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, B, or I. A = TACG, B = TACGTACGTACGATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATAGATCGCATGACGATCGCATATCGTCAGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATAGATCGCATGACGATCGCATATCGTCAGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATAGATCGCATGACGATCGCATATCGTCAGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGATCTCAGTCAGCAGC, and I = TACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGC.\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 if(toupper(temp[0]) == 'I'){
 225                     flowOrder = "TACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGC";   }
 226                 else {
 227                     m->mothurOut("[ERROR]: " + temp + " is not a valid option for order. order options are A, B, or I. A = TACG, B = TACGTACGTACGATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATAGATCGCATGACGATCGCATATCGTCAGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATAGATCGCATGACGATCGCATATCGTCAGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATAGATCGCATGACGATCGCATATCGTCAGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGATCTCAGTCAGCAGC, and I = TACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGC.\n");  abort=true;
 228                 }
 229             }
 230
 231                         if(oligoFileName == "") {       allFiles = 0;           }
 232                         else                                    {       allFiles = 1;           }
 233
 234                         numFPrimers = 0;
 235                         numRPrimers = 0;
 236             numLinkers = 0;
 237             numSpacers = 0;
 238                 }
 239         }
 240         catch(exception& e) {
 241                 m->errorOut(e, "TrimFlowsCommand", "TrimFlowsCommand");
 242                 exit(1);
 243         }
 244 }
 245
 246 //***************************************************************************************************************
 247
 248 int TrimFlowsCommand::execute(){
 249         try{
 250
 251                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 252
 253         map<string, string> variables;
 254                 variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(flowFileName));
 255         string fastaFileName = getOutputFileName("fasta",variables);
 256                 if(fasta){ outputNames.push_back(fastaFileName); outputTypes["fasta"].push_back(fastaFileName); }
 257
 258         variables["[tag]"] = "trim";
 259                 string trimFlowFileName = getOutputFileName("flow",variables);
 260                 outputNames.push_back(trimFlowFileName); outputTypes["flow"].push_back(trimFlowFileName);
 261
 262         variables["[tag]"] = "scrap";
 263                 string scrapFlowFileName = getOutputFileName("flow",variables);
 264                 outputNames.push_back(scrapFlowFileName); outputTypes["flow"].push_back(scrapFlowFileName);
 265
 266
 267
 268                 vector<unsigned long long> flowFilePos;
 269         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 270                 flowFilePos = getFlowFileBreaks();
 271                 for (int i = 0; i < (flowFilePos.size()-1); i++) {
 272                         lines.push_back(new linePair(flowFilePos[i], flowFilePos[(i+1)]));
 273                 }
 274         #else
 275                 ifstream in; m->openInputFile(flowFileName, in); in >> numFlows; in.close();
 276         ///////////////////////////////////////// until I fix multiple processors for windows //////////////////
 277                 processors = 1;
 278         ///////////////////////////////////////// until I fix multiple processors for windows //////////////////
 279                 if (processors == 1) {
 280                         lines.push_back(new linePair(0, 1000));
 281                 }else {
 282                         int numFlowLines;
 283                         flowFilePos = m->setFilePosEachLine(flowFileName, numFlowLines);
 284                         flowFilePos.erase(flowFilePos.begin() + 1); numFlowLines--;
 285
 286                         //figure out how many sequences you have to process
 287                         int numSeqsPerProcessor = numFlowLines / processors;
 288                         cout << numSeqsPerProcessor << '\t' << numFlowLines << endl;
 289                         for (int i = 0; i < processors; i++) {
 290                                 int startIndex =  i * numSeqsPerProcessor;
 291                                 if(i == (processors - 1)){      numSeqsPerProcessor = numFlowLines - i * numSeqsPerProcessor;   }
 292                                 lines.push_back(new linePair(flowFilePos[startIndex], numSeqsPerProcessor));
 293                                 cout << flowFilePos[startIndex] << '\t' << numSeqsPerProcessor << endl;
