added mergesfffiles command. added current directories to get.current commands output...

[mothur.git] / mergesfffilecommand.h

diff --git a/mergesfffilecommand.h b/mergesfffilecommand.h
new file mode 100644 (file)
index 0000000..3208e61
--- /dev/null
+++ b/mergesfffilecommand.h
@@ -0,0 +1,57 @@
+//
+//  mergesfffilecommand.h
+//  Mothur
+//
+//  Created by Sarah Westcott on 1/31/14.
+//  Copyright (c) 2014 Schloss Lab. All rights reserved.
+//
+
+#ifndef Mothur_mergesfffilecommand_h
+#define Mothur_mergesfffilecommand_h
+
+#include "command.hpp"
+
+
+/**********************************************************/
+class MergeSfffilesCommand : public Command {
+       
+public:
+       MergeSfffilesCommand(string);
+       MergeSfffilesCommand();
+       ~MergeSfffilesCommand(){}
+       
+       vector<string> setParameters();
+       string getCommandName()                 { return "merge.sfffiles";                                      }
+       string getCommandCategory()             { return "Sequence Processing";         }
+       
+       string getHelpString();
+    string getOutputPattern(string);
+       string getCitation() { return "http://www.mothur.org/wiki/merge.sfffiles"; }
+       string getDescription()         { return "merge individual sfffiles into a single .sff file"; }
+    
+       int execute();
+       void help() { m->mothurOut(getHelpString()); }
+       
+private:
+       string sffFilename, outputDir, file, currentFileName;
+       vector<string> filenames, outputNames;
+       bool abort;
+    int numTotalReads, allFilesnumFlowReads, allFileskeyLength;
+    string outputFile, outputFileHeader;
+    vector<CommonHeader> commonHeaders;
+    
+       //extract sff file functions
+       int mergeSffInfo(string, ofstream&);
+       int readCommonHeader(ifstream&, CommonHeader&);
+       int readHeader(ifstream&, Header&);
+       bool readSeqData(ifstream&, seqRead&, int, Header&, ofstream&);
+       int decodeName(string&, string&, string&, string);
+ 
+       bool sanityCheck(Header&, seqRead&);
+    int adjustCommonHeader();
+    int readFile();
+};
+
+/**********************************************************/
+
+#endif