1 #ifndef TRIMFLOWSCOMMAND_H
2 #define TRIMFLOWSCOMMAND_H
8 * Created by Pat Schloss on 12/22/10.
9 * Copyright 2010 Schloss Lab. All rights reserved.
14 #include "command.hpp"
15 #include "sequence.hpp"
18 #include "trimoligos.h"
20 class TrimFlowsCommand : public Command {
22 TrimFlowsCommand(string);
24 ~TrimFlowsCommand() {}
26 vector<string> setParameters();
27 string getCommandName() { return "trim.flows"; }
28 string getCommandCategory() { return "Sequence Processing"; }
29 string getHelpString();
30 string getCitation() { return "http://www.mothur.org/wiki/Trim.flows"; }
31 string getDescription() { return "trim.flows"; }
35 void help() { m->mothurOut(getHelpString()); }
41 unsigned long long start;
42 unsigned long long end;
43 linePair(unsigned long long i, unsigned long long j) : start(i), end(j) {}
46 vector<int> processIDS; //processid
47 vector<linePair*> lines;
49 vector<unsigned long long> getFlowFileBreaks();
50 int createProcessesCreateTrim(string, string, string, string, vector<vector<string> >);
51 int driverCreateTrim(string, string, string, string, vector<vector<string> >, linePair*);
52 string reverseOligo(string);
54 vector<string> outputNames;
55 set<string> filesToRemove;
57 void getOligos(vector<vector<string> >&); //a rewrite of what is in trimseqscommand.h
61 int numFPrimers, numRPrimers;
62 int maxFlows, minFlows, minLength, maxLength, maxHomoP, tdiffs, bdiffs, pdiffs, sdiffs, ldiffs, numLinkers, numSpacers;
68 string flowFileName, oligoFileName, outputDir;
70 map<string, int> barcodes;
71 map<string, int> primers;
72 vector<string> revPrimer;
73 vector<string> linker;
74 vector<string> spacer;
76 vector<string> primerNameVector; //needed here?
77 vector<string> barcodeNameVector; //needed here?
79 map<string, int> combos; //needed here?
80 map<string, int> groupToIndex; //needed here?
84 /**************************************************************************************************/
85 //custom data structure for threads to use.
86 // This is passed by void pointer so it can be any data type
87 // that can be passed using a single void pointer (LPVOID).
90 string trimFlowFileName;
91 string scrapFlowFileName;
94 vector<vector<string> > barcodePrimerComboFileNames;
95 map<string, int> barcodes;
96 map<string, int> primers;
97 vector<string> revPrimer;
99 unsigned long long start;
100 unsigned long long end;
103 int numFlows, maxFlows, minFlows, maxHomoP, tdiffs, bdiffs, pdiffs, threadID, count;
106 trimFlowData(string ff, string tf, string sf, string f, string fo, vector<vector<string> > bfn, map<string, int> bar, map<string, int> pri, vector<string> rev, bool fa, bool al, unsigned long long st, unsigned long long en, MothurOut* mout, float sig, float n, int numF, int maxF, int minF, int maxH, int td, int bd, int pd, int tid) {
108 trimFlowFileName = tf;
109 scrapFlowFileName = sf;
112 barcodePrimerComboFileNames = bfn;
134 /**************************************************************************************************/
135 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
137 static DWORD WINAPI MyTrimFlowThreadFunction(LPVOID lpParam){
138 trimFlowData* pDataArray;
139 pDataArray = (trimFlowData*)lpParam;
142 ofstream trimFlowFile;
143 pDataArray->m->openOutputFile(pDataArray->trimFlowFileName, trimFlowFile);
144 trimFlowFile.setf(ios::fixed, ios::floatfield); trimFlowFile.setf(ios::showpoint);
146 ofstream scrapFlowFile;