 294                         }
 295                 }
 296         #endif
 297
 298                 vector<vector<string> > barcodePrimerComboFileNames;
 299                 if(oligoFileName != ""){
 300                         getOligos(barcodePrimerComboFileNames);
 301                 }
 302
 303                 if(processors == 1){
 304                         driverCreateTrim(flowFileName, trimFlowFileName, scrapFlowFileName, fastaFileName, barcodePrimerComboFileNames, lines[0]);
 305                 }else{
 306                         createProcessesCreateTrim(flowFileName, trimFlowFileName, scrapFlowFileName, fastaFileName, barcodePrimerComboFileNames);
 307                 }
 308
 309                 if (m->control_pressed) {  return 0; }
 310
 311                 string flowFilesFileName;
 312                 ofstream output;
 313
 314                 if(allFiles){
 315                         set<string> namesAlreadyProcessed;
 316                         flowFilesFileName = getOutputFileName("file",variables);
 317                         m->openOutputFile(flowFilesFileName, output);
 318
 319                         for(int i=0;i<barcodePrimerComboFileNames.size();i++){
 320                                 for(int j=0;j<barcodePrimerComboFileNames[0].size();j++){
 321                                         if (namesAlreadyProcessed.count(barcodePrimerComboFileNames[i][j]) == 0) {
 322                         if (barcodePrimerComboFileNames[i][j] != "") {
 323                             FILE * pFile;
 324                             unsigned long long size;
 325
 326                             //get num bytes in file
 327                             pFile = fopen (barcodePrimerComboFileNames[i][j].c_str(),"rb");
 328                             if (pFile==NULL) perror ("Error opening file");
 329                             else{
 330                                 fseek (pFile, 0, SEEK_END);
 331                                 size=ftell(pFile);
 332                                 fclose (pFile);
 333                             }
 334
 335                             if(size < 10){
 336                                 m->mothurRemove(barcodePrimerComboFileNames[i][j]);
 337                             }
 338                             else{
 339                                 output << m->getFullPathName(barcodePrimerComboFileNames[i][j]) << endl;
 340                                 outputNames.push_back(barcodePrimerComboFileNames[i][j]);
 341                                 outputTypes["flow"].push_back(barcodePrimerComboFileNames[i][j]);
 342                             }
 343                             namesAlreadyProcessed.insert(barcodePrimerComboFileNames[i][j]);
 344                         }
 345                                         }
 346                                 }
 347                         }
 348                         output.close();
 349                 }
 350                 else{
 351                         flowFilesFileName = getOutputFileName("file",variables);
 352                         m->openOutputFile(flowFilesFileName, output);
 353
 354                         output << m->getFullPathName(trimFlowFileName) << endl;
 355
 356                         output.close();
 357                 }
 358                 outputTypes["file"].push_back(flowFilesFileName);
 359                 outputNames.push_back(flowFilesFileName);
 360
 361                 m->mothurOutEndLine();
 362                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 363                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 364                 m->mothurOutEndLine();
 365
 366                 return 0;
 367         }
 368         catch(exception& e) {
 369                 m->errorOut(e, "TrimSeqsCommand", "execute");
 370                 exit(1);
 371         }
 372 }
 373
 374 //***************************************************************************************************************
 375
 376 int TrimFlowsCommand::driverCreateTrim(string flowFileName, string trimFlowFileName, string scrapFlowFileName, string fastaFileName, vector<vector<string> > thisBarcodePrimerComboFileNames, linePair* line){
 377
 378         try {
 379                 ofstream trimFlowFile;
 380                 m->openOutputFile(trimFlowFileName, trimFlowFile);
 381                 trimFlowFile.setf(ios::fixed, ios::floatfield); trimFlowFile.setf(ios::showpoint);
 382
 383                 ofstream scrapFlowFile;
 384                 m->openOutputFile(scrapFlowFileName, scrapFlowFile);
 385                 scrapFlowFile.setf(ios::fixed, ios::floatfield); scrapFlowFile.setf(ios::showpoint);
 386
 387                 ofstream fastaFile;
