X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=chimerauchimecommand.h;h=735c97d1269848b94ac5a01926f93e08d1ccd5ef;hb=367747fb506bf228d3b2d645868d275ba0714e90;hp=39c3141a1bf95e6b4506887771c2bfaa85834327;hpb=f509429e06e545bde69c97cacc0eb436775bd329;p=mothur.git

diff --git a/chimerauchimecommand.h b/chimerauchimecommand.h
index 39c3141..735c97d 100644
--- a/chimerauchimecommand.h
+++ b/chimerauchimecommand.h
@@ -28,9 +28,10 @@ public:
 	vector<string> setParameters();
 	string getCommandName()			{ return "chimera.uchime";		}
 	string getCommandCategory()		{ return "Sequence Processing"; }
-	string getOutputFileNameTag(string, string);
+	
 	string getHelpString();	
-	string getCitation() { return "uchime by Robert C. Edgar\nhttp://drive5.com/uchime\nThis code is donated to the public domain.\nhttp://www.mothur.org/wiki/Chimera.uchime\nEdgar,R.C., Haas,B.J., Clemente,J.C., Quince,C. and Knight,R. (2011), UCHIME improves sensitivity and speed of chimera detection, Bioinformatics, in press.\n"; }
+    string getOutputPattern(string);	
+	string getCitation() { return "uchime by Robert C. Edgar\nhttp://drive5.com/uchime\nThis code was donated to the public domain.\nEdgar,R.C., Haas,B.J., Clemente,J.C., Quince,C. and Knight,R. (2011), UCHIME improves sensitivity and speed of chimera detection.  Bioinformatics 27:2194.\nhttp://www.mothur.org/wiki/Chimera.uchime\n"; }
 	string getDescription()		{ return "detect chimeric sequences"; }
 	
 	int execute(); 
@@ -47,7 +48,7 @@ private:
 	int driver(string, string, string, string, int&);
 	int createProcesses(string, string, string, string, int&);
 		
-	bool abort, useAbskew, chimealns, useMinH, useMindiv, useXn, useDn, useXa, useChunks, useMinchunk, useIdsmoothwindow, useMinsmoothid, useMaxp, skipgaps, skipgaps2, useMinlen, useMaxlen, ucl, useQueryfract, hasCount, hasName;
+	bool abort, useAbskew, chimealns, useMinH, useMindiv, useXn, useDn, useXa, useChunks, useMinchunk, useIdsmoothwindow, useMinsmoothid, useMaxp, skipgaps, skipgaps2, useMinlen, useMaxlen, ucl, useQueryfract, hasCount, hasName, dups;
 	string fastafile, groupfile, templatefile, outputDir, namefile, countfile, abskew, minh, mindiv, xn, dn, xa, chunks, minchunk, idsmoothwindow, minsmoothid, maxp, minlen, maxlen, queryfract, uchimeLocation;
 	int processors;
 	
@@ -758,6 +759,8 @@ static DWORD WINAPI MyUchimeSeqsThreadFunction(LPVOID lpParam){
 		for (int j = 0; j < cPara.size(); j++) {  uchimeParameters[j] = cPara[j];  commandString += toString(cPara[j]) + " "; } 
 		//int numArgs = cPara.size();
 		
+        commandString = "\"" + commandString + "\"";
+        
 		//uchime_main(numArgs, uchimeParameters); 
 		//cout << "commandString = " << commandString << endl;
         if (pDataArray->m->debug) { pDataArray->m->mothurOut("[DEBUG]: uchime command = " + commandString + ".\n"); }