5 * Created by Pat Schloss on 12/22/10.
6 * Copyright 2010 Schloss Lab. All rights reserved.
10 #include "trimflowscommand.h"
11 #include "needlemanoverlap.hpp"
14 //**********************************************************************************************************************
15 vector<string> TrimFlowsCommand::setParameters(){
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);
36 vector<string> myArray;
37 for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
41 m->errorOut(e, "TrimFlowsCommand", "setParameters");
45 //**********************************************************************************************************************
46 string TrimFlowsCommand::getHelpString(){
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";
56 m->errorOut(e, "TrimFlowsCommand", "getHelpString");
60 //**********************************************************************************************************************
61 string TrimFlowsCommand::getOutputPattern(string type) {
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; }
73 m->errorOut(e, "TrimFlowsCommand", "getOutputPattern");
77 //**********************************************************************************************************************
79 TrimFlowsCommand::TrimFlowsCommand(){
81 abort = true; calledHelp = true;
83 vector<string> tempOutNames;
84 outputTypes["flow"] = tempOutNames;
85 outputTypes["fasta"] = tempOutNames;
86 outputTypes["file"] = tempOutNames;
89 m->errorOut(e, "TrimFlowsCommand", "TrimFlowsCommand");
93 //**********************************************************************************************************************
95 TrimFlowsCommand::TrimFlowsCommand(string option) {
98 abort = false; calledHelp = false;
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;}
107 vector<string> myArray = setParameters();
109 OptionParser parser(option);
110 map<string,string> parameters = parser.getParameters();
112 ValidParameters validParameter;
113 map<string,string>::iterator it;
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; }
120 //initialize outputTypes
121 vector<string> tempOutNames;
122 outputTypes["flow"] = tempOutNames;
123 outputTypes["fasta"] = tempOutNames;
124 outputTypes["file"] = tempOutNames;
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 = ""; }
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; }
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; }
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(); }
156 m->mothurOut("No valid current flow file. You must provide a flow file."); m->mothurOutEndLine();
159 }else if (flowFileName == "not open") { flowFileName = ""; abort = true; }
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"){
164 outputDir += m->hasPath(flowFileName); //if user entered a file with a path then preserve it
168 //check for optional parameter and set defaults
169 // ...at some point should added some additional type checking...
172 temp = validParameter.validFile(parameters, "minflows", false); if (temp == "not found") { temp = "450"; }
173 m->mothurConvert(temp, minFlows);
175 temp = validParameter.validFile(parameters, "maxflows", false); if (temp == "not found") { temp = "450"; }
176 m->mothurConvert(temp, maxFlows);
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); }
184 temp = validParameter.validFile(parameters, "fasta", false); if (temp == "not found"){ fasta = 0; }
185 else if(m->isTrue(temp)) { fasta = 1; }
187 temp = validParameter.validFile(parameters, "maxhomop", false); if (temp == "not found"){ temp = "9"; }
188 m->mothurConvert(temp, maxHomoP);
190 temp = validParameter.validFile(parameters, "signal", false); if (temp == "not found"){ temp = "0.50"; }
191 m->mothurConvert(temp, signal);
193 temp = validParameter.validFile(parameters, "noise", false); if (temp == "not found"){ temp = "0.70"; }
194 m->mothurConvert(temp, noise);
196 temp = validParameter.validFile(parameters, "bdiffs", false); if (temp == "not found"){ temp = "0"; }
197 m->mothurConvert(temp, bdiffs);
199 temp = validParameter.validFile(parameters, "pdiffs", false); if (temp == "not found"){ temp = "0"; }
200 m->mothurConvert(temp, pdiffs);
202 temp = validParameter.validFile(parameters, "ldiffs", false); if (temp == "not found") { temp = "0"; }
