X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=getseqscommand.h;h=9895432b7c25d6016bbf6b38ced773487aeb0201;hp=60e471eebf7865d5924406ef7c720c3bdcdf4648;hb=b206f634aae1b4ce13978d203247fb64757d5482;hpb=ea4f373c28543cd1002b0dd7dc6e55c526647d59

diff --git a/getseqscommand.h b/getseqscommand.h
index 60e471e..9895432 100644
--- 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"; }
 
@@ -35,13 +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();