147 pDataArray->m->openOutputFile(pDataArray->scrapFlowFileName, scrapFlowFile);
148 scrapFlowFile.setf(ios::fixed, ios::floatfield); scrapFlowFile.setf(ios::showpoint);
151 if(pDataArray->fasta){ pDataArray->m->openOutputFile(pDataArray->fastaFileName, fastaFile); }
154 pDataArray->m->openInputFile(pDataArray->flowFileName, flowFile);
156 flowFile.seekg(pDataArray->start);
158 if(pDataArray->start == 0){
159 flowFile >> pDataArray->numFlows; pDataArray->m->gobble(flowFile);
160 scrapFlowFile << pDataArray->maxFlows << endl;
161 trimFlowFile << pDataArray->maxFlows << endl;
162 if(pDataArray->allFiles){
163 for(int i=0;i<pDataArray->barcodePrimerComboFileNames.size();i++){
164 for(int j=0;j<pDataArray->barcodePrimerComboFileNames[0].size();j++){
166 pDataArray->m->openOutputFile(pDataArray->barcodePrimerComboFileNames[i][j], temp);
167 temp << pDataArray->maxFlows << endl;
174 FlowData flowData(pDataArray->numFlows, pDataArray->signal, pDataArray->noise, pDataArray->maxHomoP, pDataArray->flowOrder);
175 cout << " thread flowdata address " << &flowData << '\t' << &flowFile << endl;
176 TrimOligos trimOligos(pDataArray->pdiffs, pDataArray->bdiffs, pDataArray->primers, pDataArray->barcodes, pDataArray->revPrimer);
178 pDataArray->count = pDataArray->end;
179 cout << pDataArray->threadID << '\t' << pDataArray->count << endl;
181 for(int i = 0; i < pDataArray->end; i++){ //end is the number of sequences to process
183 if (pDataArray->m->control_pressed) { break; }
184 cout << pDataArray->threadID << '\t' << count << endl;
186 int currentSeqDiffs = 0;
187 string trashCode = "";
189 flowData.getNext(flowFile);
190 cout << "thread good bit " << flowFile.good() << endl;
191 flowData.capFlows(pDataArray->maxFlows);
193 Sequence currSeq = flowData.getSequence();
194 if(!flowData.hasMinFlows(pDataArray->minFlows)){ //screen to see if sequence is of a minimum number of flows
200 int barcodeIndex = 0;
202 if(pDataArray->barcodes.size() != 0){
203 success = trimOligos.stripBarcode(currSeq, barcodeIndex);
204 if(success > pDataArray->bdiffs) { trashCode += 'b'; }
205 else{ currentSeqDiffs += success; }
208 if(pDataArray->primers.size() != 0){
209 success = trimOligos.stripForward(currSeq, primerIndex);
210 if(success > pDataArray->pdiffs) { trashCode += 'f'; }
211 else{ currentSeqDiffs += success; }
214 if (currentSeqDiffs > pDataArray->tdiffs) { trashCode += 't'; }
216 if(pDataArray->revPrimer.size() != 0){
217 success = trimOligos.stripReverse(currSeq);
218 if(!success) { trashCode += 'r'; }
221 if(trashCode.length() == 0){
223 flowData.printFlows(trimFlowFile);
225 if(pDataArray->fasta) { currSeq.printSequence(fastaFile); }
227 if(pDataArray->allFiles){
229 pDataArray->m->openOutputFileAppend(pDataArray->barcodePrimerComboFileNames[barcodeIndex][primerIndex], output);
230 output.setf(ios::fixed, ios::floatfield); trimFlowFile.setf(ios::showpoint);
232 flowData.printFlows(output);
237 flowData.printFlows(scrapFlowFile, trashCode);
241 cout << pDataArray->threadID << '\t' << currSeq.getName() << endl;
243 if((count) % 10000 == 0){ pDataArray->m->mothurOut(toString(count)); pDataArray->m->mothurOutEndLine(); }
247 if((count) % 10000 != 0){ pDataArray->m->mothurOut(toString(count)); pDataArray->m->mothurOutEndLine(); }
249 trimFlowFile.close();
250 scrapFlowFile.close();
252 if(pDataArray->fasta){ fastaFile.close(); }
255 catch(exception& e) {
256 pDataArray->m->errorOut(e, "TrimFlowsCommand", "MyTrimFlowsThreadFunction");