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-I", "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             //cout << currSeq.getName() << '\t' << currSeq.getUnaligned() << endl;
 433                         if(!flowData.hasMinFlows(minFlows)){    //screen to see if sequence is of a minimum number of flows
 434                                 success = 0;
 435                                 trashCode += 'l';
 436                         }
 437
 438                         int primerIndex = 0;
 439                         int barcodeIndex = 0;
 440
 441             if(numLinkers != 0){
 442                 success = trimOligos.stripLinker(currSeq);
 443                 if(success > ldiffs)            {       trashCode += 'k';       }
 444                 else{ currentSeqDiffs += success;  }
 445
 446             }
 447
 448             if (m->debug) { m->mothurOut("[DEBUG]: " + currSeq.getName() + " " + currSeq.getUnaligned() + "\n"); }
 449
 450                         if(barcodes.size() != 0){
 451                                 success = trimOligos.stripBarcode(currSeq, barcodeIndex);
 452                                 if(success > bdiffs)            {       trashCode += 'b';       }
 453                                 else{ currentSeqDiffs += success;  }
 454                         }
 455
 456             if(numSpacers != 0){
 457                 success = trimOligos.stripSpacer(currSeq);
 458                 if(success > sdiffs)            {       trashCode += 's';       }
 459                 else{ currentSeqDiffs += success;  }
 460
 461             }
 462
 463                         if(numFPrimers != 0){
 464                                 success = trimOligos.stripForward(currSeq, primerIndex);
 465                                 if(success > pdiffs)            {       trashCode += 'f';       }
 466                                 else{ currentSeqDiffs += success;  }
 467                         }
 468
 469                         if (currentSeqDiffs > tdiffs)   {       trashCode += 't';   }
 470
 471                         if(numRPrimers != 0){
 472                                 success = trimOligos.stripReverse(currSeq);
 473                                 if(!success)                            {       trashCode += 'r';       }
 474                         }
 475
 476                         if(trashCode.length() == 0){
 477                 string thisGroup = "";
 478                 if(barcodes.size() != 0){
 479                     thisGroup = barcodeNameVector[barcodeIndex];
 480                     if (primers.size() != 0) {
 481                         if (primerNameVector[primerIndex] != "") {
 482                             if(thisGroup != "") {
 483                                 thisGroup += "." + primerNameVector[primerIndex];
 484                             }else {
 485                                 thisGroup = primerNameVector[primerIndex];
 486                             }
 487                         }
 488                     }
 489                 }
 490
 491                 int pos = thisGroup.find("ignore");
 492                 if (pos == string::npos) {
 493                     flowData.printFlows(trimFlowFile);
 494
 495                     if(fasta)   { currSeq.printSequence(fastaFile);     }
 496
 497                     if(allFiles){
 498                         ofstream output;
 499                         m->openOutputFileAppend(thisBarcodePrimerComboFileNames[barcodeIndex][primerIndex], output);
 500                         output.setf(ios::fixed, ios::floatfield); trimFlowFile.setf(ios::showpoint);
 501
 502                         flowData.printFlows(output);
 503                         output.close();
 504                     }
 505                 }
 506                         }
 507                         else{
 508                                 flowData.printFlows(scrapFlowFile, trashCode);
 509                         }
 510
 511                         count++;
 512                         //cout << "driver" << '\t' << currSeq.getName() << endl;
 513                         //report progress
 514                         if((count) % 10000 == 0){       m->mothurOut(toString(count)); m->mothurOutEndLine();           }
 515
 516 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 517                         unsigned long long pos = flowFile.tellg();
 518
 519                         if ((pos == -1) || (pos >= line->end)) { break; }
 520 #else
 521                         if (flowFile.eof()) { break; }
 522 #endif
 523
 524                 }
 525                 //report progress
 526                 if((count) % 10000 != 0){       m->mothurOut(toString(count)); m->mothurOutEndLine();           }
 527
 528                 trimFlowFile.close();
 529                 scrapFlowFile.close();
 530                 flowFile.close();
 531                 if(fasta){      fastaFile.close();      }
 532
 533                 return count;
 534         }
 535         catch(exception& e) {
 536                 m->errorOut(e, "TrimSeqsCommand", "driverCreateTrim");
 537                 exit(1);
 538         }
 539 }
 540
 541 //***************************************************************************************************************
 542
 543 void TrimFlowsCommand::getOligos(vector<vector<string> >& outFlowFileNames){
 544         try {
 545                 ifstream oligosFile;
 546                 m->openInputFile(oligoFileName, oligosFile);
 547
 548                 string type, oligo, group;
 549
 550                 int indexPrimer = 0;
 551                 int indexBarcode = 0;
 552
 553                 while(!oligosFile.eof()){
 554
 555                         oligosFile >> type;     //get the first column value of the row - is it a comment or a feature we are interested in?
