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 += "The order parameter options are A, B or I.  Default=A. A = TACG and B = TACGTACGTACGATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATAGATCGCATGACGATCGCATATCGTCAGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATAGATCGCATGACGATCGCATATCGTCAGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATAGATCGCATGACGATCGCATATCGTCAGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGATCTCAGTCAGCAGC and I = TACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGC.\n";
  51                 helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n";
  52                 helpString += "For more details please check out the wiki http://www.mothur.org/wiki/Trim.flows.\n";
  53                 return helpString;
  54         }
  55         catch(exception& e) {
  56                 m->errorOut(e, "TrimFlowsCommand", "getHelpString");
  57                 exit(1);
  58         }
  59 }
  60 //**********************************************************************************************************************
  61 string TrimFlowsCommand::getOutputPattern(string type) {
  62     try {
  63         string pattern = "";
  64
  65         if (type == "flow") {  pattern = "[filename],[tag],flow"; }
  66         else if (type == "fasta") {  pattern = "[filename],flow.fasta"; }
  67         else if (type == "file") {  pattern = "[filename],flow.files"; }
  68         else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true;  }
  69
  70         return pattern;
  71     }
  72     catch(exception& e) {
  73         m->errorOut(e, "TrimFlowsCommand", "getOutputPattern");
  74         exit(1);
  75     }
  76 }
  77 //**********************************************************************************************************************
  78
  79 TrimFlowsCommand::TrimFlowsCommand(){
  80         try {
  81                 abort = true; calledHelp = true;
  82                 setParameters();
  83                 vector<string> tempOutNames;
  84                 outputTypes["flow"] = tempOutNames;
  85                 outputTypes["fasta"] = tempOutNames;
  86         outputTypes["file"] = tempOutNames;
  87         }
  88         catch(exception& e) {
  89                 m->errorOut(e, "TrimFlowsCommand", "TrimFlowsCommand");
  90                 exit(1);
  91         }
  92 }
  93 //**********************************************************************************************************************
  94
  95 TrimFlowsCommand::TrimFlowsCommand(string option)  {
  96         try {
  97
  98                 abort = false; calledHelp = false;
  99                 comboStarts = 0;
 100
 101                 //allow user to run help
 102                 if(option == "help") { help(); abort = true; calledHelp = true; }
 103                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
 104
 105                 else {
 106
 107                         vector<string> myArray = setParameters();
 108
 109                         OptionParser parser(option);
 110                         map<string,string> parameters = parser.getParameters();
 111
 112                         ValidParameters validParameter;
 113                         map<string,string>::iterator it;
 114
 115                         //check to make sure all parameters are valid for command
 116                         for (it = parameters.begin(); it != parameters.end(); it++) {
 117                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 118                         }
 119
 120                         //initialize outputTypes
 121                         vector<string> tempOutNames;
 122                         outputTypes["flow"] = tempOutNames;
 123                         outputTypes["fasta"] = tempOutNames;
 124             outputTypes["file"] = tempOutNames;
 125
 126                         //if the user changes the input directory command factory will send this info to us in the output parameter
 127                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 128                         if (inputDir == "not found"){   inputDir = "";          }
 129                         else {
 130                                 string path;
 131                                 it = parameters.find("flow");
 132                                 //user has given a template file
 133                                 if(it != parameters.end()){
 134                                         path = m->hasPath(it->second);
 135                                         //if the user has not given a path then, add inputdir. else leave path alone.
 136                                         if (path == "") {       parameters["flow"] = inputDir + it->second;             }
 137                                 }
 138
 139                                 it = parameters.find("oligos");
 140                                 //user has given a template file
 141                                 if(it != parameters.end()){
 142                                         path = m->hasPath(it->second);
 143                                         //if the user has not given a path then, add inputdir. else leave path alone.
 144                                         if (path == "") {       parameters["oligos"] = inputDir + it->second;           }
 145                                 }
 146
 147                         }
 148
 149
 150                         //check for required parameters
 151                         flowFileName = validParameter.validFile(parameters, "flow", true);
 152                         if (flowFileName == "not found") {
 153                                 flowFileName = m->getFlowFile();
 154                                 if (flowFileName != "") {  m->mothurOut("Using " + flowFileName + " as input file for the flow parameter."); m->mothurOutEndLine(); }
 155                                 else {
 156                                         m->mothurOut("No valid current flow file. You must provide a flow file."); m->mothurOutEndLine();
 157                                         abort = true;
 158                                 }
 159                         }else if (flowFileName == "not open") { flowFileName = ""; abort = true; }
 160
 161                         //if the user changes the output directory command factory will send this info to us in the output parameter
 162                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){
 163                                 outputDir = "";
 164                                 outputDir += m->hasPath(flowFileName); //if user entered a file with a path then preserve it
 165                         }
 166
 167
 168                         //check for optional parameter and set defaults
 169                         // ...at some point should added some additional type checking...
