X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=getseqscommand.h;h=9895432b7c25d6016bbf6b38ced773487aeb0201;hb=6b32d112bb60e9f7eb6d4407a4eed4c49b67bced;hp=42070e53a57cf05c6d5674e022c602636fa374bf;hpb=deba0af0ccdcb6005ed5b2b82649b137c63fbdf7;p=mothur.git

diff --git a/getseqscommand.h b/getseqscommand.h
index 42070e5..9895432 100644
--- 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();