//
#include "command.hpp"
+#include "sffinfocommand.h"
+#include "seqsummarycommand.h"
+#include "trimflowscommand.h"
+#include "shhhercommand.h"
+#include "trimseqscommand.h"
class SffMultipleCommand : public Command {
vector<string> setParameters();
string getCommandName() { return "sff.multiple"; }
string getCommandCategory() { return "Sequence Processing"; }
- string getOutputFileNameTag(string, string);
+
string getHelpString();
+ string getOutputPattern(string);
string getCitation() { return "http://www.mothur.org/wiki/Sff.multiple"; }
string getDescription() { return "run multiple sff files through, sffinfo, trim.flow, shhh.flows and trim.seqs combining the results"; }
int end;
linePair(int i, int j) : start(i), end(j) {}
};
-
- string filename, outputDir, flowOrder;
+
+ string inputDir;
+ string filename, outputDir, flowOrder, lookupFileName, minDelta;
vector<string> outputNames;
- bool abort, trim, large, flip, qtrim, allFiles, keepforward;
- int maxFlows, minFlows, minLength, maxLength, maxHomoP, tdiffs, bdiffs, pdiffs, sdiffs, ldiffs, numLinkers, numSpacers;
- int numFlows, numFPrimers, numRPrimers, processors, maxIters, largeSize;
- float signal, noise, cutoff, sigma, minDelta;
- int qWindowSize, qWindowStep, keepFirst, removeLast, maxAmbig;
- double qRollAverage, qThreshold, qWindowAverage, qAverage;
+ bool abort, trim, large, flip, allFiles, keepforward, append, makeGroup;
+ int maxFlows, minFlows, minLength, maxLength, maxHomoP, tdiffs, bdiffs, pdiffs, sdiffs, ldiffs;
+ int processors, maxIters, largeSize;
+ float signal, noise, cutoff, sigma;
+ int keepFirst, removeLast, maxAmbig;
int readFile(vector<string>& sffFiles, vector<string>& oligosFiles);
- int createProcesses(vector<string> sffFiles, vector<string> oligosFiles);
- int driver(vector<string> sffFiles, vector<string> oligosFiles, int start, int end);
+ int createProcesses(vector<string> sffFiles, vector<string> oligosFiles, string, string, string);
+ int driver(vector<string> sffFiles, vector<string> oligosFiles, int start, int end, string, string, string);
+ int mergeOutputFileList(map<string, vector<string> >& files, map<string, vector<string> >& temp);
+
};
-
#endif