 170
 171                         string temp;
 172                         temp = validParameter.validFile(parameters, "minflows", false); if (temp == "not found") { temp = "450"; }
 173                         m->mothurConvert(temp, minFlows);
 174
 175                         temp = validParameter.validFile(parameters, "maxflows", false); if (temp == "not found") { temp = "450"; }
 176                         m->mothurConvert(temp, maxFlows);
 177
 178
 179                         temp = validParameter.validFile(parameters, "oligos", true);
 180                         if (temp == "not found")        {       oligoFileName = "";             }
 181                         else if(temp == "not open")     {       abort = true;                   }
 182                         else                                            {       oligoFileName = temp;   m->setOligosFile(oligoFileName); }
 183
 184                         temp = validParameter.validFile(parameters, "fasta", false);            if (temp == "not found"){       fasta = 0;              }
 185                         else if(m->isTrue(temp))        {       fasta = 1;      }
 186
 187                         temp = validParameter.validFile(parameters, "maxhomop", false);         if (temp == "not found"){       temp = "9";             }
 188                         m->mothurConvert(temp, maxHomoP);
 189
 190                         temp = validParameter.validFile(parameters, "signal", false);           if (temp == "not found"){       temp = "0.50";  }
 191                         m->mothurConvert(temp, signal);
 192
 193                         temp = validParameter.validFile(parameters, "noise", false);            if (temp == "not found"){       temp = "0.70";  }
 194                         m->mothurConvert(temp, noise);
 195
 196                         temp = validParameter.validFile(parameters, "bdiffs", false);           if (temp == "not found"){       temp = "0";             }
 197                         m->mothurConvert(temp, bdiffs);
 198
 199                         temp = validParameter.validFile(parameters, "pdiffs", false);           if (temp == "not found"){       temp = "0";             }
 200                         m->mothurConvert(temp, pdiffs);
 201
 202             temp = validParameter.validFile(parameters, "ldiffs", false);               if (temp == "not found") { temp = "0"; }
 203                         m->mothurConvert(temp, ldiffs);
 204
 205             temp = validParameter.validFile(parameters, "sdiffs", false);               if (temp == "not found") { temp = "0"; }
 206                         m->mothurConvert(temp, sdiffs);
 207
 208                         temp = validParameter.validFile(parameters, "tdiffs", false);           if (temp == "not found") { int tempTotal = pdiffs + bdiffs + ldiffs + sdiffs;  temp = toString(tempTotal); }
 209                         m->mothurConvert(temp, tdiffs);
 210
 211                         if(tdiffs == 0){        tdiffs = bdiffs + pdiffs + ldiffs + sdiffs;     }
 212
 213
 214                         temp = validParameter.validFile(parameters, "processors", false);       if (temp == "not found"){       temp = m->getProcessors();      }
 215                         m->setProcessors(temp);
 216                         m->mothurConvert(temp, processors);
 217
 218                         temp = validParameter.validFile(parameters, "order", false);  if (temp == "not found"){         temp = "A";     }
 219             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;
 220             }
 221             else {
 222                 if (toupper(temp[0]) == 'A') {  flowOrder = "TACG";   }
 223                 else if(toupper(temp[0]) == 'B'){
 224                     flowOrder = "TACGTACGTACGATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATAGATCGCATGACGATCGCATATCGTCAGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATAGATCGCATGACGATCGCATATCGTCAGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATAGATCGCATGACGATCGCATATCGTCAGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGATCTCAGTCAGCAGC";   }
 225                 else if(toupper(temp[0]) == 'I'){
 226                     flowOrder = "TACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGC";   }
 227                 else {
 228                     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             }
 231
 232                         if(oligoFileName == "") {       allFiles = 0;           }
 233                         else                                    {       allFiles = 1;           }
 234
 235                         numFPrimers = 0;
 236                         numRPrimers = 0;
 237             numLinkers = 0;
 238             numSpacers = 0;
 239                 }
 240         }
 241         catch(exception& e) {
 242                 m->errorOut(e, "TrimFlowsCommand", "TrimFlowsCommand");
 243                 exit(1);
 244         }
 245 }
 246
 247 //***************************************************************************************************************
 248
 249 int TrimFlowsCommand::execute(){
 250         try{
 251
 252                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 253
 254         map<string, string> variables;
 255                 variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(flowFileName));
 256         string fastaFileName = getOutputFileName("fasta",variables);
 257                 if(fasta){ outputNames.push_back(fastaFileName); outputTypes["fasta"].push_back(fastaFileName); }
 258
 259         variables["[tag]"] = "trim";
 260                 string trimFlowFileName = getOutputFileName("flow",variables);
 261                 outputNames.push_back(trimFlowFileName); outputTypes["flow"].push_back(trimFlowFileName);
 262
 263         variables["[tag]"] = "scrap";
 264                 string scrapFlowFileName = getOutputFileName("flow",variables);
 265                 outputNames.push_back(scrapFlowFileName); outputTypes["flow"].push_back(scrapFlowFileName);
 266
 267
 268
 269                 vector<unsigned long long> flowFilePos;
 270         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 271                 flowFilePos = getFlowFileBreaks();
 272                 for (int i = 0; i < (flowFilePos.size()-1); i++) {
 273                         lines.push_back(new linePair(flowFilePos[i], flowFilePos[(i+1)]));
 274                 }
 275         #else
 276                 ifstream in; m->openInputFile(flowFileName, in); in >> numFlows; in.close();
 277         ///////////////////////////////////////// until I fix multiple processors for windows //////////////////
 278                 processors = 1;
 279         ///////////////////////////////////////// until I fix multiple processors for windows //////////////////
 280                 if (processors == 1) {
 281                         lines.push_back(new linePair(0, 1000));
