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#ifndef TRIMSEQSCOMMAND_H
#define TRIMSEQSCOMMAND_H
/*
* trimseqscommand.h
* Mothur
*
* Created by Pat Schloss on 6/6/09.
* Copyright 2009 Patrick D. Schloss. All rights reserved.
*
*/
#include "mothur.h"
#include "command.hpp"
#include "sequence.hpp"
#include "qualityscores.h"
#include "trimoligos.h"
#include "counttable.h"
#include "writer.h"
#include "splitgroupscommand.h"
#include "oligos.h"
class TrimSeqsCommand : public Command {
public:
TrimSeqsCommand(string);
~TrimSeqsCommand(){}
vector<string> setParameters();
string getCommandName() { return "trim.seqs"; }
string getCommandCategory() { return "Sequence Processing"; }
string getHelpString();
string getOutputPattern(string);
string getCitation() { return "http://www.mothur.org/wiki/Trim.seqs"; }
string getDescription() { return "provides the preprocessing features needed to screen and sort pyrosequences"; }
int execute();
void help() { m->mothurOut(getHelpString()); }
private:
bool abort, createGroup;
string fastaFile, oligoFile, qFileName, nameFile, countfile;
bool flip, allFiles, qtrim, keepforward, pairedOligos, reorient, logtransform;
int maxAmbig, maxHomoP, minLength, maxLength, processors, tdiffs, bdiffs, pdiffs, ldiffs, sdiffs, comboStarts;
int qWindowSize, qWindowStep, keepFirst, removeLast;
double qRollAverage, qThreshold, qWindowAverage, qAverage;
vector<string> outputNames;
set<string> filesToRemove;
vector<string> groupVector;
map<string, int> groupCounts;
map<string, int> nameCount; //for countfile name -> repCount
map<string, string> seq2Group;
vector<linePair> lines;
vector<linePair> qLines;
long long createProcessesCreateTrim(string, string, string, string, string, string, unordered_set<string>&);
int processNamesCountFiles(string trimFasta, unordered_set<string> badNames, string trimCountFileName, string scrapCountFileName);
int setLines(string, string);
};
/**************************************************************************************************/
#endif
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