X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=clustersplitcommand.h;h=e1f17b1bd0b8c4088d5deb3c06691fb3ccf26999;hp=e079197c1ea60d15e2454ad7433e90d2cfbbc611;hb=1a20e24ee786195ab0e1cccd4f5aede7a88f3f4e;hpb=28bcfc4a41b8b82f66636587e0d4d355d07cbdd1

diff --git a/clustersplitcommand.h b/clustersplitcommand.h
index e079197..e1f17b1 100644
--- a/clustersplitcommand.h
+++ b/clustersplitcommand.h
@@ -35,9 +35,10 @@ public:
 	vector<string> setParameters();
 	string getCommandName()			{ return "cluster.split";		}
 	string getCommandCategory()		{ return "Clustering";			}
-	string getOutputFileNameTag(string, string);
+	
 	string getHelpString();	
-	string getCitation() { return "Schloss PD, Westcott SL (2011). Assessing and improving methods used in OTU-based approaches for 16S rRNA gene sequence analysis. Appl Environ Microbiol. \nhttp://www.mothur.org/wiki/Cluster.split"; }
+    string getOutputPattern(string);	
+	string getCitation() { return "Schloss PD, Westcott SL (2011). Assessing and improving methods used in OTU-based approaches for 16S rRNA gene sequence analysis. Appl Environ Microbiol 77:3219. \nhttp://www.mothur.org/wiki/Cluster.split"; }
 	string getDescription()		{ return "splits your sequences by distance or taxonomy then clusters into OTUs"; }
 	
 	int execute(); 
@@ -50,7 +51,7 @@ private:
 	string method, fileroot, tag, outputDir, phylipfile, columnfile, namefile, countfile, distfile, format, showabund, timing, splitmethod, taxFile, fastafile;
 	double cutoff, splitcutoff;
 	int precision, length, processors, taxLevelCutoff;
-	bool print_start, abort, hard, large, classic;
+	bool print_start, abort, hard, large, classic, runCluster;
 	time_t start;
 	ofstream outList, outRabund, outSabund;