 282                 }else {
 283                         int numFlowLines;
 284                         flowFilePos = m->setFilePosEachLine(flowFileName, numFlowLines);
 285                         flowFilePos.erase(flowFilePos.begin() + 1); numFlowLines--;
 286
 287                         //figure out how many sequences you have to process
 288                         int numSeqsPerProcessor = numFlowLines / processors;
 289                         cout << numSeqsPerProcessor << '\t' << numFlowLines << endl;
 290                         for (int i = 0; i < processors; i++) {
 291                                 int startIndex =  i * numSeqsPerProcessor;
 292                                 if(i == (processors - 1)){      numSeqsPerProcessor = numFlowLines - i * numSeqsPerProcessor;   }
 293                                 lines.push_back(new linePair(flowFilePos[startIndex], numSeqsPerProcessor));
 294                                 cout << flowFilePos[startIndex] << '\t' << numSeqsPerProcessor << endl;
 295                         }
 296                 }
 297         #endif
 298
 299                 vector<vector<string> > barcodePrimerComboFileNames;
 300                 if(oligoFileName != ""){
 301                         getOligos(barcodePrimerComboFileNames);
 302                 }
 303
 304                 if(processors == 1){
 305                         driverCreateTrim(flowFileName, trimFlowFileName, scrapFlowFileName, fastaFileName, barcodePrimerComboFileNames, lines[0]);
 306                 }else{
 307                         createProcessesCreateTrim(flowFileName, trimFlowFileName, scrapFlowFileName, fastaFileName, barcodePrimerComboFileNames);
 308                 }
 309
 310                 if (m->control_pressed) {  return 0; }
 311
 312                 string flowFilesFileName;
 313                 ofstream output;
 314
 315                 if(allFiles){
 316                         set<string> namesAlreadyProcessed;
 317                         flowFilesFileName = getOutputFileName("file",variables);
 318                         m->openOutputFile(flowFilesFileName, output);
 319
 320                         for(int i=0;i<barcodePrimerComboFileNames.size();i++){
 321                                 for(int j=0;j<barcodePrimerComboFileNames[0].size();j++){
 322                                         if (namesAlreadyProcessed.count(barcodePrimerComboFileNames[i][j]) == 0) {
 323                         if (barcodePrimerComboFileNames[i][j] != "") {
 324                             FILE * pFile;
 325                             unsigned long long size;
 326
 327                             //get num bytes in file
 328                             pFile = fopen (barcodePrimerComboFileNames[i][j].c_str(),"rb");
 329                             if (pFile==NULL) perror ("Error opening file");
 330                             else{
 331                                 fseek (pFile, 0, SEEK_END);
 332                                 size=ftell(pFile);
 333                                 fclose (pFile);
 334                             }
 335
 336                             if(size < 10){
 337                                 m->mothurRemove(barcodePrimerComboFileNames[i][j]);
 338                             }
 339                             else{
 340                                 output << m->getFullPathName(barcodePrimerComboFileNames[i][j]) << endl;
 341                                 outputNames.push_back(barcodePrimerComboFileNames[i][j]);
 342                                 outputTypes["flow"].push_back(barcodePrimerComboFileNames[i][j]);
 343                             }
 344                             namesAlreadyProcessed.insert(barcodePrimerComboFileNames[i][j]);
 345                         }
 346                                         }
 347                                 }
 348                         }
 349                         output.close();
 350                 }
 351                 else{
 352                         flowFilesFileName = getOutputFileName("file",variables);
 353                         m->openOutputFile(flowFilesFileName, output);
 354
 355                         output << m->getFullPathName(trimFlowFileName) << endl;
 356
 357                         output.close();
 358                 }
 359                 outputTypes["file"].push_back(flowFilesFileName);
 360                 outputNames.push_back(flowFilesFileName);
 361
 362                 m->mothurOutEndLine();
 363                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 364                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 365                 m->mothurOutEndLine();
 366
 367                 return 0;
 368         }
 369         catch(exception& e) {
 370                 m->errorOut(e, "TrimSeqsCommand", "execute");
 371                 exit(1);
 372         }
 373 }
 374
 375 //***************************************************************************************************************
 376
 377 int TrimFlowsCommand::driverCreateTrim(string flowFileName, string trimFlowFileName, string scrapFlowFileName, string fastaFileName, vector<vector<string> > thisBarcodePrimerComboFileNames, linePair* line){
 378
 379         try {
 380                 ofstream trimFlowFile;
 381                 m->openOutputFile(trimFlowFileName, trimFlowFile);
 382                 trimFlowFile.setf(ios::fixed, ios::floatfield); trimFlowFile.setf(ios::showpoint);
 383
 384                 ofstream scrapFlowFile;
 385                 m->openOutputFile(scrapFlowFileName, scrapFlowFile);
 386                 scrapFlowFile.setf(ios::fixed, ios::floatfield); scrapFlowFile.setf(ios::showpoint);
 387
 388                 ofstream fastaFile;
 389                 if(fasta){      m->openOutputFile(fastaFileName, fastaFile);    }
 390
 391                 ifstream flowFile;
 392                 m->openInputFile(flowFileName, flowFile);
 393
 394                 flowFile.seekg(line->start);
 395
 396                 if(line->start == 0){
 397                         flowFile >> numFlows; m->gobble(flowFile);
 398                         scrapFlowFile << numFlows << endl;
 399                         trimFlowFile << maxFlows << endl;
 400                         if(allFiles){
 401                                 for(int i=0;i<thisBarcodePrimerComboFileNames.size();i++){
 402                                         for(int j=0;j<thisBarcodePrimerComboFileNames[0].size();j++){
 403                         if (thisBarcodePrimerComboFileNames[i][j] != "") {
 404                             ofstream temp;
 405                             m->openOutputFile(thisBarcodePrimerComboFileNames[i][j], temp);
 406                             temp << maxFlows << endl;
 407                             temp.close();
 408                         }
 409                                         }
 410                                 }