 388                 if(fasta){      m->openOutputFile(fastaFileName, fastaFile);    }
 389
 390                 ifstream flowFile;
 391                 m->openInputFile(flowFileName, flowFile);
 392
 393                 flowFile.seekg(line->start);
 394
 395                 if(line->start == 0){
 396                         flowFile >> numFlows; m->gobble(flowFile);
 397                         scrapFlowFile << maxFlows << endl;
 398                         trimFlowFile << maxFlows << endl;
 399                         if(allFiles){
 400                                 for(int i=0;i<thisBarcodePrimerComboFileNames.size();i++){
 401                                         for(int j=0;j<thisBarcodePrimerComboFileNames[0].size();j++){
 402                         if (thisBarcodePrimerComboFileNames[i][j] != "") {
 403                             ofstream temp;
 404                             m->openOutputFile(thisBarcodePrimerComboFileNames[i][j], temp);
 405                             temp << maxFlows << endl;
 406                             temp.close();
 407                         }
 408                                         }
 409                                 }
 410                         }
 411                 }
 412
 413                 FlowData flowData(numFlows, signal, noise, maxHomoP, flowOrder);
 414                 //cout << " driver flowdata address " <<  &flowData  << &flowFile << endl;
 415                 int count = 0;
 416                 bool moreSeqs = 1;
 417
 418                 TrimOligos trimOligos(pdiffs, bdiffs, ldiffs, sdiffs, primers, barcodes, revPrimer, linker, spacer);
 419
 420                 while(moreSeqs) {
 421
 422                         if (m->control_pressed) { break; }
 423
 424                         int success = 1;
 425                         int currentSeqDiffs = 0;
 426                         string trashCode = "";
 427
 428                         flowData.getNext(flowFile);
 429                         flowData.capFlows(maxFlows);
 430
 431                         Sequence currSeq = flowData.getSequence();
 432                         if(!flowData.hasMinFlows(minFlows)){    //screen to see if sequence is of a minimum number of flows
 433                                 success = 0;
 434                                 trashCode += 'l';
 435                         }
 436
 437                         int primerIndex = 0;
 438                         int barcodeIndex = 0;
 439
 440             if(numLinkers != 0){
 441                 success = trimOligos.stripLinker(currSeq);
 442                 if(success > ldiffs)            {       trashCode += 'k';       }
 443                 else{ currentSeqDiffs += success;  }
 444
 445             }
 446
 447             if (m->debug) { m->mothurOut("[DEBUG]: " + currSeq.getName() + " " + currSeq.getUnaligned() + "\n"); }
 448
 449                         if(barcodes.size() != 0){
 450                                 success = trimOligos.stripBarcode(currSeq, barcodeIndex);
 451                                 if(success > bdiffs)            {       trashCode += 'b';       }
 452                                 else{ currentSeqDiffs += success;  }
 453                         }
 454
 455             if(numSpacers != 0){
 456                 success = trimOligos.stripSpacer(currSeq);
 457                 if(success > sdiffs)            {       trashCode += 's';       }
 458                 else{ currentSeqDiffs += success;  }
 459
 460             }
 461
 462                         if(numFPrimers != 0){
 463                                 success = trimOligos.stripForward(currSeq, primerIndex);
 464                                 if(success > pdiffs)            {       trashCode += 'f';       }
 465                                 else{ currentSeqDiffs += success;  }
 466                         }
 467
 468                         if (currentSeqDiffs > tdiffs)   {       trashCode += 't';   }
 469
 470                         if(numRPrimers != 0){
 471                                 success = trimOligos.stripReverse(currSeq);
 472                                 if(!success)                            {       trashCode += 'r';       }
 473                         }
 474
 475                         if(trashCode.length() == 0){
 476                 string thisGroup = "";
 477                 if(barcodes.size() != 0){
 478                     thisGroup = barcodeNameVector[barcodeIndex];
 479                     if (primers.size() != 0) {
 480                         if (primerNameVector[primerIndex] != "") {
 481                             if(thisGroup != "") {
 482                                 thisGroup += "." + primerNameVector[primerIndex];
 483                             }else {
 484                                 thisGroup = primerNameVector[primerIndex];