 556
 557             if (m->debug) { m->mothurOut("[DEBUG]: type = " + type + ".\n"); }
 558
 559                         if(type[0] == '#'){     //igore the line because there's a comment
 560                                 while (!oligosFile.eof())       {       char c = oligosFile.get(); if (c == 10 || c == 13){     break;  }       }
 561                 m->gobble(oligosFile);// get rest of line if there's any crap there
 562                         }
 563                         else{                           //there's a feature we're interested in
 564                 m->gobble(oligosFile);
 565                                 for(int i=0;i<type.length();i++){       type[i] = toupper(type[i]);  }                                  //make type case insensitive
 566
 567                                 oligosFile >> oligo;    //get the DNA sequence for the feature
 568
 569                                 for(int i=0;i<oligo.length();i++){      //make type case insensitive and change any U's to T's
 570                                         oligo[i] = toupper(oligo[i]);
 571                                         if(oligo[i] == 'U')     {       oligo[i] = 'T'; }
 572                                 }
 573
 574                 if (m->debug) { m->mothurOut("[DEBUG]: oligos = " + oligo + ".\n"); }
 575
 576                                 if(type == "FORWARD"){  //if the feature is a forward primer...
 577                                         group = "";
 578
 579                                         while (!oligosFile.eof())       {       // get rest of line in case there is a primer name = will have the name of the primer
 580                                                 char c = oligosFile.get();
 581                                                 if (c == 10 || c == 13 || c == -1){     break;  }
 582                                                 else if (c == 32 || c == 9){;} //space or tab
 583                                                 else {  group += c;  }
 584                                         }
 585
 586                                         //have we seen this primer already?
 587                                         map<string, int>::iterator itPrimer = primers.find(oligo);
 588                                         if (itPrimer != primers.end()) { m->mothurOut("primer " + oligo + " is in your oligos file already."); m->mothurOutEndLine();  }
 589
 590                                         primers[oligo]=indexPrimer; indexPrimer++;
 591                                         primerNameVector.push_back(group);
 592
 593                                 }
 594                                 else if(type == "REVERSE"){
 595                                         string oligoRC = reverseOligo(oligo);
 596                                         revPrimer.push_back(oligoRC);
 597                                 }
 598                                 else if(type == "BARCODE"){
 599                                         oligosFile >> group;
 600
 601                                         //check for repeat barcodes
 602                                         map<string, int>::iterator itBar = barcodes.find(oligo);
 603                                         if (itBar != barcodes.end()) { m->mothurOut("barcode " + oligo + " is in your oligos file already."); m->mothurOutEndLine();  }
 604
 605                     if (m->debug) { m->mothurOut("[DEBUG]: group = " + group + ".\n"); }
 606
 607                                         barcodes[oligo]=indexBarcode; indexBarcode++;
 608                                         barcodeNameVector.push_back(group);
 609                                 }else if(type == "LINKER"){
 610                                         linker.push_back(oligo);
 611                                 }else if(type == "SPACER"){
 612                                         spacer.push_back(oligo);
 613                                 }
 614                                 else{
 615                                         m->mothurOut(type + " is not recognized as a valid type. Choices are forward, reverse, and barcode. Ignoring " + oligo + "."); m->mothurOutEndLine();
 616                                 }
 617                         }
 618
 619                         m->gobble(oligosFile);
 620                 }
 621                 oligosFile.close();
 622
 623                 if(barcodeNameVector.size() == 0 && primerNameVector[0] == ""){ allFiles = 0;   }
 624
 625                 //add in potential combos