 411                         }
 412                 }
 413
 414                 FlowData flowData(numFlows, signal, noise, maxHomoP, flowOrder);
 415                 //cout << " driver flowdata address " <<  &flowData  << &flowFile << endl;
 416                 int count = 0;
 417                 bool moreSeqs = 1;
 418
 419                 TrimOligos trimOligos(pdiffs, bdiffs, ldiffs, sdiffs, primers, barcodes, revPrimer, linker, spacer);
 420
 421                 while(moreSeqs) {
 422
 423                         if (m->control_pressed) { break; }
 424
 425                         int success = 1;
 426                         int currentSeqDiffs = 0;
 427                         string trashCode = "";
 428
 429                         flowData.getNext(flowFile);
 430                         flowData.capFlows(maxFlows);
 431
 432                         Sequence currSeq = flowData.getSequence();
 433             //cout << currSeq.getName() << '\t' << currSeq.getUnaligned() << endl;
 434                         if(!flowData.hasMinFlows(minFlows)){    //screen to see if sequence is of a minimum number of flows
 435                                 success = 0;
 436                                 trashCode += 'l';
 437                         }
 438             if(!flowData.hasGoodHomoP()){       //screen to see if sequence meets the maximum homopolymer limit
 439                                 success = 0;
 440                                 trashCode += 'h';
 441                         }
 442
 443                         int primerIndex = 0;
 444                         int barcodeIndex = 0;
 445
 446             if(numLinkers != 0){
 447                 success = trimOligos.stripLinker(currSeq);
 448                 if(success > ldiffs)            {       trashCode += 'k';       }
 449                 else{ currentSeqDiffs += success;  }
 450
 451             }
 452
 453             if (m->debug) { m->mothurOut("[DEBUG]: " + currSeq.getName() + " " + currSeq.getUnaligned() + "\n"); }
 454
 455                         if(barcodes.size() != 0){
 456                                 success = trimOligos.stripBarcode(currSeq, barcodeIndex);
 457                                 if(success > bdiffs)            {       trashCode += 'b';       }
 458                                 else{ currentSeqDiffs += success;  }
 459                         }
 460
 461             if(numSpacers != 0){
 462                 success = trimOligos.stripSpacer(currSeq);
 463                 if(success > sdiffs)            {       trashCode += 's';       }
 464                 else{ currentSeqDiffs += success;  }
 465
 466             }
 467
 468                         if(numFPrimers != 0){
 469                                 success = trimOligos.stripForward(currSeq, primerIndex);
 470                                 if(success > pdiffs)            {       trashCode += 'f';       }
 471                                 else{ currentSeqDiffs += success;  }
 472                         }
 473
 474                         if (currentSeqDiffs > tdiffs)   {       trashCode += 't';   }
 475
 476                         if(numRPrimers != 0){
 477                                 success = trimOligos.stripReverse(currSeq);
 478                                 if(!success)                            {       trashCode += 'r';       }
 479                         }
 480
 481                         if(trashCode.length() == 0){
 482                 string thisGroup = "";
 483                 if(barcodes.size() != 0){
 484                     thisGroup = barcodeNameVector[barcodeIndex];
 485                     if (primers.size() != 0) {
 486                         if (primerNameVector[primerIndex] != "") {
 487                             if(thisGroup != "") {
 488                                 thisGroup += "." + primerNameVector[primerIndex];
 489                             }else {
 490                                 thisGroup = primerNameVector[primerIndex];
 491                             }
 492                         }
 493                     }
 494                 }
 495
 496                 int pos = thisGroup.find("ignore");
 497                 if (pos == string::npos) {
 498                     flowData.printFlows(trimFlowFile);
 499
 500                     if(fasta)   { currSeq.printSequence(fastaFile);     }
 501
 502                     if(allFiles){
 503                         ofstream output;
 504                         m->openOutputFileAppend(thisBarcodePrimerComboFileNames[barcodeIndex][primerIndex], output);
 505                         output.setf(ios::fixed, ios::floatfield); trimFlowFile.setf(ios::showpoint);
 506
 507                         flowData.printFlows(output);
 508                         output.close();
 509                     }
 510                 }
 511                         }
 512                         else{
 513                                 flowData.printFlows(scrapFlowFile, trashCode);
 514                         }
 515
 516                         count++;
 517                         //cout << "driver" << '\t' << currSeq.getName() << endl;
 518                         //report progress
 519                         if((count) % 10000 == 0){       m->mothurOut(toString(count)); m->mothurOutEndLine();           }
 520
 521 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 522                         unsigned long long pos = flowFile.tellg();
 523
 524                         if ((pos == -1) || (pos >= line->end)) { break; }
 525 #else
 526                         if (flowFile.eof()) { break; }
 527 #endif
 528
 529                 }
 530                 //report progress
 531                 if((count) % 10000 != 0){       m->mothurOut(toString(count)); m->mothurOutEndLine();           }
 532
 533                 trimFlowFile.close();
 534                 scrapFlowFile.close();
 535                 flowFile.close();
 536                 if(fasta){      fastaFile.close();      }
 537
 538                 return count;
 539         }
 540         catch(exception& e) {
 541                 m->errorOut(e, "TrimSeqsCommand", "driverCreateTrim");
 542                 exit(1);
 543         }
 544 }
 545
 546 //***************************************************************************************************************
 547
 548 void TrimFlowsCommand::getOligos(vector<vector<string> >& outFlowFileNames){
 549         try {
 550                 ifstream oligosFile;
 551                 m->openInputFile(oligoFileName, oligosFile);
 552
 553                 string type, oligo, group;
 554
 555                 int indexPrimer = 0;
 556                 int indexBarcode = 0;
 557
 558                 while(!oligosFile.eof()){
 559
 560                         oligosFile >> type;     //get the first column value of the row - is it a comment or a feature we are interested in?
