fixes while testing 1.33.0

[mothur.git] / getseqscommand.h

diff --git a/getseqscommand.h b/getseqscommand.h
index 42070e53a57cf05c6d5674e022c602636fa374bf..9895432b7c25d6016bbf6b38ced773487aeb0201 100644 (file)
--- a/getseqscommand.h
+++ b/getseqscommand.h
@@ -36,13 +36,14 @@ class GetSeqsCommand : public Command {
        private:
                set<string> names;
                vector<string> outputNames;
-               string accnosfile, accnosfile2, fastafile, namefile, countfile, groupfile, alignfile, listfile, taxfile, qualfile, outputDir;
+               string accnosfile, accnosfile2, fastafile, fastqfile, 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.
                
                int readFasta();
+        int readFastq();
                int readName();
                int readGroup();
         int readCount();