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//
// chimeravsearchcommand.h
// Mothur
//
// Created by Sarah Westcott on 6/16/16.
// Copyright (c) 2016 Schloss Lab. All rights reserved.
//
#ifndef __Mothur__chimeravsearchcommand__
#define __Mothur__chimeravsearchcommand__
#include "command.hpp"
#include "sequenceparser.h"
#include "counttable.h"
#include "sequencecountparser.h"
/**************************************************************************************************/
struct vsearchVariables {
bool dups, useAbskew, chimealns, useMinH, useMindiv, useXn, useDn, useXa, hasCount, useMindiffs;
string abskew, minh, mindiv, xn, dn, mindiffs;
vsearchVariables() = default;
void setBooleans(bool dps, bool Abskew, bool calns, bool MinH, bool Mindiv, bool Xn, bool Dn, bool mindif, bool hc) {
useAbskew = Abskew;
chimealns = calns;
useMinH = MinH;
useMindiv = Mindiv;
useMindiffs = mindif;
useXn = Xn;
useDn = Dn;
hasCount = hc;
dups = dps;
}
void setVariables(string abske, string min, string mindi, string x, string d, string mind) {
abskew = abske;
minh = min;
mindiv = mindi;
mindiffs = mind;
xn = x;
dn = d;
}
};
/**************************************************************************************************/
struct vsearchData {
string dupsfile;
string outputFName;
string accnos, alns, formattedFastaFilename, templatefile, vsearchLocation;
string driverAccnos, driverAlns, driverOutputFName;
map<string, vector<string> > parsedFiles;
map<string, vector<string> > seqs2RemoveByGroup;
int count, numChimeras, processors;
vector<string> groups;
vsearchVariables* vars;
MothurOut* m;
Utils util;
vsearchData(){}
vsearchData(int proc, map<string, vector<string> > g2f, string o, string uloc, string t, string file, string n, string ac, string al, string nc, vector<string> gr, vsearchVariables* vs) {
dupsfile = n;
formattedFastaFilename = file;
outputFName = o;
templatefile = t;
accnos = ac;
alns = al;
m = MothurOut::getInstance();
groups = gr;
count = 0;
numChimeras = 0;
vsearchLocation = uloc;
vars = vs;
driverAccnos = ac;
driverAlns = al;
driverOutputFName = o;
parsedFiles = g2f;
processors = proc;
}
void setDriverNames(string o, string al, string ac) {
driverAccnos = ac;
driverAlns = al;
driverOutputFName = o;
}
};
/***********************************************************/
class ChimeraVsearchCommand : public Command {
public:
ChimeraVsearchCommand(string);
~ChimeraVsearchCommand() = default;
vector<string> setParameters();
string getCommandName() { return "chimera.vsearch"; }
string getCommandCategory() { return "Sequence Processing"; }
string getHelpString();
string getCommonQuestions();
string getOutputPattern(string);
string getCitation() { return "vsearch by https://github.com/torognes/vsearch.\nhttp://www.mothur.org/wiki/Chimera.vsearch\n"; }
string getDescription() { return "detect chimeric sequences"; }
int execute();
void help() { m->mothurOut(getHelpString()); }
private:
bool abort, useAbskew, chimealns, useMinH, useMindiv, useXn, useDn, ucl, useMindiffs, hasCount, dups, removeChimeras;
string fastafile, templatefile, countfile, abskew, minh, mindiv, xn, dn, mindiffs, vsearchLocation;
int processors;
vsearchVariables* vars;
vector<string> outputNames;
string getCountFile(string&);
int readFasta(string, map<string, string>&);
int deconvoluteResults(string, string, string, long long&);
int prepFile(string filename, string);
int createProcessesGroups(map<string, vector<string> >& groups2Files, string outputFName, string filename, string accnos, string alns, string newCountFile, vector<string> groups, map<string, vector<string> >&);
};
#endif
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