 561
 562             if (m->debug) { m->mothurOut("[DEBUG]: type = " + type + ".\n"); }
 563
 564                         if(type[0] == '#'){     //igore the line because there's a comment
 565                                 while (!oligosFile.eof())       {       char c = oligosFile.get(); if (c == 10 || c == 13){     break;  }       }
 566                 m->gobble(oligosFile);// get rest of line if there's any crap there
 567                         }
 568                         else{                           //there's a feature we're interested in
 569                 m->gobble(oligosFile);
 570                                 for(int i=0;i<type.length();i++){       type[i] = toupper(type[i]);  }                                  //make type case insensitive
 571
 572                                 oligosFile >> oligo;    //get the DNA sequence for the feature
 573
 574                                 for(int i=0;i<oligo.length();i++){      //make type case insensitive and change any U's to T's
 575                                         oligo[i] = toupper(oligo[i]);
 576                                         if(oligo[i] == 'U')     {       oligo[i] = 'T'; }
 577                                 }
 578
 579                 if (m->debug) { m->mothurOut("[DEBUG]: oligos = " + oligo + ".\n"); }
 580
 581                                 if(type == "FORWARD"){  //if the feature is a forward primer...
 582                                         group = "";
 583
 584                                         while (!oligosFile.eof())       {       // get rest of line in case there is a primer name = will have the name of the primer
 585                                                 char c = oligosFile.get();
 586                                                 if (c == 10 || c == 13 || c == -1){     break;  }
 587                                                 else if (c == 32 || c == 9){;} //space or tab
 588                                                 else {  group += c;  }
 589                                         }
 590
 591                                         //have we seen this primer already?
 592                                         map<string, int>::iterator itPrimer = primers.find(oligo);
 593                                         if (itPrimer != primers.end()) { m->mothurOut("primer " + oligo + " is in your oligos file already."); m->mothurOutEndLine();  }
 594
 595                                         primers[oligo]=indexPrimer; indexPrimer++;
 596                                         primerNameVector.push_back(group);
 597
 598                                 }
 599                                 else if(type == "REVERSE"){
 600                                         string oligoRC = reverseOligo(oligo);
 601                                         revPrimer.push_back(oligoRC);
 602                     if (m->debug) { m->mothurOut("[DEBUG]: reverse oligos = " + oligoRC + ".\n"); }
 603                                 }
 604                                 else if(type == "BARCODE"){
 605                                         oligosFile >> group;
 606
 607                                         //check for repeat barcodes
 608                                         map<string, int>::iterator itBar = barcodes.find(oligo);
 609                                         if (itBar != barcodes.end()) { m->mothurOut("barcode " + oligo + " is in your oligos file already."); m->mothurOutEndLine();  }
 610
 611                     if (m->debug) { m->mothurOut("[DEBUG]: group = " + group + ".\n"); }
 612
 613                                         barcodes[oligo]=indexBarcode; indexBarcode++;
 614                                         barcodeNameVector.push_back(group);
 615                                 }else if(type == "LINKER"){
 616                                         linker.push_back(oligo);
 617                                 }else if(type == "SPACER"){
 618                                         spacer.push_back(oligo);
 619                                 }
 620                                 else{
 621                                         m->mothurOut(type + " is not recognized as a valid type. Choices are forward, reverse, and barcode. Ignoring " + oligo + "."); m->mothurOutEndLine();
 622                                 }
 623                         }
 624
 625                         m->gobble(oligosFile);
 626                 }
 627                 oligosFile.close();
 628
 629                 if(barcodeNameVector.size() == 0 && primerNameVector[0] == ""){ allFiles = 0;   }
 630
 631                 //add in potential combos
 632                 if(barcodeNameVector.size() == 0){
 633                         barcodes[""] = 0;
 634                         barcodeNameVector.push_back("");
 635                 }
 636
 637                 if(primerNameVector.size() == 0){
 638                         primers[""] = 0;
 639                         primerNameVector.push_back("");
 640                 }
 641
 642                 outFlowFileNames.resize(barcodeNameVector.size());
 643                 for(int i=0;i<outFlowFileNames.size();i++){
 644                         outFlowFileNames[i].assign(primerNameVector.size(), "");
 645                 }
 646
 647                 if(allFiles){
 648
 649                         for(map<string, int>::iterator itBar = barcodes.begin();itBar != barcodes.end();itBar++){
 650                                 for(map<string, int>::iterator itPrimer = primers.begin();itPrimer != primers.end(); itPrimer++){
 651
 652                                         string primerName = primerNameVector[itPrimer->second];
