sffinfo bug with flow grams right index when clipQualRight=0

[mothur.git] / getseqscommand.h

diff --git a/getseqscommand.h b/getseqscommand.h
index 60e471eebf7865d5924406ef7c720c3bdcdf4648..c5b6ca4141afc00c12b646ea34604b898b1c4131 100644 (file)
--- a/getseqscommand.h
+++ b/getseqscommand.h
@@ -23,8 +23,9 @@ class GetSeqsCommand : public Command {
                vector<string> setParameters();
                string getCommandName()                 { return "get.seqs";                            }
                string getCommandCategory()             { return "Sequence Processing";         }
-               string getOutputFileNameTag(string, string);
+               
        string getHelpString(); 
+    string getOutputPattern(string);   
                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"; }
 
@@ -37,7 +38,7 @@ class GetSeqsCommand : public Command {
                vector<string> outputNames;
                string accnosfile, accnosfile2, fastafile, namefile, countfile, groupfile, alignfile, listfile, taxfile, qualfile, outputDir;
                bool abort, dups;
-    
+        map<string, string> uniqueMap;
         //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.