X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=summaryqualcommand.h;fp=summaryqualcommand.h;h=bbd103c1d14f7b40badd9654152aec0fd2b47a10;hb=0caf3fbabaa3ece404f8ce77f4c883dc5b1bf1dc;hp=0000000000000000000000000000000000000000;hpb=1b73ff67c83892a025e597dabd9df6fe7b58206a;p=mothur.git

diff --git a/summaryqualcommand.h b/summaryqualcommand.h
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+#ifndef SUMMARYQUALCOMMAND_H
+#define SUMMARYQUALCOMMAND_H
+
+/*
+ *  summaryqualcommand.h
+ *  Mothur
+ *
+ *  Created by westcott on 11/28/11.
+ *  Copyright 2011 Schloss Lab. All rights reserved.
+ *
+ */
+
+
+#include "command.hpp"
+#include "qualityscores.h"
+
+/**************************************************************************************************/
+
+class SummaryQualCommand : public Command {
+public:
+	SummaryQualCommand(string);
+	SummaryQualCommand();
+	~SummaryQualCommand(){}
+	
+	vector<string> setParameters();
+	string getCommandName()			{ return "summary.qual";			}
+	string getCommandCategory()		{ return "Sequence Processing";		}
+	string getHelpString();	
+	string getCitation() { return "http://www.mothur.org/wiki/Summary.qual"; }
+	string getDescription()		{ return "summarize the quality of a set of sequences"; }
+	
+	int execute(); 
+	void help() { m->mothurOut(getHelpString()); }	
+	
+private:
+	bool abort;
+	string qualfile, outputDir, namefile;
+	vector<string> outputNames;
+	map<string, int> nameMap;
+	int processors;
+	
+	struct linePair {
+		unsigned long long start;
+		unsigned long long end;
+		linePair(unsigned long long i, unsigned long long j) : start(i), end(j) {}
+	};
+	
+	vector<linePair> lines;
+	vector<int> processIDS;
+	
+	int createProcessesCreateSummary(vector<int>&, vector<int>&, vector< vector<int> >&, string);
+	int driverCreateSummary(vector<int>&, vector<int>&, vector< vector<int> >&, string, linePair);	
+	int printQual(string, vector<int>&, vector<int>&, vector< vector<int> >&);
+};
+
+/**************************************************************************************************/
+//custom data structure for threads to use.
+// This is passed by void pointer so it can be any data type
+// that can be passed using a single void pointer (LPVOID).
+struct seqSumQualData {
+	vector<int> position;
+	vector<int> averageQ;
+	vector< vector<int> > scores; 
+	string filename, namefile; 
+	unsigned long long start;
+	unsigned long long end;
+	int count;
+	MothurOut* m;
+	map<string, int> nameMap;
+	
+	~seqSumQualData(){}
+	seqSumQualData(string f, MothurOut* mout, unsigned long long st, unsigned long long en, string n, map<string, int> nam) {
+		filename = f;
+		m = mout;
+		start = st;
+		end = en;
+		namefile = n;
+		nameMap = nam;
+		count = 0;
+	}
+};
+
+/**************************************************************************************************/
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+#else
+static DWORD WINAPI MySeqSumQualThreadFunction(LPVOID lpParam){ 
+	seqSumQualData* pDataArray;
+	pDataArray = (seqSumQualData*)lpParam;
+	
+	try {
+		ifstream in;
+		pDataArray->m->openInputFile(pDataArray->filename, in);
+		
+		//print header if you are process 0
+		if ((pDataArray->start == 0) || (pDataArray->start == 1)) {
+			in.seekg(0);
+		}else { //this accounts for the difference in line endings. 
+			in.seekg(pDataArray->start-1); pDataArray->m->gobble(in); 
+		}
+		
+		int count = 0;
+		for(int i = 0; i < pDataArray->end; i++){ //end is the number of sequences to process
+				
+			if (pDataArray->m->control_pressed) { in.close(); pDataArray->count = 1; return 1; }
+			
+			QualityScores current(in); pDataArray->m->gobble(in);
+			
+			if (current.getName() != "") {
+			
+				int num = 1;
+				if (pDataArray->namefile != "") {
+					//make sure this sequence is in the namefile, else error 
+					map<string, int>::iterator it = pDataArray->nameMap.find(current.getName());
+					
+					if (it == pDataArray->nameMap.end()) { pDataArray->m->mothurOut("[ERROR]: " + current.getName() + " is not in your namefile, please correct."); pDataArray->m->mothurOutEndLine(); pDataArray->m->control_pressed = true; }
+					else { num = it->second; }
+				}
+				
+				vector<int> thisScores = current.getQualityScores();
+				
+				//resize to num of positions setting number of seqs with that size to 1
+				if (pDataArray->position.size() < thisScores.size()) { pDataArray->position.resize(thisScores.size(), 0); }
+				if (pDataArray->averageQ.size() < thisScores.size()) { pDataArray->averageQ.resize(thisScores.size(), 0); }
+				if (pDataArray->scores.size() < thisScores.size()) { 
+					pDataArray->scores.resize(thisScores.size()); 
+					for (int i = 0; i < pDataArray->scores.size(); i++) { pDataArray->scores.at(i).resize(41, 0); }
+				}
+				
+				//increase counts of number of seqs with this position
+				//average is really the total, we will average in execute
+				for (int i = 0; i < thisScores.size(); i++) { 
+					pDataArray->position.at(i) += num; 
+					pDataArray->averageQ.at(i) += (thisScores[i] * num); //weighting for namesfile
+					if (thisScores[i] > 40) { pDataArray->m->mothurOut("[ERROR]: " + current.getName() + " has a quality scores of " + toString(thisScores[i]) + ", expecting values to be less than 40."); pDataArray->m->mothurOutEndLine(); pDataArray->m->control_pressed = true; }
+					else { pDataArray->scores.at(i)[thisScores[i]] += num; }  
+				}
+				
+				count += num;
+			}
+		}
+		
+		pDataArray->count = count;
+		in.close();
+		
+		return 0;
+		
+	}
+	catch(exception& e) {
+		pDataArray->m->errorOut(e, "SummaryQualCommand", "MySeqSumQualThreadFunction");
+		exit(1);
+	}
+} 
+#endif
+
+
+/**************************************************************************************************/
+
+
+#endif
+