203 m->mothurConvert(temp, ldiffs);
205 temp = validParameter.validFile(parameters, "sdiffs", false); if (temp == "not found") { temp = "0"; }
206 m->mothurConvert(temp, sdiffs);
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);
211 if(tdiffs == 0){ tdiffs = bdiffs + pdiffs + ldiffs + sdiffs; }
214 temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = m->getProcessors(); }
215 m->setProcessors(temp);
216 m->mothurConvert(temp, processors);
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;
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"; }
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;
232 if(oligoFileName == "") { allFiles = 0; }
233 else { allFiles = 1; }
241 catch(exception& e) {
242 m->errorOut(e, "TrimFlowsCommand", "TrimFlowsCommand");
247 //***************************************************************************************************************
249 int TrimFlowsCommand::execute(){
252 if (abort == true) { if (calledHelp) { return 0; } return 2; }
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); }
259 variables["[tag]"] = "trim";
260 string trimFlowFileName = getOutputFileName("flow",variables);
261 outputNames.push_back(trimFlowFileName); outputTypes["flow"].push_back(trimFlowFileName);
263 variables["[tag]"] = "scrap";
264 string scrapFlowFileName = getOutputFileName("flow",variables);
265 outputNames.push_back(scrapFlowFileName); outputTypes["flow"].push_back(scrapFlowFileName);
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)]));
276 ifstream in; m->openInputFile(flowFileName, in); in >> numFlows; in.close();
277 ///////////////////////////////////////// until I fix multiple processors for windows //////////////////
279 ///////////////////////////////////////// until I fix multiple processors for windows //////////////////
280 if (processors == 1) {
281 lines.push_back(new linePair(0, 1000));
284 flowFilePos = m->setFilePosEachLine(flowFileName, numFlowLines);
285 flowFilePos.erase(flowFilePos.begin() + 1); numFlowLines--;
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;
299 vector<vector<string> > barcodePrimerComboFileNames;
300 if(oligoFileName != ""){
301 getOligos(barcodePrimerComboFileNames);
305 driverCreateTrim(flowFileName, trimFlowFileName, scrapFlowFileName, fastaFileName, barcodePrimerComboFileNames, lines[0]);
307 createProcessesCreateTrim(flowFileName, trimFlowFileName, scrapFlowFileName, fastaFileName, barcodePrimerComboFileNames);
310 if (m->control_pressed) { return 0; }
312 string flowFilesFileName;
316 set<string> namesAlreadyProcessed;
317 flowFilesFileName = getOutputFileName("file",variables);
318 m->openOutputFile(flowFilesFileName, output);
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] != "") {
325 unsigned long long size;
327 //get num bytes in file
328 pFile = fopen (barcodePrimerComboFileNames[i][j].c_str(),"rb");
329 if (pFile==NULL) perror ("Error opening file");
331 fseek (pFile, 0, SEEK_END);
337 m->mothurRemove(barcodePrimerComboFileNames[i][j]);
340 output << m->getFullPathName(barcodePrimerComboFileNames[i][j]) << endl;
341 outputNames.push_back(barcodePrimerComboFileNames[i][j]);
342 outputTypes["flow"].push_back(barcodePrimerComboFileNames[i][j]);
344 namesAlreadyProcessed.insert(barcodePrimerComboFileNames[i][j]);
352 flowFilesFileName = getOutputFileName("file",variables);
353 m->openOutputFile(flowFilesFileName, output);
355 output << m->getFullPathName(trimFlowFileName) << endl;
359 outputTypes["file"].push_back(flowFilesFileName);
360 outputNames.push_back(flowFilesFileName);
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();
369 catch(exception& e) {
370 m->errorOut(e, "TrimSeqsCommand", "execute");
375 //***************************************************************************************************************
377 int TrimFlowsCommand::driverCreateTrim(string flowFileName, string trimFlowFileName, string scrapFlowFileName, string fastaFileName, vector<vector<string> > thisBarcodePrimerComboFileNames, linePair* line){
380 ofstream trimFlowFile;
381 m->openOutputFile(trimFlowFileName, trimFlowFile);
382 trimFlowFile.setf(ios::fixed, ios::floatfield); trimFlowFile.setf(ios::showpoint);
384 ofstream scrapFlowFile;