 653                                         string barcodeName = barcodeNameVector[itBar->second];
 654
 655                                         if ((primerName == "ignore") || (barcodeName == "ignore")) { } //do nothing
 656                                         else {
 657                         string comboGroupName = "";
 658                         string fileName = "";
 659
 660                         map<string, string> variables;
 661                         variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(flowFileName));
 662
 663                         if(primerName == ""){
 664                             comboGroupName = barcodeNameVector[itBar->second];
 665                             variables["[tag]"] = comboGroupName;
 666                             fileName = getOutputFileName("flow", variables);
 667                         }
 668                         else{
 669                             if(barcodeName == ""){
 670                                 comboGroupName = primerNameVector[itPrimer->second];
 671                             }
 672                             else{
 673                                 comboGroupName = barcodeNameVector[itBar->second] + "." + primerNameVector[itPrimer->second];
 674                             }
 675                             variables["[tag]"] = comboGroupName;
 676                             fileName = getOutputFileName("flow", variables);
 677                         }
 678
 679                         outFlowFileNames[itBar->second][itPrimer->second] = fileName;
 680
 681                         ofstream temp;
 682                         m->openOutputFile(fileName, temp);
 683                         temp.close();
 684                     }
 685                                 }
 686                         }
 687                 }
 688
 689                 numFPrimers = primers.size();
 690                 numRPrimers = revPrimer.size();
 691         numLinkers = linker.size();
 692         numSpacers = spacer.size();
 693
 694         }
 695         catch(exception& e) {
 696                 m->errorOut(e, "TrimSeqsCommand", "getOligos");
 697                 exit(1);
 698         }
 699 }
 700 //********************************************************************/
 701 string TrimFlowsCommand::reverseOligo(string oligo){
 702         try {
 703         string reverse = "";
 704
 705         for(int i=oligo.length()-1;i>=0;i--){
 706
 707             if(oligo[i] == 'A')         {       reverse += 'T'; }
 708             else if(oligo[i] == 'T'){   reverse += 'A'; }
 709             else if(oligo[i] == 'U'){   reverse += 'A'; }
 710
 711             else if(oligo[i] == 'G'){   reverse += 'C'; }
 712             else if(oligo[i] == 'C'){   reverse += 'G'; }
 713
 714             else if(oligo[i] == 'R'){   reverse += 'Y'; }
 715             else if(oligo[i] == 'Y'){   reverse += 'R'; }
 716
 717             else if(oligo[i] == 'M'){   reverse += 'K'; }
 718             else if(oligo[i] == 'K'){   reverse += 'M'; }
 719
 720             else if(oligo[i] == 'W'){   reverse += 'W'; }
 721             else if(oligo[i] == 'S'){   reverse += 'S'; }
 722
 723             else if(oligo[i] == 'B'){   reverse += 'V'; }
 724             else if(oligo[i] == 'V'){   reverse += 'B'; }
 725
 726             else if(oligo[i] == 'D'){   reverse += 'H'; }
 727             else if(oligo[i] == 'H'){   reverse += 'D'; }
 728
 729             else                                                {       reverse += 'N'; }
 730         }
 731
 732
 733         return reverse;
 734     }
 735         catch(exception& e) {
 736                 m->errorOut(e, "TrimFlowsCommand", "reverseOligo");
 737                 exit(1);
 738         }
 739 }
 740
 741 /**************************************************************************************************/
 742 vector<unsigned long long> TrimFlowsCommand::getFlowFileBreaks() {
 743
 744         try{
 745
 746                 vector<unsigned long long> filePos;
 747                 filePos.push_back(0);
 748
 749                 FILE * pFile;
 750                 unsigned long long size;
 751
 752                 //get num bytes in file
 753                 pFile = fopen (flowFileName.c_str(),"rb");
 754                 if (pFile==NULL) perror ("Error opening file");
 755                 else{
 756                         fseek (pFile, 0, SEEK_END);
 757                         size=ftell (pFile);
 758                         fclose (pFile);
 759                 }
 760
 761                 //estimate file breaks
 762                 unsigned long long chunkSize = 0;
 763                 chunkSize = size / processors;
 764
 765                 //file too small to divide by processors
 766                 if (chunkSize == 0)  {  processors = 1; filePos.push_back(size); return filePos;        }
 767
 768                 //for each process seekg to closest file break and search for next '>' char. make that the filebreak
 769                 for (int i = 0; i < processors; i++) {
 770                         unsigned long long spot = (i+1) * chunkSize;
 771
 772                         ifstream in;
 773                         m->openInputFile(flowFileName, in);
 774                         in.seekg(spot);
 775
 776                         string dummy = m->getline(in);
 777
 778                         //there was not another sequence before the end of the file
 779                         unsigned long long sanityPos = in.tellg();
 780
 781 //                      if (sanityPos == -1) {  break;  }
 782 //                      else {  filePos.push_back(newSpot);  }
