added dups parameter to chimera.uchime. working on make.contigs command.

[mothur.git] / chimerauchimecommand.h

diff --git a/chimerauchimecommand.h b/chimerauchimecommand.h
index 39c3141a1bf95e6b4506887771c2bfaa85834327..a5b42751dfd74ea3eb1fc3dc4ccf9bfa5bb9822b 100644 (file)
--- a/chimerauchimecommand.h
+++ b/chimerauchimecommand.h
@@ -47,7 +47,7 @@ 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 +758,8 @@ 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"); }