 485                             }
 486                         }
 487                     }
 488                 }
 489
 490                 int pos = thisGroup.find("ignore");
 491                 if (pos == string::npos) {
 492                     flowData.printFlows(trimFlowFile);
 493
 494                     if(fasta)   { currSeq.printSequence(fastaFile);     }
 495
 496                     if(allFiles){
 497                         ofstream output;
 498                         m->openOutputFileAppend(thisBarcodePrimerComboFileNames[barcodeIndex][primerIndex], output);
 499                         output.setf(ios::fixed, ios::floatfield); trimFlowFile.setf(ios::showpoint);
 500
 501                         flowData.printFlows(output);
 502                         output.close();
 503                     }
 504                 }
 505                         }
 506                         else{
 507                                 flowData.printFlows(scrapFlowFile, trashCode);
 508                         }
 509
 510                         count++;
 511                         //cout << "driver" << '\t' << currSeq.getName() << endl;
 512                         //report progress
 513                         if((count) % 10000 == 0){       m->mothurOut(toString(count)); m->mothurOutEndLine();           }
 514
 515 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 516                         unsigned long long pos = flowFile.tellg();
 517
 518                         if ((pos == -1) || (pos >= line->end)) { break; }
 519 #else
 520                         if (flowFile.eof()) { break; }
 521 #endif
 522
 523                 }
 524                 //report progress
 525                 if((count) % 10000 != 0){       m->mothurOut(toString(count)); m->mothurOutEndLine();           }
 526
 527                 trimFlowFile.close();
 528                 scrapFlowFile.close();
 529                 flowFile.close();
 530                 if(fasta){      fastaFile.close();      }
 531
 532                 return count;
 533         }
 534         catch(exception& e) {
 535                 m->errorOut(e, "TrimSeqsCommand", "driverCreateTrim");
 536                 exit(1);
 537         }
 538 }
 539
 540 //***************************************************************************************************************
 541
 542 void TrimFlowsCommand::getOligos(vector<vector<string> >& outFlowFileNames){
 543         try {
 544                 ifstream oligosFile;
 545                 m->openInputFile(oligoFileName, oligosFile);
 546
 547                 string type, oligo, group;
 548
 549                 int indexPrimer = 0;
 550                 int indexBarcode = 0;
 551
 552                 while(!oligosFile.eof()){
 553
 554                         oligosFile >> type; m->gobble(oligosFile);      //get the first column value of the row - is it a comment or a feature we are interested in?
 555
 556                         if(type[0] == '#'){     //igore the line because there's a comment
 557                                 while (!oligosFile.eof())       {       char c = oligosFile.get(); if (c == 10 || c == 13){     break;  }       } // get rest of line if there's any crap there
 558                         }
 559                         else{                           //there's a feature we're interested in
 560
 561                                 for(int i=0;i<type.length();i++){       type[i] = toupper(type[i]);  }                                  //make type case insensitive
 562
 563                                 oligosFile >> oligo;    //get the DNA sequence for the feature
 564
 565                                 for(int i=0;i<oligo.length();i++){      //make type case insensitive and change any U's to T's
 566                                         oligo[i] = toupper(oligo[i]);
 567                                         if(oligo[i] == 'U')     {       oligo[i] = 'T'; }
 568                                 }
 569
 570                                 if(type == "FORWARD"){  //if the feature is a forward primer...
 571                                         group = "";
 572
 573                                         while (!oligosFile.eof())       {       // get rest of line in case there is a primer name = will have the name of the primer
 574                                                 char c = oligosFile.get();
 575                                                 if (c == 10 || c == 13){        break;  }
 576                                                 else if (c == 32 || c == 9){;} //space or tab
 577                                                 else {  group += c;  }
 578                                         }
 579
 580                                         //have we seen this primer already?