385 m->openOutputFile(scrapFlowFileName, scrapFlowFile);
386 scrapFlowFile.setf(ios::fixed, ios::floatfield); scrapFlowFile.setf(ios::showpoint);
389 if(fasta){ m->openOutputFile(fastaFileName, fastaFile); }
392 m->openInputFile(flowFileName, flowFile);
394 flowFile.seekg(line->start);
396 if(line->start == 0){
397 flowFile >> numFlows; m->gobble(flowFile);
398 scrapFlowFile << maxFlows << endl;
399 trimFlowFile << maxFlows << endl;
401 for(int i=0;i<thisBarcodePrimerComboFileNames.size();i++){
402 for(int j=0;j<thisBarcodePrimerComboFileNames[0].size();j++){
403 if (thisBarcodePrimerComboFileNames[i][j] != "") {
405 m->openOutputFile(thisBarcodePrimerComboFileNames[i][j], temp);
406 temp << maxFlows << endl;
414 FlowData flowData(numFlows, signal, noise, maxHomoP, flowOrder);
415 //cout << " driver flowdata address " << &flowData << &flowFile << endl;
419 TrimOligos trimOligos(pdiffs, bdiffs, ldiffs, sdiffs, primers, barcodes, revPrimer, linker, spacer);
423 if (m->control_pressed) { break; }
426 int currentSeqDiffs = 0;
427 string trashCode = "";
429 flowData.getNext(flowFile);
430 flowData.capFlows(maxFlows);
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
438 if(!flowData.hasGoodHomoP()){ //screen to see if sequence meets the maximum homopolymer limit
444 int barcodeIndex = 0;
447 success = trimOligos.stripLinker(currSeq);
448 if(success > ldiffs) { trashCode += 'k'; }
449 else{ currentSeqDiffs += success; }
453 if (m->debug) { m->mothurOut("[DEBUG]: " + currSeq.getName() + " " + currSeq.getUnaligned() + "\n"); }
455 if(barcodes.size() != 0){
456 success = trimOligos.stripBarcode(currSeq, barcodeIndex);
457 if(success > bdiffs) { trashCode += 'b'; }
458 else{ currentSeqDiffs += success; }
462 success = trimOligos.stripSpacer(currSeq);
463 if(success > sdiffs) { trashCode += 's'; }
464 else{ currentSeqDiffs += success; }
468 if(numFPrimers != 0){
469 success = trimOligos.stripForward(currSeq, primerIndex);
470 if(success > pdiffs) { trashCode += 'f'; }
471 else{ currentSeqDiffs += success; }
474 if (currentSeqDiffs > tdiffs) { trashCode += 't'; }
476 if(numRPrimers != 0){
477 success = trimOligos.stripReverse(currSeq);
478 if(!success) { trashCode += 'r'; }
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];
490 thisGroup = primerNameVector[primerIndex];
496 int pos = thisGroup.find("ignore");
497 if (pos == string::npos) {
498 flowData.printFlows(trimFlowFile);
500 if(fasta) { currSeq.printSequence(fastaFile); }
504 m->openOutputFileAppend(thisBarcodePrimerComboFileNames[barcodeIndex][primerIndex], output);
505 output.setf(ios::fixed, ios::floatfield); trimFlowFile.setf(ios::showpoint);
507 flowData.printFlows(output);
513 flowData.printFlows(scrapFlowFile, trashCode);
517 //cout << "driver" << '\t' << currSeq.getName() << endl;
519 if((count) % 10000 == 0){ m->mothurOut(toString(count)); m->mothurOutEndLine(); }
521 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
522 unsigned long long pos = flowFile.tellg();
524 if ((pos == -1) || (pos >= line->end)) { break; }
526 if (flowFile.eof()) { break; }
531 if((count) % 10000 != 0){ m->mothurOut(toString(count)); m->mothurOutEndLine(); }
533 trimFlowFile.close();
534 scrapFlowFile.close();
536 if(fasta){ fastaFile.close(); }
540 catch(exception& e) {
541 m->errorOut(e, "TrimSeqsCommand", "driverCreateTrim");
546 //***************************************************************************************************************
548 void TrimFlowsCommand::getOligos(vector<vector<string> >& outFlowFileNames){
551 m->openInputFile(oligoFileName, oligosFile);
553 string type, oligo, group;
556 int indexBarcode = 0;
558 while(!oligosFile.eof()){
560 oligosFile >> type; //get the first column value of the row - is it a comment or a feature we are interested in?
562 if (m->debug) { m->mothurOut("[DEBUG]: type = " + type + ".\n"); }
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
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
572 oligosFile >> oligo; //get the DNA sequence for the feature
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'; }
579 if (m->debug) { m->mothurOut("[DEBUG]: oligos = " + oligo + ".\n"); }
581 if(type == "FORWARD"){ //if the feature is a forward primer...