 783                         if (sanityPos == -1) {  break;  }
 784                         else {  filePos.push_back(sanityPos);  }
 785
 786                         in.close();
 787                 }
 788
 789                 //save end pos
 790                 filePos.push_back(size);
 791
 792                 //sanity check filePos
 793                 for (int i = 0; i < (filePos.size()-1); i++) {
 794                         if (filePos[(i+1)] <= filePos[i]) {  filePos.erase(filePos.begin()+(i+1)); i--; }
 795                 }
 796
 797                 ifstream in;
 798                 m->openInputFile(flowFileName, in);
 799                 in >> numFlows;
 800                 m->gobble(in);
 801                 //unsigned long long spot = in.tellg();
 802                 //filePos[0] = spot;
 803                 in.close();
 804
 805                 processors = (filePos.size() - 1);
 806
 807                 return filePos;
 808         }
 809         catch(exception& e) {
 810                 m->errorOut(e, "TrimSeqsCommand", "getFlowFileBreaks");
 811                 exit(1);
 812         }
 813 }
 814
 815 /**************************************************************************************************/
 816
 817 int TrimFlowsCommand::createProcessesCreateTrim(string flowFileName, string trimFlowFileName, string scrapFlowFileName, string fastaFileName, vector<vector<string> > barcodePrimerComboFileNames){
 818
 819         try {
 820                 processIDS.clear();
 821                 int exitCommand = 1;
 822
 823 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 824                 int process = 1;
 825
 826                 //loop through and create all the processes you want
 827                 while (process != processors) {
 828                         int pid = fork();
 829
 830                         if (pid > 0) {
 831                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
 832                                 process++;
 833                         }else if (pid == 0){
 834
 835                                 vector<vector<string> > tempBarcodePrimerComboFileNames = barcodePrimerComboFileNames;
 836                                 if(allFiles){
 837                                         for(int i=0;i<tempBarcodePrimerComboFileNames.size();i++){
 838                                                 for(int j=0;j<tempBarcodePrimerComboFileNames[0].size();j++){
 839                             if (tempBarcodePrimerComboFileNames[i][j] != "") {
 840                                 tempBarcodePrimerComboFileNames[i][j] += toString(getpid()) + ".temp";
 841                                 ofstream temp;
 842                                 m->openOutputFile(tempBarcodePrimerComboFileNames[i][j], temp);
 843                                 temp.close();
 844                             }
 845                                                 }
 846                                         }
 847                                 }
 848                                 driverCreateTrim(flowFileName,
 849                                                                  (trimFlowFileName + toString(getpid()) + ".temp"),
 850                                                                  (scrapFlowFileName + toString(getpid()) + ".temp"),
 851                                                                  (fastaFileName + toString(getpid()) + ".temp"),
 852                                                                  tempBarcodePrimerComboFileNames, lines[process]);
 853
 854                                 exit(0);
 855                         }else {
 856                                 m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
 857                                 for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
 858                                 exit(0);
 859                         }
 860                 }
 861
 862                 //parent do my part
 863                 ofstream temp;
 864                 m->openOutputFile(trimFlowFileName, temp);
 865                 temp.close();
 866
 867                 m->openOutputFile(scrapFlowFileName, temp);
 868                 temp.close();
 869
 870                 if(fasta){
 871                         m->openOutputFile(fastaFileName, temp);
 872                         temp.close();
 873                 }
 874
 875                 driverCreateTrim(flowFileName, trimFlowFileName, scrapFlowFileName, fastaFileName, barcodePrimerComboFileNames, lines[0]);
 876
 877                 //force parent to wait until all the processes are done
 878                 for (int i=0;i<processIDS.size();i++) {
 879                         int temp = processIDS[i];
 880                         wait(&temp);
 881                 }
 882 #else
 883                 //////////////////////////////////////////////////////////////////////////////////////////////////////
 884                 //Windows version shared memory, so be careful when passing variables through the trimFlowData struct.
 885                 //Above fork() will clone, so memory is separate, but that's not the case with windows,
 886                 //////////////////////////////////////////////////////////////////////////////////////////////////////
 887
 888                 vector<trimFlowData*> pDataArray;
 889                 DWORD   dwThreadIdArray[processors-1];
 890                 HANDLE  hThreadArray[processors-1];
 891
 892                 //Create processor worker threads.
 893                 for( int i=0; i<processors-1; i++ ){
 894                         // Allocate memory for thread data.
