[0] == ""){ allFiles = 0;   }
 614
 615                 //add in potential combos
 616                 if(barcodeNameVector.size() == 0){
 617                         barcodes[""] = 0;
 618                         barcodeNameVector.push_back("");
 619                 }
 620
 621                 if(primerNameVector.size() == 0){
 622                         primers[""] = 0;
 623                         primerNameVector.push_back("");
 624                 }
 625
 626
 627                 outFlowFileNames.resize(barcodeNameVector.size());
 628                 for(int i=0;i<outFlowFileNames.size();i++){
 629                         outFlowFileNames[i].assign(primerNameVector.size(), "");
 630                 }
 631
 632                 if(allFiles){
 633
 634                         for(map<string, int>::iterator itBar = barcodes.begin();itBar != barcodes.end();itBar++){
 635                                 for(map<string, int>::iterator itPrimer = primers.begin();itPrimer != primers.end(); itPrimer++){
 636
 637                                         string primerName = primerNameVector[itPrimer->second];
 638                                         string barcodeName = barcodeNameVector[itBar->second];
 639
 640                                         if ((primerName == "ignore") || (barcodeName == "ignore")) { } //do nothing
 641                                         else {
 642                         string comboGroupName = "";
 643                         string fileName = "";
 644
 645                         map<string, string> variables;
 646                         variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(flowFileName));
 647
 648                         if(primerName == ""){
 649                             comboGroupName = barcodeNameVector[itBar->second];
 650                             variables["[tag]"] = comboGroupName;
 651                             fileName = getOutputFileName("flow", variables);
 652                         }
 653                         else{
 654                             if(barcodeName == ""){
 655                                 comboGroupName = primerNameVector[itPrimer->second];
 656                             }
 657                             else{
 658                                 comboGroupName = barcodeNameVector[itBar->second] + "." + primerNameVector[itPrimer->second];
 659                             }
 660                             variables["[tag]"] = comboGroupName;
 661                             fileName = getOutputFileName("flow", variables);
 662                         }
 663
 664                         outFlowFileNames[itBar->second][itPrimer->second] = fileName;
 665
 666                         ofstream temp;
 667                         m->openOutputFile(fileName, temp);
 668                         temp.close();
 669                     }
 670                                 }
 671                         }
 672                 }
 673
 674                 numFPrimers = primers.size();
 675                 numRPrimers = revPrimer.size();
 676         numLinkers = linker.size();
 677         numSpacers = spacer.size();
 678
 679         }
 680         catch(exception& e) {
 681                 m->errorOut(e, "TrimSeqsCommand", "getOligos");
 682                 exit(1);
 683         }
 684 }
 685 //********************************************************************/
 686 string TrimFlowsCommand::reverseOligo(string oligo){
 687         try {
 688         string reverse = "";
 689
 690         for(int i=oligo.length()-1;i>=0;i--){
 691
 692             if(oligo[i] == 'A')         {       reverse += 'T'; }
 693             else if(oligo[i] == 'T'){   reverse += 'A'; }
 694             else if(oligo[i] == 'U'){   reverse += 'A'; }
 695
 696             else if(oligo[i] == 'G'){   reverse += 'C'; }
 697             else if(oligo[i] == 'C'){   reverse += 'G'; }
 698
 699             else if(oligo[i] == 'R'){   reverse += 'Y'; }
 700             else if(oligo[i] == 'Y'){   reverse += 'R'; }
 701
 702             else if(oligo[i] == 'M'){   reverse += 'K'; }
 703             else if(oligo[i] == 'K'){   reverse += 'M'; }
 704
 705             else if(oligo[i] == 'W'){   reverse += 'W'; }
 706             else if(oligo[i] == 'S'){   reverse += 'S'; }
 707
 708             else if(oligo[i] == 'B'){   reverse += 'V'; }
 709             else if(oligo[i] == 'V'){   reverse += 'B'; }
 710
 711             else if(oligo[i] == 'D'){   reverse += 'H'; }
 712             else if(oligo[i] == 'H'){   reverse += 'D'; }
 713