 626                 if(barcodeNameVector.size() == 0){
 627                         barcodes[""] = 0;
 628                         barcodeNameVector.push_back("");
 629                 }
 630
 631                 if(primerNameVector.size() == 0){
 632                         primers[""] = 0;
 633                         primerNameVector.push_back("");
 634                 }
 635
 636
 637                 outFlowFileNames.resize(barcodeNameVector.size());
 638                 for(int i=0;i<outFlowFileNames.size();i++){
 639                         outFlowFileNames[i].assign(primerNameVector.size(), "");
 640                 }
 641
 642                 if(allFiles){
 643
 644                         for(map<string, int>::iterator itBar = barcodes.begin();itBar != barcodes.end();itBar++){
 645                                 for(map<string, int>::iterator itPrimer = primers.begin();itPrimer != primers.end(); itPrimer++){
 646
 647                                         string primerName = primerNameVector[itPrimer->second];
 648                                         string barcodeName = barcodeNameVector[itBar->second];
 649
 650                                         if ((primerName == "ignore") || (barcodeName == "ignore")) { } //do nothing
 651                                         else {
 652                         string comboGroupName = "";
 653                         string fileName = "";
 654
 655                         map<string, string> variables;
 656                         variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(flowFileName));
 657
 658                         if(primerName == ""){
 659                             comboGroupName = barcodeNameVector[itBar->second];
 660                             variables["[tag]"] = comboGroupName;
 661                             fileName = getOutputFileName("flow", variables);
 662                         }
 663                         else{
 664                             if(barcodeName == ""){
 665                                 comboGroupName = primerNameVector[itPrimer->second];
 666                             }
 667                             else{
 668                                 comboGroupName = barcodeNameVector[itBar->second] + "." + primerNameVector[itPrimer->second];
 669                             }
 670                             variables["[tag]"] = comboGroupName;
 671                             fileName = getOutputFileName("flow", variables);
 672                         }
 673
 674                         outFlowFileNames[itBar->second][itPrimer->second] = fileName;
 675
 676                         ofstream temp;
 677                         m->openOutputFile(fileName, temp);
 678                         temp.close();
 679                     }
 680                                 }
 681                         }
 682                 }
 683
 684                 numFPrimers = primers.size();
 685                 numRPrimers = revPrimer.size();
 686         numLinkers = linker.size();
 687         numSpacers = spacer.size();
 688
 689         }
 690         catch(exception& e) {
 691                 m->errorOut(e, "TrimSeqsCommand", "getOligos");
 692                 exit(1);
 693         }
 694 }
 695 //********************************************************************/
 696 string TrimFlowsCommand::reverseOligo(string oligo){
 697         try {
 698         string reverse = "";
 699
 700         for(int i=oligo.length()-1;i>=0;i--){
 701
 702             if(oligo[i] == 'A')         {       reverse += 'T'; }
 703             else if(oligo[i] == 'T'){   reverse += 'A'; }
 704             else if(oligo[i] == 'U'){   reverse += 'A'; }
 705
 706             else if(oligo[i] == 'G'){   reverse += 'C'; }
 707             else if(oligo[i] == 'C'){   reverse += 'G'; }
 708
 709             else if(oligo[i] == 'R'){   reverse += 'Y'; }
 710             else if(oligo[i] == 'Y'){   reverse += 'R'; }
 711
 712             else if(oligo[i] == 'M'){   reverse += 'K'; }
 713             else if(oligo[i] == 'K'){   reverse += 'M'; }
 714
 715             else if(oligo[i] == 'W'){   reverse += 'W'; }
 716             else if(oligo[i] == 'S'){   reverse += 'S'; }
 717
 718             else if(oligo[i] == 'B'){   reverse += 'V'; }
 719             else if(oligo[i] == 'V'){   reverse += 'B'; }
 720
 721             else if(oligo[i] == 'D'){   reverse += 'H'; }
 722             else if(oligo[i] == 'H'){   reverse += 'D'; }
 723
 724             else                                                {       reverse += 'N'; }
