1 #ifndef SUMMARYQUALCOMMAND_H
2 #define SUMMARYQUALCOMMAND_H
8 * Created by westcott on 11/28/11.
9 * Copyright 2011 Schloss Lab. All rights reserved.
14 #include "command.hpp"
15 #include "qualityscores.h"
17 /**************************************************************************************************/
19 class SummaryQualCommand : public Command {
21 SummaryQualCommand(string);
23 ~SummaryQualCommand(){}
25 vector<string> setParameters();
26 string getCommandName() { return "summary.qual"; }
27 string getCommandCategory() { return "Sequence Processing"; }
28 string getHelpString();
29 string getCitation() { return "http://www.mothur.org/wiki/Summary.qual"; }
30 string getDescription() { return "summarize the quality of a set of sequences"; }
33 void help() { m->mothurOut(getHelpString()); }
37 string qualfile, outputDir, namefile;
38 vector<string> outputNames;
39 map<string, int> nameMap;
43 unsigned long long start;
44 unsigned long long end;
45 linePair(unsigned long long i, unsigned long long j) : start(i), end(j) {}
48 vector<linePair> lines;
49 vector<int> processIDS;
51 int createProcessesCreateSummary(vector<int>&, vector<int>&, vector< vector<int> >&, string);
52 int driverCreateSummary(vector<int>&, vector<int>&, vector< vector<int> >&, string, linePair);
53 int printQual(string, vector<int>&, vector<int>&, vector< vector<int> >&);
56 /**************************************************************************************************/
57 //custom data structure for threads to use.
58 // This is passed by void pointer so it can be any data type
59 // that can be passed using a single void pointer (LPVOID).
60 struct seqSumQualData {
63 vector< vector<int> > scores;
64 string filename, namefile;
65 unsigned long long start;
66 unsigned long long end;
69 map<string, int> nameMap;
72 seqSumQualData(string f, MothurOut* mout, unsigned long long st, unsigned long long en, string n, map<string, int> nam) {
83 /**************************************************************************************************/
84 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
86 static DWORD WINAPI MySeqSumQualThreadFunction(LPVOID lpParam){
87 seqSumQualData* pDataArray;
88 pDataArray = (seqSumQualData*)lpParam;
92 pDataArray->m->openInputFile(pDataArray->filename, in);
94 //print header if you are process 0
95 if ((pDataArray->start == 0) || (pDataArray->start == 1)) {
97 }else { //this accounts for the difference in line endings.
98 in.seekg(pDataArray->start-1); pDataArray->m->gobble(in);
102 for(int i = 0; i < pDataArray->end; i++){ //end is the number of sequences to process
104 if (pDataArray->m->control_pressed) { in.close(); pDataArray->count = 1; return 1; }
106 QualityScores current(in); pDataArray->m->gobble(in);
108 if (current.getName() != "") {
111 if (pDataArray->namefile != "") {
112 //make sure this sequence is in the namefile, else error
113 map<string, int>::iterator it = pDataArray->nameMap.find(current.getName());
115 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; }
116 else { num = it->second; }
119 vector<int> thisScores = current.getQualityScores();
121 //resize to num of positions setting number of seqs with that size to 1
122 if (pDataArray->position.size() < thisScores.size()) { pDataArray->position.resize(thisScores.size(), 0); }
123 if (pDataArray->averageQ.size() < thisScores.size()) { pDataArray->averageQ.resize(thisScores.size(), 0); }
124 if (pDataArray->scores.size() < thisScores.size()) {
125 pDataArray->scores.resize(thisScores.size());
126 for (int i = 0; i < pDataArray->scores.size(); i++) { pDataArray->scores.at(i).resize(41, 0); }
129 //increase counts of number of seqs with this position
130 //average is really the total, we will average in execute
131 for (int i = 0; i < thisScores.size(); i++) {
132 pDataArray->position.at(i) += num;
133 pDataArray->averageQ.at(i) += (thisScores[i] * num); //weighting for namesfile
134 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; }
135 else { pDataArray->scores.at(i)[thisScores[i]] += num; }
142 pDataArray->count = count;
148 catch(exception& e) {
149 pDataArray->m->errorOut(e, "SummaryQualCommand", "MySeqSumQualThreadFunction");
156 /**************************************************************************************************/