+++ /dev/null
-#ifndef SEQSUMMARYCOMMAND_H
-#define SEQSUMMARYCOMMAND_H
-
-/*
- * seqcoordcommand.h
- * Mothur
- *
- * Created by Pat Schloss on 5/30/09.
- * Copyright 2009 Patrick D. Schloss. All rights reserved.
- *
- */
-
-#include "mothur.h"
-#include "command.hpp"
-#include "sequence.hpp"
-
-/**************************************************************************************************/
-
-class SeqSummaryCommand : public Command {
-public:
- SeqSummaryCommand(string);
- SeqSummaryCommand();
- ~SeqSummaryCommand(){}
-
- vector<string> setParameters();
- string getCommandName() { return "summary.seqs"; }
- string getCommandCategory() { return "Sequence Processing"; }
- string getHelpString();
- string getCitation() { return "http://www.mothur.org/wiki/Summary.seqs"; }
- string getDescription() { return "summarize the quality of sequences in an unaligned or aligned fasta file"; }
-
- int execute();
- void help() { m->mothurOut(getHelpString()); }
-private:
- bool abort;
- string fastafile, outputDir, namefile;
- int processors;
- vector<string> outputNames;
- map<string, int> nameMap;
-
- 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<int>&, vector<int>&, vector<int>&, string, string);
- int driverCreateSummary(vector<int>&, vector<int>&, vector<int>&, vector<int>&, vector<int>&, string, string, linePair*);
-
- #ifdef USE_MPI
- int MPICreateSummary(int, int, vector<int>&, vector<int>&, vector<int>&, vector<int>&, vector<int>&, MPI_File&, MPI_File&, vector<unsigned long long>&);
- #endif
-
-
-};
-
-/**************************************************************************************************/
-//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 seqSumData {
- vector<int> startPosition;
- vector<int> endPosition;
- vector<int> seqLength;
- vector<int> ambigBases;
- vector<int> longHomoPolymer;
- string filename;
- string sumFile;
- unsigned long long start;
- unsigned long long end;
- int count;
- MothurOut* m;
- string namefile;
- map<string, int> nameMap;
-
-
- seqSumData(){}
- seqSumData(string f, string sf, MothurOut* mout, unsigned long long st, unsigned long long en, string na, map<string, int> nam) {
- filename = f;
- sumFile = sf;
- m = mout;
- start = st;
- end = en;
- namefile = na;
- nameMap = nam;
- count = 0;
- }
-};
-
-/**************************************************************************************************/
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
-#else
-static DWORD WINAPI MySeqSumThreadFunction(LPVOID lpParam){
- seqSumData* pDataArray;
- pDataArray = (seqSumData*)lpParam;
-
- try {
- ofstream outSummary;
- pDataArray->m->openOutputFile(pDataArray->sumFile, outSummary);
-
- ifstream in;
- pDataArray->m->openInputFile(pDataArray->filename, in);
-
- //print header if you are process 0
- if ((pDataArray->start == 0) || (pDataArray->start == 1)) {
- outSummary << "seqname\tstart\tend\tnbases\tambigs\tpolymer\tnumSeqs" << endl;
- in.seekg(0);
- }else { //this accounts for the difference in line endings.
- in.seekg(pDataArray->start-1); pDataArray->m->gobble(in);
- }
-
- pDataArray->count = pDataArray->end;
- for(int i = 0; i < pDataArray->end; i++){ //end is the number of sequences to process
-
- if (pDataArray->m->control_pressed) { in.close(); outSummary.close(); pDataArray->count = 1; return 1; }
-
- Sequence 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; }
- }
-
- //for each sequence this sequence represents
- for (int i = 0; i < num; i++) {
- pDataArray->startPosition.push_back(current.getStartPos());
- pDataArray->endPosition.push_back(current.getEndPos());
- pDataArray->seqLength.push_back(current.getNumBases());
- pDataArray->ambigBases.push_back(current.getAmbigBases());
- pDataArray->longHomoPolymer.push_back(current.getLongHomoPolymer());
- }
-
- outSummary << current.getName() << '\t';
- outSummary << current.getStartPos() << '\t' << current.getEndPos() << '\t';
- outSummary << current.getNumBases() << '\t' << current.getAmbigBases() << '\t';
- outSummary << current.getLongHomoPolymer() << '\t' << num << endl;
- }
- }
-
- in.close();
- outSummary.close();
-
- return 0;
-
- }
- catch(exception& e) {
- pDataArray->m->errorOut(e, "SeqSummaryCommand", "MySeqSumThreadFunction");
- exit(1);
- }
-}
-#endif
-
-
-
-
-#endif
-
-/**************************************************************************************************/
-
-
projects / mothur.git / blobdiff