 714             else                                                {       reverse += 'N'; }
 715         }
 716
 717
 718         return reverse;
 719     }
 720         catch(exception& e) {
 721                 m->errorOut(e, "TrimFlowsCommand", "reverseOligo");
 722                 exit(1);
 723         }
 724 }
 725
 726 /**************************************************************************************************/
 727 vector<unsigned long long> TrimFlowsCommand::getFlowFileBreaks() {
 728
 729         try{
 730
 731                 vector<unsigned long long> filePos;
 732                 filePos.push_back(0);
 733
 734                 FILE * pFile;
 735                 unsigned long long size;
 736
 737                 //get num bytes in file
 738                 pFile = fopen (flowFileName.c_str(),"rb");
 739                 if (pFile==NULL) perror ("Error opening file");
 740                 else{
 741                         fseek (pFile, 0, SEEK_END);
 742                         size=ftell (pFile);
 743                         fclose (pFile);
 744                 }
 745
 746                 //estimate file breaks
 747                 unsigned long long chunkSize = 0;
 748                 chunkSize = size / processors;
 749
 750                 //file too small to divide by processors
 751                 if (chunkSize == 0)  {  processors = 1; filePos.push_back(size); return filePos;        }
 752
 753                 //for each process seekg to closest file break and search for next '>' char. make that the filebreak
 754                 for (int i = 0; i < processors; i++) {
 755                         unsigned long long spot = (i+1) * chunkSize;
 756
 757                         ifstream in;
 758                         m->openInputFile(flowFileName, in);
 759                         in.seekg(spot);
 760
 761                         string dummy = m->getline(in);
 762
 763                         //there was not another sequence before the end of the file
 764                         unsigned long long sanityPos = in.tellg();
 765
 766 //                      if (sanityPos == -1) {  break;  }
 767 //                      else {  filePos.push_back(newSpot);  }
 768                         if (sanityPos == -1) {  break;  }
 769                         else {  filePos.push_back(sanityPos);  }
 770
 771                         in.close();
 772                 }
 773
 774                 //save end pos
 775                 filePos.push_back(size);
 776
 777                 //sanity check filePos
 778                 for (int i = 0; i < (filePos.size()-1); i++) {
 779                         if (filePos[(i+1)] <= filePos[i]) {  filePos.erase(filePos.begin()+(i+1)); i--; }
 780                 }
 781
 782                 ifstream in;
 783                 m->openInputFile(flowFileName, in);
 784                 in >> numFlows;
 785                 m->gobble(in);
 786                 //unsigned long long spot = in.tellg();
 787                 //filePos[0] = spot;
 788                 in.close();
 789
 790                 processors = (filePos.size() - 1);
 791
 792                 return filePos;
 793         }
 794         catch(exception& e) {
 795                 m->errorOut(e, "TrimSeqsCommand", "getFlowFileBreaks");
 796                 exit(1);
 797         }
 798 }
 799
 800 /**************************************************************************************************/
 801
 802 int TrimFlowsCommand::createProcessesCreateTrim(string flowFileName, string trimFlowFileName, string scrapFlowFileName, string fastaFileName, vector<vector<string> > barcodePrimerComboFileNames){
 803
 804         try {
 805                 processIDS.clear();
 806                 int exitCommand = 1;
 807
 808 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 809                 int process = 1;
 810
 811                 //loop through and create all the processes you want
 812                 while (process != processors) {
 813                         int pid = fork();
 814
 815                         if (pid > 0) {
 816                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
 817                                 process++;
 818                         }else if (pid == 0){
 819
 820                                 vector<vector<string> > tempBarcodePrimerComboFileNames = barcodePrimerComboFileNames;
 821                                 if(allFiles){
 822                                         for(int i=0;i<tempBarcodePrimerComboFileNames.size();i++){
 823                                                 for(int j=0;j<tempBarcodePrimerComboFileNames[0].size();j++){