 581                                         map<string, int>::iterator itPrimer = primers.find(oligo);
 582                                         if (itPrimer != primers.end()) { m->mothurOut("primer " + oligo + " is in your oligos file already."); m->mothurOutEndLine();  }
 583
 584                                         primers[oligo]=indexPrimer; indexPrimer++;
 585                                         primerNameVector.push_back(group);
 586
 587                                 }
 588                                 else if(type == "REVERSE"){
 589                                         string oligoRC = reverseOligo(oligo);
 590                                         revPrimer.push_back(oligoRC);
 591                                 }
 592                                 else if(type == "BARCODE"){
 593                                         oligosFile >> group;
 594
 595                                         //check for repeat barcodes
 596                                         map<string, int>::iterator itBar = barcodes.find(oligo);
 597                                         if (itBar != barcodes.end()) { m->mothurOut("barcode " + oligo + " is in your oligos file already."); m->mothurOutEndLine();  }
 598
 599                                         barcodes[oligo]=indexBarcode; indexBarcode++;
 600                                         barcodeNameVector.push_back(group);
 601                                 }else if(type == "LINKER"){
 602                                         linker.push_back(oligo);
 603                                 }else if(type == "SPACER"){
 604                                         spacer.push_back(oligo);
 605                                 }
 606                                 else{
 607                                         m->mothurOut(type + " is not recognized as a valid type. Choices are forward, reverse, and barcode. Ignoring " + oligo + "."); m->mothurOutEndLine();
 608                                 }
 609                         }
 610
 611                         m->gobble(oligosFile);
 612                 }
 613                 oligosFile.close();
 614
 615                 if(barcodeNameVector.size() == 0 && primerNameVector[0] == ""){ allFiles = 0;   }
 616
 617                 //add in potential combos
 618                 if(barcodeNameVector.size() == 0){
 619                         barcodes[""] = 0;
 620                         barcodeNameVector.push_back("");
 621                 }
 622
 623                 if(primerNameVector.size() == 0){
 624                         primers[""] = 0;
 625                         primerNameVector.push_back("");
 626                 }
 627
 628
 629                 outFlowFileNames.resize(barcodeNameVector.size());
 630                 for(int i=0;i<outFlowFileNames.size();i++){
 631                         outFlowFileNames[i].assign(primerNameVector.size(), "");
 632                 }
 633
 634                 if(allFiles){
 635
 636                         for(map<string, int>::iterator itBar = barcodes.begin();itBar != barcodes.end();itBar++){
 637                                 for(map<string, int>::iterator itPrimer = primers.begin();itPrimer != primers.end(); itPrimer++){
 638
 639                                         string primerName = primerNameVector[itPrimer->second];
 640                                         string barcodeName = barcodeNameVector[itBar->second];
 641
 642                                         if ((primerName == "ignore") || (barcodeName == "ignore")) { } //do nothing
 643                                         else {
 644                         string comboGroupName = "";
 645                         string fileName = "";
 646
 647                         map<string, string> variables;
 648                         variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(flowFileName));
 649
 650                         if(primerName == ""){
 651                             comboGroupName = barcodeNameVector[itBar->second];
 652                             variables["[tag]"] = comboGroupName;
 653                             fileName = getOutputFileName("flow", variables);
 654                         }
 655                         else{
 656                             if(barcodeName == ""){
 657                                 comboGroupName = primerNameVector[itPrimer->second];
 658                             }
 659                             else{
 660                                 comboGroupName = barcodeNameVector[itBar->second] + "." + primerNameVector[itPrimer->second];
 661                             }
 662                             variables["[tag]"] = comboGroupName;
 663                             fileName = getOutputFileName("flow", variables);
 664                         }
 665
 666                         outFlowFileNames[itBar->second][itPrimer->second] = fileName;
 667
 668                         ofstream temp;
 669                         m->openOutputFile(fileName, temp);
 670                         temp.close();
 671                     }
 672                                 }
 673                         }
 674                 }
 675
 676                 numFPrimers = primers.size();
 677                 numRPrimers = revPrimer.size();
 678         numLinkers = linker.size();