 725         }
 726
 727
 728         return reverse;
 729     }
 730         catch(exception& e) {
 731                 m->errorOut(e, "TrimFlowsCommand", "reverseOligo");
 732                 exit(1);
 733         }
 734 }
 735
 736 /**************************************************************************************************/
 737 vector<unsigned long long> TrimFlowsCommand::getFlowFileBreaks() {
 738
 739         try{
 740
 741                 vector<unsigned long long> filePos;
 742                 filePos.push_back(0);
 743
 744                 FILE * pFile;
 745                 unsigned long long size;
 746
 747                 //get num bytes in file
 748                 pFile = fopen (flowFileName.c_str(),"rb");
 749                 if (pFile==NULL) perror ("Error opening file");
 750                 else{
 751                         fseek (pFile, 0, SEEK_END);
 752                         size=ftell (pFile);
 753                         fclose (pFile);
 754                 }
 755
 756                 //estimate file breaks
 757                 unsigned long long chunkSize = 0;
 758                 chunkSize = size / processors;
 759
 760                 //file too small to divide by processors
 761                 if (chunkSize == 0)  {  processors = 1; filePos.push_back(size); return filePos;        }
 762
 763                 //for each process seekg to closest file break and search for next '>' char. make that the filebreak
 764                 for (int i = 0; i < processors; i++) {
 765                         unsigned long long spot = (i+1) * chunkSize;
 766
 767                         ifstream in;
 768                         m->openInputFile(flowFileName, in);
 769                         in.seekg(spot);
 770
 771                         string dummy = m->getline(in);
 772
 773                         //there was not another sequence before the end of the file
 774                         unsigned long long sanityPos = in.tellg();
 775
 776 //                      if (sanityPos == -1) {  break;  }
 777 //                      else {  filePos.push_back(newSpot);  }
 778                         if (sanityPos == -1) {  break;  }
 779                         else {  filePos.push_back(sanityPos);  }
 780
 781                         in.close();
 782                 }
 783
 784                 //save end pos
 785                 filePos.push_back(size);
 786
 787                 //sanity check filePos
 788                 for (int i = 0; i < (filePos.size()-1); i++) {
 789                         if (filePos[(i+1)] <= filePos[i]) {  filePos.erase(filePos.begin()+(i+1)); i--; }
 790                 }
 791
 792                 ifstream in;
 793                 m->openInputFile(flowFileName, in);
 794                 in >> numFlows;
 795                 m->gobble(in);
 796                 //unsigned long long spot = in.tellg();
 797                 //filePos[0] = spot;
 798                 in.close();
 799
 800                 processors = (filePos.size() - 1);
 801
 802                 return filePos;
 803         }
 804         catch(exception& e) {
 805                 m->errorOut(e, "TrimSeqsCommand", "getFlowFileBreaks");
 806                 exit(1);
 807         }
 808 }
 809
 810 /**************************************************************************************************/
 811
 812 int TrimFlowsCommand::createProcessesCreateTrim(string flowFileName, string trimFlowFileName, string scrapFlowFileName, string fastaFileName, vector<vector<string> > barcodePrimerComboFileNames){
 813
 814         try {
 815                 processIDS.clear();
 816                 int exitCommand = 1;
 817
 818 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 819                 int process = 1;
 820
 821                 //loop through and create all the processes you want
 822                 while (process != processors) {
 823                         int pid = fork();
 824
 825                         if (pid > 0) {
 826                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
 827                                 process++;
 828                         }else if (pid == 0){
 829
 830                                 vector<vector<string> > tempBarcodePrimerComboFileNames = barcodePrimerComboFileNames;
 831                                 if(allFiles){
 832                                         for(int i=0;i<tempBarcodePrimerComboFileNames.size();i++){
 833                                                 for(int j=0;j<tempBarcodePrimerComboFileNames[0].size();j++){