 824                             if (tempBarcodePrimerComboFileNames[i][j] != "") {
 825                                 tempBarcodePrimerComboFileNames[i][j] += toString(getpid()) + ".temp";
 826                                 ofstream temp;
 827                                 m->openOutputFile(tempBarcodePrimerComboFileNames[i][j], temp);
 828                                 temp.close();
 829                             }
 830                                                 }
 831                                         }
 832                                 }
 833                                 driverCreateTrim(flowFileName,
 834                                                                  (trimFlowFileName + toString(getpid()) + ".temp"),
 835                                                                  (scrapFlowFileName + toString(getpid()) + ".temp"),
 836                                                                  (fastaFileName + toString(getpid()) + ".temp"),
 837                                                                  tempBarcodePrimerComboFileNames, lines[process]);
 838
 839                                 exit(0);
 840                         }else {
 841                                 m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
 842                                 for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
 843                                 exit(0);
 844                         }
 845                 }
 846
 847                 //parent do my part
 848                 ofstream temp;
 849                 m->openOutputFile(trimFlowFileName, temp);
 850                 temp.close();
 851
 852                 m->openOutputFile(scrapFlowFileName, temp);
 853                 temp.close();
 854
 855                 if(fasta){
 856                         m->openOutputFile(fastaFileName, temp);
 857                         temp.close();
 858                 }
 859
 860                 driverCreateTrim(flowFileName, trimFlowFileName, scrapFlowFileName, fastaFileName, barcodePrimerComboFileNames, lines[0]);
 861
 862                 //force parent to wait until all the processes are done
 863                 for (int i=0;i<processIDS.size();i++) {
 864                         int temp = processIDS[i];
 865                         wait(&temp);
 866                 }
 867 #else
 868                 //////////////////////////////////////////////////////////////////////////////////////////////////////
 869                 //Windows version shared memory, so be careful when passing variables through the trimFlowData struct.
 870                 //Above fork() will clone, so memory is separate, but that's not the case with windows,
 871                 //////////////////////////////////////////////////////////////////////////////////////////////////////
 872
 873                 vector<trimFlowData*> pDataArray;
 874                 DWORD   dwThreadIdArray[processors-1];
 875                 HANDLE  hThreadArray[processors-1];
 876
 877                 //Create processor worker threads.
 878                 for( int i=0; i<processors-1; i++ ){
 879                         // Allocate memory for thread data.
 880                         string extension = "";
 881                         if (i != 0) { extension = toString(i) + ".temp"; processIDS.push_back(i); }
 882
 883                         vector<vector<string> > tempBarcodePrimerComboFileNames = barcodePrimerComboFileNames;
 884                         if(allFiles){
 885                                 for(int i=0;i<tempBarcodePrimerComboFileNames.size();i++){
 886                                         for(int j=0;j<tempBarcodePrimerComboFileNames[0].size();j++){
 887                         if (tempBarcodePrimerComboFileNames[i][j] != "") {
 888                             tempBarcodePrimerComboFileNames[i][j] += extension;
 889                             ofstream temp;
 890                             m->openOutputFile(tempBarcodePrimerComboFileNames[i][j], temp);
 891                             temp.close();
 892                                                 }
 893                                         }
 894                                 }
 895                         }
 896
 897                         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);
 898                         pDataArray.push_back(tempflow);
 899
 900                         //MyTrimFlowThreadFunction is in header. It must be global or static to work with the threads.