 679         numSpacers = spacer.size();
 680
 681         }
 682         catch(exception& e) {
 683                 m->errorOut(e, "TrimSeqsCommand", "getOligos");
 684                 exit(1);
 685         }
 686 }
 687 //********************************************************************/
 688 string TrimFlowsCommand::reverseOligo(string oligo){
 689         try {
 690         string reverse = "";
 691
 692         for(int i=oligo.length()-1;i>=0;i--){
 693
 694             if(oligo[i] == 'A')         {       reverse += 'T'; }
 695             else if(oligo[i] == 'T'){   reverse += 'A'; }
 696             else if(oligo[i] == 'U'){   reverse += 'A'; }
 697
 698             else if(oligo[i] == 'G'){   reverse += 'C'; }
 699             else if(oligo[i] == 'C'){   reverse += 'G'; }
 700
 701             else if(oligo[i] == 'R'){   reverse += 'Y'; }
 702             else if(oligo[i] == 'Y'){   reverse += 'R'; }
 703
 704             else if(oligo[i] == 'M'){   reverse += 'K'; }
 705             else if(oligo[i] == 'K'){   reverse += 'M'; }
 706
 707             else if(oligo[i] == 'W'){   reverse += 'W'; }
 708             else if(oligo[i] == 'S'){   reverse += 'S'; }
 709
 710             else if(oligo[i] == 'B'){   reverse += 'V'; }
 711             else if(oligo[i] == 'V'){   reverse += 'B'; }
 712
 713             else if(oligo[i] == 'D'){   reverse += 'H'; }
 714             else if(oligo[i] == 'H'){   reverse += 'D'; }
 715
 716             else                                                {       reverse += 'N'; }
 717         }
 718
 719
 720         return reverse;
 721     }
 722         catch(exception& e) {
 723                 m->errorOut(e, "TrimFlowsCommand", "reverseOligo");
 724                 exit(1);
 725         }
 726 }
 727
 728 /**************************************************************************************************/
 729 vector<unsigned long long> TrimFlowsCommand::getFlowFileBreaks() {
 730
 731         try{
 732
 733                 vector<unsigned long long> filePos;
 734                 filePos.push_back(0);
 735
 736                 FILE * pFile;
 737                 unsigned long long size;
 738
 739                 //get num bytes in file
 740                 pFile = fopen (flowFileName.c_str(),"rb");
 741                 if (pFile==NULL) perror ("Error opening file");
 742                 else{
 743                         fseek (pFile, 0, SEEK_END);
 744                         size=ftell (pFile);
 745                         fclose (pFile);
 746                 }
 747
 748                 //estimate file breaks
 749                 unsigned long long chunkSize = 0;
 750                 chunkSize = size / processors;
 751
 752                 //file too small to divide by processors
 753                 if (chunkSize == 0)  {  processors = 1; filePos.push_back(size); return filePos;        }
 754
 755                 //for each process seekg to closest file break and search for next '>' char. make that the filebreak
 756                 for (int i = 0; i < processors; i++) {
 757                         unsigned long long spot = (i+1) * chunkSize;
 758
 759                         ifstream in;
 760                         m->openInputFile(flowFileName, in);
 761                         in.seekg(spot);
 762
 763                         string dummy = m->getline(in);
 764
 765                         //there was not another sequence before the end of the file
 766                         unsigned long long sanityPos = in.tellg();
 767
 768 //                      if (sanityPos == -1) {  break;  }
 769 //                      else {  filePos.push_back(newSpot);  }
 770                         if (sanityPos == -1) {  break;  }
 771                         else {  filePos.push_back(sanityPos);  }
 772
 773                         in.close();
 774                 }
 775
 776                 //save end pos
 777                 filePos.push_back(size);
 778
 779                 //sanity check filePos
 780                 for (int i = 0; i < (filePos.size()-1); i++) {
 781                         if (filePos[(i+1)] <= filePos[i]) {  filePos.erase(filePos.begin()+(i+1)); i--; }
 782                 }
 783
 784                 ifstream in;
 785                 m->openInputFile(flowFileName, in);
 786                 in >> numFlows;
 787                 m->gobble(in);
 788                 //unsigned long long spot = in.tellg();
 789                 //filePos[0] = spot;
 790                 in.close();
 791
 792                 processors = (filePos.size() - 1);
 793
 794                 return filePos;
 795         }
 796         catch(exception& e) {
 797                 m->errorOut(e, "TrimSeqsCommand", "getFlowFileBreaks");
 798                 exit(1);
 799         }
 800 }
 801
 802 /**************************************************************************************************/
 803
 804 int TrimFlowsCommand::createProcessesCreateTrim(string flowFileName, string trimFlowFileName, string scrapFlowFileName, string fastaFileName, vector<vector<string> > barcodePrimerComboFileNames){
 805
 806         try {
 807                 processIDS.clear();
 808                 int exitCommand = 1;
 809
 810 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 811                 int process = 1;
 812
