+++ /dev/null
-#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
-
projects / mothur.git / blobdiff