 834                             if (tempBarcodePrimerComboFileNames[i][j] != "") {
 835                                 tempBarcodePrimerComboFileNames[i][j] += toString(getpid()) + ".temp";
 836                                 ofstream temp;
 837                                 m->openOutputFile(tempBarcodePrimerComboFileNames[i][j], temp);
 838                                 temp.close();
 839                             }
 840                                                 }
 841                                         }
 842                                 }
 843                                 driverCreateTrim(flowFileName,
 844                                                                  (trimFlowFileName + toString(getpid()) + ".temp"),
 845                                                                  (scrapFlowFileName + toString(getpid()) + ".temp"),
 846                                                                  (fastaFileName + toString(getpid()) + ".temp"),
 847                                                                  tempBarcodePrimerComboFileNames, lines[process]);
 848
 849                                 exit(0);
 850                         }else {
 851                                 m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
 852                                 for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
 853                                 exit(0);
 854                         }
 855                 }
 856
 857                 //parent do my part
 858                 ofstream temp;
 859                 m->openOutputFile(trimFlowFileName, temp);
 860                 temp.close();
 861
 862                 m->openOutputFile(scrapFlowFileName, temp);
 863                 temp.close();
 864
 865                 if(fasta){
 866                         m->openOutputFile(fastaFileName, temp);
 867                         temp.close();
 868                 }
 869
 870                 driverCreateTrim(flowFileName, trimFlowFileName, scrapFlowFileName, fastaFileName, barcodePrimerComboFileNames, lines[0]);
 871
 872                 //force parent to wait until all the processes are done
 873                 for (int i=0;i<processIDS.size();i++) {
 874                         int temp = processIDS[i];
 875                         wait(&temp);
 876                 }
 877 #else
 878                 //////////////////////////////////////////////////////////////////////////////////////////////////////
 879                 //Windows version shared memory, so be careful when passing variables through the trimFlowData struct.
 880                 //Above fork() will clone, so memory is separate, but that's not the case with windows,
 881                 //////////////////////////////////////////////////////////////////////////////////////////////////////
 882
 883                 vector<trimFlowData*> pDataArray;
 884                 DWORD   dwThreadIdArray[processors-1];
 885                 HANDLE  hThreadArray[processors-1];
 886
 887                 //Create processor worker threads.
 888                 for( int i=0; i<processors-1; i++ ){
 889                         // Allocate memory for thread data.
 890                         string extension = "";
 891                         if (i != 0) { extension = toString(i) + ".temp"; processIDS.push_back(i); }
 892
 893                         vector<vector<string> > tempBarcodePrimerComboFileNames = barcodePrimerComboFileNames;
 894                         if(allFiles){
 895                                 for(int i=0;i<tempBarcodePrimerComboFileNames.size();i++){
 896                                         for(int j=0;j<tempBarcodePrimerComboFileNames[0].size();j++){
 897                         if (tempBarcodePrimerComboFileNames[i][j] != "") {
 898                             tempBarcodePrimerComboFileNames[i][j] += extension;
 899                             ofstream temp;
 900                             m->openOutputFile(tempBarcodePrimerComboFileNames[i][j], temp);
 901                             temp.close();
 902                                                 }
 903                                         }
 904                                 }
 905                         }
 906
 907                         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);
 908                         pDataArray.push_back(tempflow);
 909
 910                         //MyTrimFlowThreadFunction is in header. It must be global or static to work with the threads.
