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#ifndef REMOVESEQSCOMMAND_H
#define REMOVESEQSCOMMAND_H
/*
* removeseqscommand.h
* Mothur
*
* Created by Sarah Westcott on 7/8/09.
* Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
*
*/
#include "command.hpp"
class RemoveSeqsCommand : public Command {
public:
RemoveSeqsCommand(string);
RemoveSeqsCommand(string, pair<string, string> dupsFile, string dupsFileType);
RemoveSeqsCommand(unordered_set<string>, pair<string, string> dupsFile, string dupsFileType);
~RemoveSeqsCommand(){}
vector<string> setParameters();
string getCommandName() { return "remove.seqs"; }
string getCommandCategory() { return "Sequence Processing"; }
string getHelpString();
string getOutputPattern(string);
string getCitation() { return "http://www.mothur.org/wiki/Remove.seqs"; }
string getDescription() { return "removes sequences from a list, fasta, name, group, alignreport, contigsreport, quality or taxonomy file"; }
int execute();
void help() { m->mothurOut(getHelpString()); }
private:
unordered_set<string> names;
vector<string> fastafiles, namefiles, groupfiles, countfiles, alignfiles, listfiles, taxfiles, fastqfiles, contigsreportfiles, qualityfiles, outputNames;
string accnosfile, format;
bool abort, dups;
map<string, string> uniqueMap;
void readFasta(string);
void readFastq(string);
void readGZFastq(string);
void readName(string); //inputNameFile, mothur generates output name
void readName(string, string); //inputNameFile, outputName (internal use)
void readGroup(string);
void readCount(string); //inputCountFile, mothur generates output name
void readCount(string, string); //inputCountFile, outputName (internal use)
void readAlign(string);
void readContigs(string);
void readList(string);
void readTax(string);
void readQual(string);
};
#endif
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