added forward and reverse barcodes to trim.seqs to process illumina seqs

[mothur.git] / getseqscommand.h

diff --git a/getseqscommand.h b/getseqscommand.h
index ea93b5a1c4e0427cc43157a5d77f995bb3f2308b..0f606ffb59ac884b46ac97d861aa3542786d1793 100644 (file)
--- a/getseqscommand.h
+++ b/getseqscommand.h
@@ -18,20 +18,27 @@ class GetSeqsCommand : public Command {
        
                GetSeqsCommand(string);
                GetSeqsCommand();
-               ~GetSeqsCommand(){};
-               vector<string> getRequiredParameters();
-               vector<string> getValidParameters();
-               vector<string> getRequiredFiles();
-               map<string, vector<string> > getOutputFiles() { return outputTypes; }
-               int execute();
-               void help();    
-               
+               ~GetSeqsCommand(){}
+       
+               vector<string> setParameters();
+               string getCommandName()                 { return "get.seqs";                            }
+               string getCommandCategory()             { return "Sequence Processing";         }
+               string getHelpString(); 
+               string getCitation() { return "http://www.mothur.org/wiki/Get.seqs"; }
+               string getDescription()         { return "gets sequences from a list, fasta, name, group, alignreport, quality or taxonomy file"; }
+
+               int execute(); 
+               void help() { m->mothurOut(getHelpString()); }  
+       
+       
        private:
                set<string> names;
                vector<string> outputNames;
-               string accnosfile, fastafile, namefile, groupfile, alignfile, listfile, taxfile, outputDir;
+               string accnosfile, accnosfile2, fastafile, namefile, groupfile, alignfile, listfile, taxfile, qualfile, outputDir;
                bool abort, dups;
-               map<string, vector<string> > outputTypes;
+    
+        //for debug
+        map<string, set<string> > sanity; //maps file type to names chosen for file. something like "fasta" -> vector<string>. If running in debug mode this is filled and we check to make sure all the files have the same names. If they don't we output the differences for the user.
                
                int readFasta();
                int readName();
@@ -40,6 +47,11 @@ class GetSeqsCommand : public Command {
                int readAccnos();
                int readList();
                int readTax();
+               int readQual();
+               int compareAccnos();
+        int runSanityCheck();
+        int createMisMatchFile(ofstream&, string, string, set<string>, set<string>);
+
                
 };