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
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(); }
595 primers[oligo]=indexPrimer; indexPrimer++;
596 primerNameVector.push_back(group);
599 else if(type == "REVERSE"){
600 string oligoRC = reverseOligo(oligo);
601 revPrimer.push_back(oligoRC);
603 else if(type == "BARCODE"){
606 //check for repeat barcodes
607 map<string, int>::iterator itBar = barcodes.find(oligo);
608 if (itBar != barcodes.end()) { m->mothurOut("barcode " + oligo + " is in your oligos file already."); m->mothurOutEndLine(); }
610 if (m->debug) { m->mothurOut("[DEBUG]: group = " + group + ".\n"); }
612 barcodes[oligo]=indexBarcode; indexBarcode++;
613 barcodeNameVector.push_back(group);
614 }else if(type == "LINKER"){
615 linker.push_back(oligo);
616 }else if(type == "SPACER"){
617 spacer.push_back(oligo);
620 m->mothurOut(type + " is not recognized as a valid type. Choices are forward, reverse, and barcode. Ignoring " + oligo + "."); m->mothurOutEndLine();
624 m->gobble(oligosFile);
628 if(barcodeNameVector.size() == 0 && primerNameVector[0] == ""){ allFiles = 0; }
630 //add in potential combos
631 if(barcodeNameVector.size() == 0){
633 barcodeNameVector.push_back("");
636 if(primerNameVector.size() == 0){
638 primerNameVector.push_back("");
642 outFlowFileNames.resize(barcodeNameVector.size());
643 for(int i=0;i<outFlowFileNames.size();i++){
644 outFlowFileNames[i].assign(primerNameVector.size(), "");
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++){
652 string primerName = primerNameVector[itPrimer->second];
653 string barcodeName = barcodeNameVector[itBar->second];
655 if ((primerName == "ignore") || (barcodeName == "ignore")) { } //do nothing
657 string comboGroupName = "";
658 string fileName = "";
660 map<string, string> variables;
661 variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(flowFileName));
663 if(primerName == ""){
664 comboGroupName = barcodeNameVector[itBar->second];
665 variables["[tag]"] = comboGroupName;
666 fileName = getOutputFileName("flow", variables);
669 if(barcodeName == ""){
670 comboGroupName = primerNameVector[itPrimer->second];
673 comboGroupName = barcodeNameVector[itBar->second] + "." + primerNameVector[itPrimer->second];
675 variables["[tag]"] = comboGroupName;
676 fileName = getOutputFileName("flow", variables);
679 outFlowFileNames[itBar->second][itPrimer->second] = fileName;
682 m->openOutputFile(fileName, temp);
689 numFPrimers = primers.size();
690 numRPrimers = revPrimer.size();
691 numLinkers = linker.size();
692 numSpacers = spacer.size();
695 catch(exception& e) {
696 m->errorOut(e, "TrimSeqsCommand", "getOligos");
700 //********************************************************************/
701 string TrimFlowsCommand::reverseOligo(string oligo){
705 for(int i=oligo.length()-1;i>=0;i--){
707 if(oligo[i] == 'A') { reverse += 'T'; }
708 else if(oligo[i] == 'T'){ reverse += 'A'; }
709 else if(oligo[i] == 'U'){ reverse += 'A'; }
711 else if(oligo[i] == 'G'){ reverse += 'C'; }
712 else if(oligo[i] == 'C'){ reverse += 'G'; }
714 else if(oligo[i] == 'R'){ reverse += 'Y'; }
715 else if(oligo[i] == 'Y'){ reverse += 'R'; }
717 else if(oligo[i] == 'M'){ reverse += 'K'; }
718 else if(oligo[i] == 'K'){ reverse += 'M'; }
720 else if(oligo[i] == 'W'){ reverse += 'W'; }
721 else if(oligo[i] == 'S'){ reverse += 'S'; }
723 else if(oligo[i] == 'B'){ reverse += 'V'; }
724 else if(oligo[i] == 'V'){ reverse += 'B'; }
726 else if(oligo[i] == 'D'){ reverse += 'H'; }
727 else if(oligo[i] == 'H'){ reverse += 'D'; }
729 else { reverse += 'N'; }
735 catch(exception& e) {
736 m->errorOut(e, "TrimFlowsCommand", "reverseOligo");
741 /**************************************************************************************************/
742 vector<unsigned long long> TrimFlowsCommand::getFlowFileBreaks() {
746 vector<unsigned long long> filePos;
747 filePos.push_back(0);
750 unsigned long long size;
752 //get num bytes in file
753 pFile = fopen (flowFileName.c_str(),"rb");
754 if (pFile==NULL) perror ("Error opening file");
756 fseek (pFile, 0, SEEK_END);
761 //estimate file breaks
762 unsigned long long chunkSize = 0;
763 chunkSize = size / processors;