 813                 //loop through and create all the processes you want
 814                 while (process != processors) {
 815                         int pid = fork();
 816
 817                         if (pid > 0) {
 818                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
 819                                 process++;
 820                         }else if (pid == 0){
 821
 822                                 vector<vector<string> > tempBarcodePrimerComboFileNames = barcodePrimerComboFileNames;
 823                                 if(allFiles){
 824                                         for(int i=0;i<tempBarcodePrimerComboFileNames.size();i++){
 825                                                 for(int j=0;j<tempBarcodePrimerComboFileNames[0].size();j++){
 826                             if (tempBarcodePrimerComboFileNames[i][j] != "") {
 827                                 tempBarcodePrimerComboFileNames[i][j] += toString(getpid()) + ".temp";
 828                                 ofstream temp;
 829                                 m->openOutputFile(tempBarcodePrimerComboFileNames[i][j], temp);
 830                                 temp.close();
 831                             }
 832                                                 }
 833                                         }
 834                                 }
 835                                 driverCreateTrim(flowFileName,
 836                                                                  (trimFlowFileName + toString(getpid()) + ".temp"),
 837                                                                  (scrapFlowFileName + toString(getpid()) + ".temp"),
 838                                                                  (fastaFileName + toString(getpid()) + ".temp"),
 839                                                                  tempBarcodePrimerComboFileNames, lines[process]);
 840
 841                                 exit(0);
 842                         }else {
 843                                 m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
 844                                 for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
 845                                 exit(0);
 846                         }
 847                 }
 848
 849                 //parent do my part
 850                 ofstream temp;
 851                 m->openOutputFile(trimFlowFileName, temp);
 852                 temp.close();
 853
 854                 m->openOutputFile(scrapFlowFileName, temp);
 855                 temp.close();
 856
 857                 if(fasta){
 858                         m->openOutputFile(fastaFileName, temp);
 859                         temp.close();
 860                 }
 861
 862                 driverCreateTrim(flowFileName, trimFlowFileName, scrapFlowFileName, fastaFileName, barcodePrimerComboFileNames, lines[0]);
 863
 864                 //force parent to wait until all the processes are done
 865                 for (int i=0;i<processIDS.size();i++) {
 866                         int temp = processIDS[i];
 867                         wait(&temp);
 868                 }
 869 #else
 870                 //////////////////////////////////////////////////////////////////////////////////////////////////////
 871                 //Windows version shared memory, so be careful when passing variables through the trimFlowData struct.
 872                 //Above fork() will clone, so memory is separate, but that's not the case with windows,
 873                 //////////////////////////////////////////////////////////////////////////////////////////////////////
 874
 875                 vector<trimFlowData*> pDataArray;
 876                 DWORD   dwThreadIdArray[processors-1];
 877                 HANDLE  hThreadArray[processors-1];
 878
 879                 //Create processor worker threads.
 880                 for( int i=0; i<processors-1; i++ ){
 881                         // Allocate memory for thread data.
 882                         string extension = "";
 883                         if (i != 0) { extension = toString(i) + ".temp"; processIDS.push_back(i); }
 884
 885                         vector<vector<string> > tempBarcodePrimerComboFileNames = barcodePrimerComboFileNames;
 886                         if(allFiles){
 887                                 for(int i=0;i<tempBarcodePrimerComboFileNames.size();i++){
 888                                         for(int j=0;j<tempBarcodePrimerComboFileNames[0].size();j++){
 889                         if (tempBarcodePrimerComboFileNames[i][j] != "") {
 890                             tempBarcodePrimerComboFileNames[i][j] += extension;
 891                             ofstream temp;
 892                             m->openOutputFile(tempBarcodePrimerComboFileNames[i][j], temp);
 893                             temp.close();
 894                                                 }
 895                                         }
 896                                 }
 897                         }
 898
 899                         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);
 900                         pDataArray.push_back(tempflow);
 901
 902                         //MyTrimFlowThreadFunction is in header. It must be global or static to work with the threads.