 911                         //default security attributes, thread function name, argument to thread function, use default creation flags, returns the thread identifier
 912                         hThreadArray[i] = CreateThread(NULL, 0, MyTrimFlowThreadFunction, pDataArray[i], 0, &dwThreadIdArray[i]);
 913                 }
 914
 915                 //using the main process as a worker saves time and memory
 916                 ofstream temp;
 917                 m->openOutputFile(trimFlowFileName, temp);
 918                 temp.close();
 919
 920                 m->openOutputFile(scrapFlowFileName, temp);
 921                 temp.close();
 922
 923                 if(fasta){
 924                         m->openOutputFile(fastaFileName, temp);
 925                         temp.close();
 926                 }
 927
 928                 vector<vector<string> > tempBarcodePrimerComboFileNames = barcodePrimerComboFileNames;
 929                 if(allFiles){
 930                         for(int i=0;i<tempBarcodePrimerComboFileNames.size();i++){
 931                                 for(int j=0;j<tempBarcodePrimerComboFileNames[0].size();j++){
 932                     if (tempBarcodePrimerComboFileNames[i][j] != "") {
 933                         tempBarcodePrimerComboFileNames[i][j] += toString(processors-1) + ".temp";
 934                         ofstream temp;
 935                         m->openOutputFile(tempBarcodePrimerComboFileNames[i][j], temp);
 936                         temp.close();
 937                     }
 938
 939                                 }
 940                         }
 941                 }
 942
 943                 //do my part - do last piece because windows is looking for eof
 944                 int num = driverCreateTrim(flowFileName, (trimFlowFileName  + toString(processors-1) + ".temp"), (scrapFlowFileName  + toString(processors-1) + ".temp"), (fastaFileName + toString(processors-1) + ".temp"), tempBarcodePrimerComboFileNames, lines[processors-1]);
 945                 processIDS.push_back((processors-1));
 946
 947                 //Wait until all threads have terminated.
 948                 WaitForMultipleObjects(processors-1, hThreadArray, TRUE, INFINITE);
 949
 950                 //Close all thread handles and free memory allocations.
 951                 for(int i=0; i < pDataArray.size(); i++){
 952                         num += pDataArray[i]->count;
 953                         CloseHandle(hThreadArray[i]);
 954                         delete pDataArray[i];
 955                 }
 956
 957
 958 #endif
 959                 //append files
 960                 m->mothurOutEndLine();
 961                 for(int i=0;i<processIDS.size();i++){
 962
 963                         m->mothurOut("Appending files from process " + toString(processIDS[i])); m->mothurOutEndLine();
 964
 965                         m->appendFiles((trimFlowFileName + toString(processIDS[i]) + ".temp"), trimFlowFileName);
 966                         m->mothurRemove((trimFlowFileName + toString(processIDS[i]) + ".temp"));
 967 //                      m->mothurOut("\tDone with trim.flow file"); m->mothurOutEndLine();
 968
 969                         m->appendFiles((scrapFlowFileName + toString(processIDS[i]) + ".temp"), scrapFlowFileName);
 970                         m->mothurRemove((scrapFlowFileName + toString(processIDS[i]) + ".temp"));
 971 //                      m->mothurOut("\tDone with scrap.flow file"); m->mothurOutEndLine();
 972
 973                         if(fasta){
 974                                 m->appendFiles((fastaFileName + toString(processIDS[i]) + ".temp"), fastaFileName);
 975                                 m->mothurRemove((fastaFileName + toString(processIDS[i]) + ".temp"));
 976 //                              m->mothurOut("\tDone with flow.fasta file"); m->mothurOutEndLine();
 977                         }
 978                         if(allFiles){
 979                                 for (int j = 0; j < barcodePrimerComboFileNames.size(); j++) {
 980                                         for (int k = 0; k < barcodePrimerComboFileNames[0].size(); k++) {
 981                         if (barcodePrimerComboFileNames[j][k] != "") {
 982                             m->appendFiles((barcodePrimerComboFileNames[j][k] + toString(processIDS[i]) + ".temp"), barcodePrimerComboFileNames[j][k]);
 983                             m->mothurRemove((barcodePrimerComboFileNames[j][k] + toString(processIDS[i]) + ".temp"));
 984                         }
 985                                         }
 986                                 }
 987                         }
 988                 }
 989
 990                 return exitCommand;
 991
 992         }
 993         catch(exception& e) {
 994                 m->errorOut(e, "TrimFlowsCommand", "createProcessesCreateTrim");
 995                 exit(1);
 996         }
 997 }
 998
 999 //***************************************************************************************************************