765 //file too small to divide by processors
766 if (chunkSize == 0) { processors = 1; filePos.push_back(size); return filePos; }
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;
773 m->openInputFile(flowFileName, in);
776 string dummy = m->getline(in);
778 //there was not another sequence before the end of the file
779 unsigned long long sanityPos = in.tellg();
781 // if (sanityPos == -1) { break; }
782 // else { filePos.push_back(newSpot); }
783 if (sanityPos == -1) { break; }
784 else { filePos.push_back(sanityPos); }
790 filePos.push_back(size);
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--; }
798 m->openInputFile(flowFileName, in);
801 //unsigned long long spot = in.tellg();
805 processors = (filePos.size() - 1);
809 catch(exception& e) {
810 m->errorOut(e, "TrimSeqsCommand", "getFlowFileBreaks");
815 /**************************************************************************************************/
817 int TrimFlowsCommand::createProcessesCreateTrim(string flowFileName, string trimFlowFileName, string scrapFlowFileName, string fastaFileName, vector<vector<string> > barcodePrimerComboFileNames){
823 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
826 //loop through and create all the processes you want
827 while (process != processors) {
831 processIDS.push_back(pid); //create map from line number to pid so you can append files in correct order later
835 vector<vector<string> > tempBarcodePrimerComboFileNames = barcodePrimerComboFileNames;
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";
842 m->openOutputFile(tempBarcodePrimerComboFileNames[i][j], temp);
848 driverCreateTrim(flowFileName,
849 (trimFlowFileName + toString(getpid()) + ".temp"),
850 (scrapFlowFileName + toString(getpid()) + ".temp"),
851 (fastaFileName + toString(getpid()) + ".temp"),
852 tempBarcodePrimerComboFileNames, lines[process]);
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); }
864 m->openOutputFile(trimFlowFileName, temp);
867 m->openOutputFile(scrapFlowFileName, temp);
871 m->openOutputFile(fastaFileName, temp);
875 driverCreateTrim(flowFileName, trimFlowFileName, scrapFlowFileName, fastaFileName, barcodePrimerComboFileNames, lines[0]);
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];
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 //////////////////////////////////////////////////////////////////////////////////////////////////////
888 vector<trimFlowData*> pDataArray;
889 DWORD dwThreadIdArray[processors-1];
890 HANDLE hThreadArray[processors-1];
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); }
898 vector<vector<string> > tempBarcodePrimerComboFileNames = barcodePrimerComboFileNames;
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;
905 m->openOutputFile(tempBarcodePrimerComboFileNames[i][j], temp);
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);
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]);
920 //using the main process as a worker saves time and memory
922 m->openOutputFile(trimFlowFileName, temp);
925 m->openOutputFile(scrapFlowFileName, temp);
929 m->openOutputFile(fastaFileName, temp);
933 vector<vector<string> > tempBarcodePrimerComboFileNames = barcodePrimerComboFileNames;
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";
940 m->openOutputFile(tempBarcodePrimerComboFileNames[i][j], temp);
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));
952 //Wait until all threads have terminated.
953 WaitForMultipleObjects(processors-1, hThreadArray, TRUE, INFINITE);
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];
965 m->mothurOutEndLine();
966 for(int i=0;i<processIDS.size();i++){
968 m->mothurOut("Appending files from process " + toString(processIDS[i])); m->mothurOutEndLine();
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();
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();
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();
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"));
998 catch(exception& e) {
999 m->errorOut(e, "TrimFlowsCommand", "createProcessesCreateTrim");
1004 //***************************************************************************************************************