X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=getseqscommand.h;h=9895432b7c25d6016bbf6b38ced773487aeb0201;hp=c71b5f2804a71190c6919f0dc80bf80d32f15508;hb=b206f634aae1b4ce13978d203247fb64757d5482;hpb=49d2b7459c5027557564b21e9487dadafbbbdc96

diff --git a/getseqscommand.h b/getseqscommand.h
index c71b5f2..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"; }
 
@@ -35,15 +36,17 @@ class GetSeqsCommand : public Command {
 	private:
 		set<string> names;
 		vector<string> outputNames;
-		string accnosfile, accnosfile2, fastafile, namefile, 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();
 		int readAlign();
 		int readList();
 		int readTax();