 901                         //default security attributes, thread function name, argument to thread function, use default creation flags, returns the thread identifier
 902                         hThreadArray[i] = CreateThread(NULL, 0, MyTrimFlowThreadFunction, pDataArray[i], 0, &dwThreadIdArray[i]);
 903                 }
 904
 905                 //using the main process as a worker saves time and memory
 906                 ofstream temp;
 907                 m->openOutputFile(trimFlowFileName, temp);
 908                 temp.close();
 909
 910                 m->openOutputFile(scrapFlowFileName, temp);
 911                 temp.close();
 912
 913                 if(fasta){
 914                         m->openOutputFile(fastaFileName, temp);
 915                         temp.close();
 916                 }
 917
 918                 vector<vector<string> > tempBarcodePrimerComboFileNames = barcodePrimerComboFileNames;
 919                 if(allFiles){
 920                         for(int i=0;i<tempBarcodePrimerComboFileNames.size();i++){
 921                                 for(int j=0;j<tempBarcodePrimerComboFileNames[0].size();j++){
 922                     if (tempBarcodePrimerComboFileNames[i][j] != "") {
 923                         tempBarcodePrimerComboFileNames[i][j] += toString(processors-1) + ".temp";
 924                         ofstream temp;
 925                         m->openOutputFile(tempBarcodePrimerComboFileNames[i][j], temp);
 926                         temp.close();
 927                     }
 928
 929                                 }
 930                         }
 931                 }
 932
 933                 //do my part - do last piece because windows is looking for eof
 934                 int num = driverCreateTrim(flowFileName, (trimFlowFileName  + toString(processors-1) + ".temp"), (scrapFlowFileName  + toString(processors-1) + ".temp"), (fastaFileName + toString(processors-1) + ".temp"), tempBarcodePrimerComboFileNames, lines[processors-1]);
 935                 processIDS.push_back((processors-1));
 936
 937                 //Wait until all threads have terminated.
 938                 WaitForMultipleObjects(processors-1, hThreadArray, TRUE, INFINITE);
 939
 940                 //Close all thread handles and free memory allocations.
 941                 for(int i=0; i < pDataArray.size(); i++){
 942                         num += pDataArray[i]->count;
 943                         CloseHandle(hThreadArray[i]);
 944                         delete pDataArray[i];
 945                 }
 946
 947
 948 #endif
 949                 //append files
 950                 m->mothurOutEndLine();
 951                 for(int i=0;i<processIDS.size();i++){
 952
 953                         m->mothurOut("Appending files from process " + toString(processIDS[i])); m->mothurOutEndLine();
 954
 955                         m->appendFiles((trimFlowFileName + toString(processIDS[i]) + ".temp"), trimFlowFileName);
 956                         m->mothurRemove((trimFlowFileName + toString(processIDS[i]) + ".temp"));
 957 //                      m->mothurOut("\tDone with trim.flow file"); m->mothurOutEndLine();
 958
 959                         m->appendFiles((scrapFlowFileName + toString(processIDS[i]) + ".temp"), scrapFlowFileName);
 960                         m->mothurRemove((scrapFlowFileName + toString(processIDS[i]) + ".temp"));
 961 //                      m->mothurOut("\tDone with scrap.flow file"); m->mothurOutEndLine();
 962
 963                         if(fasta){
 964                                 m->appendFiles((fastaFileName + toString(processIDS[i]) + ".temp"), fastaFileName);
 965                                 m->mothurRemove((fastaFileName + toString(processIDS[i]) + ".temp"));
 966 //                              m->mothurOut("\tDone with flow.fasta file"); m->mothurOutEndLine();
 967                         }
 968                         if(allFiles){
 969                                 for (int j = 0; j < barcodePrimerComboFileNames.size(); j++) {
 970                                         for (int k = 0; k < barcodePrimerComboFileNames[0].size(); k++) {
 971                         if (barcodePrimerComboFileNames[j][k] != "") {
 972                             m->appendFiles((barcodePrimerComboFileNames[j][k] + toString(processIDS[i]) + ".temp"), barcodePrimerComboFileNames[j][k]);
 973                             m->mothurRemove((barcodePrimerComboFileNames[j][k] + toString(processIDS[i]) + ".temp"));
 974                         }
 975                                         }
 976                                 }
 977                         }
 978                 }
 979
 980                 return exitCommand;
 981
 982         }
 983         catch(exception& e) {
 984                 m->errorOut(e, "TrimFlowsCommand", "createProcessesCreateTrim");
 985                 exit(1);
 986         }
 987 }
 988
 989 //***************************************************************************************************************