 903                         //default security attributes, thread function name, argument to thread function, use default creation flags, returns the thread identifier
 904                         hThreadArray[i] = CreateThread(NULL, 0, MyTrimFlowThreadFunction, pDataArray[i], 0, &dwThreadIdArray[i]);
 905                 }
 906
 907                 //using the main process as a worker saves time and memory
 908                 ofstream temp;
 909                 m->openOutputFile(trimFlowFileName, temp);
 910                 temp.close();
 911
 912                 m->openOutputFile(scrapFlowFileName, temp);
 913                 temp.close();
 914
 915                 if(fasta){
 916                         m->openOutputFile(fastaFileName, temp);
 917                         temp.close();
 918                 }
 919
 920                 vector<vector<string> > tempBarcodePrimerComboFileNames = barcodePrimerComboFileNames;
 921                 if(allFiles){
 922                         for(int i=0;i<tempBarcodePrimerComboFileNames.size();i++){
 923                                 for(int j=0;j<tempBarcodePrimerComboFileNames[0].size();j++){
 924                     if (tempBarcodePrimerComboFileNames[i][j] != "") {
 925                         tempBarcodePrimerComboFileNames[i][j] += toString(processors-1) + ".temp";
 926                         ofstream temp;
 927                         m->openOutputFile(tempBarcodePrimerComboFileNames[i][j], temp);
 928                         temp.close();
 929                     }
 930
 931                                 }
 932                         }
 933                 }
 934
 935                 //do my part - do last piece because windows is looking for eof
 936                 int num = driverCreateTrim(flowFileName, (trimFlowFileName  + toString(processors-1) + ".temp"), (scrapFlowFileName  + toString(processors-1) + ".temp"), (fastaFileName + toString(processors-1) + ".temp"), tempBarcodePrimerComboFileNames, lines[processors-1]);
 937                 processIDS.push_back((processors-1));
 938
 939                 //Wait until all threads have terminated.
 940                 WaitForMultipleObjects(processors-1, hThreadArray, TRUE, INFINITE);
 941
 942                 //Close all thread handles and free memory allocations.
 943                 for(int i=0; i < pDataArray.size(); i++){
 944                         num += pDataArray[i]->count;
 945                         CloseHandle(hThreadArray[i]);
 946                         delete pDataArray[i];
 947                 }
 948
 949
 950 #endif
 951                 //append files
 952                 m->mothurOutEndLine();
 953                 for(int i=0;i<processIDS.size();i++){
 954
 955                         m->mothurOut("Appending files from process " + toString(processIDS[i])); m->mothurOutEndLine();
 956
 957                         m->appendFiles((trimFlowFileName + toString(processIDS[i]) + ".temp"), trimFlowFileName);
 958                         m->mothurRemove((trimFlowFileName + toString(processIDS[i]) + ".temp"));
 959 //                      m->mothurOut("\tDone with trim.flow file"); m->mothurOutEndLine();
 960
 961                         m->appendFiles((scrapFlowFileName + toString(processIDS[i]) + ".temp"), scrapFlowFileName);
 962                         m->mothurRemove((scrapFlowFileName + toString(processIDS[i]) + ".temp"));
 963 //                      m->mothurOut("\tDone with scrap.flow file"); m->mothurOutEndLine();
 964
 965                         if(fasta){
 966                                 m->appendFiles((fastaFileName + toString(processIDS[i]) + ".temp"), fastaFileName);
 967                                 m->mothurRemove((fastaFileName + toString(processIDS[i]) + ".temp"));
 968 //                              m->mothurOut("\tDone with flow.fasta file"); m->mothurOutEndLine();
 969                         }
 970                         if(allFiles){
 971                                 for (int j = 0; j < barcodePrimerComboFileNames.size(); j++) {
 972                                         for (int k = 0; k < barcodePrimerComboFileNames[0].size(); k++) {
 973                         if (barcodePrimerComboFileNames[j][k] != "") {
 974                             m->appendFiles((barcodePrimerComboFileNames[j][k] + toString(processIDS[i]) + ".temp"), barcodePrimerComboFileNames[j][k]);
 975                             m->mothurRemove((barcodePrimerComboFileNames[j][k] + toString(processIDS[i]) + ".temp"));
 976                         }
 977                                         }
 978                                 }
 979                         }
 980                 }
 981
 982                 return exitCommand;
 983
 984         }
 985         catch(exception& e) {
 986                 m->errorOut(e, "TrimFlowsCommand", "createProcessesCreateTrim");
 987                 exit(1);
 988         }
 989 }
 990
 991 //***************************************************************************************************************