 895                         string extension = "";
 896                         if (i != 0) { extension = toString(i) + ".temp"; processIDS.push_back(i); }
 897
 898                         vector<vector<string> > tempBarcodePrimerComboFileNames = barcodePrimerComboFileNames;
 899                         if(allFiles){
 900                                 for(int i=0;i<tempBarcodePrimerComboFileNames.size();i++){
 901                                         for(int j=0;j<tempBarcodePrimerComboFileNames[0].size();j++){
 902                         if (tempBarcodePrimerComboFileNames[i][j] != "") {
 903                             tempBarcodePrimerComboFileNames[i][j] += extension;
 904                             ofstream temp;
 905                             m->openOutputFile(tempBarcodePrimerComboFileNames[i][j], temp);
 906                             temp.close();
 907                                                 }
 908                                         }
 909                                 }
 910                         }
 911
 912                         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);
 913                         pDataArray.push_back(tempflow);
 914
 915                         //MyTrimFlowThreadFunction is in header. It must be global or static to work with the threads.
 916                         //default security attributes, thread function name, argument to thread function, use default creation flags, returns the thread identifier
 917                         hThreadArray[i] = CreateThread(NULL, 0, MyTrimFlowThreadFunction, pDataArray[i], 0, &dwThreadIdArray[i]);
 918                 }
 919
 920                 //using the main process as a worker saves time and memory
 921                 ofstream temp;
 922                 m->openOutputFile(trimFlowFileName, temp);
 923                 temp.close();
 924
 925                 m->openOutputFile(scrapFlowFileName, temp);
 926                 temp.close();
 927
 928                 if(fasta){
 929                         m->openOutputFile(fastaFileName, temp);
 930                         temp.close();
 931                 }
 932
 933                 vector<vector<string> > tempBarcodePrimerComboFileNames = barcodePrimerComboFileNames;
 934                 if(allFiles){
 935                         for(int i=0;i<tempBarcodePrimerComboFileNames.size();i++){
 936                                 for(int j=0;j<tempBarcodePrimerComboFileNames[0].size();j++){
 937                     if (tempBarcodePrimerComboFileNames[i][j] != "") {
 938                         tempBarcodePrimerComboFileNames[i][j] += toString(processors-1) + ".temp";
 939                         ofstream temp;
 940                         m->openOutputFile(tempBarcodePrimerComboFileNames[i][j], temp);
 941                         temp.close();
 942                     }
 943
 944                                 }
 945                         }
 946                 }
 947
 948                 //do my part - do last piece because windows is looking for eof
 949                 int num = driverCreateTrim(flowFileName, (trimFlowFileName  + toString(processors-1) + ".temp"), (scrapFlowFileName  + toString(processors-1) + ".temp"), (fastaFileName + toString(processors-1) + ".temp"), tempBarcodePrimerComboFileNames, lines[processors-1]);
 950                 processIDS.push_back((processors-1));
 951
 952                 //Wait until all threads have terminated.
 953                 WaitForMultipleObjects(processors-1, hThreadArray, TRUE, INFINITE);
 954
 955                 //Close all thread handles and free memory allocations.
 956                 for(int i=0; i < pDataArray.size(); i++){
 957                         num += pDataArray[i]->count;
 958                         CloseHandle(hThreadArray[i]);
 959                         delete pDataArray[i];
 960                 }
 961
 962
 963 #endif
 964                 //append files
 965                 m->mothurOutEndLine();
 966                 for(int i=0;i<processIDS.size();i++){
 967
 968                         m->mothurOut("Appending files from process " + toString(processIDS[i])); m->mothurOutEndLine();
 969
 970                         m->appendFiles((trimFlowFileName + toString(processIDS[i]) + ".temp"), trimFlowFileName);
 971                         m->mothurRemove((trimFlowFileName + toString(processIDS[i]) + ".temp"));
 972 //                      m->mothurOut("\tDone with trim.flow file"); m->mothurOutEndLine();
 973
 974                         m->appendFiles((scrapFlowFileName + toString(processIDS[i]) + ".temp"), scrapFlowFileName);
 975                         m->mothurRemove((scrapFlowFileName + toString(processIDS[i]) + ".temp"));
 976 //                      m->mothurOut("\tDone with scrap.flow file"); m->mothurOutEndLine();
 977
 978                         if(fasta){
 979                                 m->appendFiles((fastaFileName + toString(processIDS[i]) + ".temp"), fastaFileName);
 980                                 m->mothurRemove((fastaFileName + toString(processIDS[i]) + ".temp"));
 981 //                              m->mothurOut("\tDone with flow.fasta file"); m->mothurOutEndLine();
 982                         }
 983                         if(allFiles){
 984                                 for (int j = 0; j < barcodePrimerComboFileNames.size(); j++) {
 985                                         for (int k = 0; k < barcodePrimerComboFileNames[0].size(); k++) {
 986                         if (barcodePrimerComboFileNames[j][k] != "") {
 987                             m->appendFiles((barcodePrimerComboFileNames[j][k] + toString(processIDS[i]) + ".temp"), barcodePrimerComboFileNames[j][k]);
 988                             m->mothurRemove((barcodePrimerComboFileNames[j][k] + toString(processIDS[i]) + ".temp"));
 989                         }
 990                                         }
 991                                 }
 992                         }
 993                 }
 994
 995                 return exitCommand;
 996
 997         }
 998         catch(exception& e) {
 999                 m->errorOut(e, "TrimFlowsCommand", "createProcessesCreateTrim");
1000                 exit(1);
1001         }
1002 }
1003
1004 //***************************************************************************************************************