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