added primer.design command. fixed bug with linux unifrac subsampling, metastats...

[mothur.git] / chimerauchimecommand.h

diff --git a/chimerauchimecommand.h b/chimerauchimecommand.h
index 67c77f24f4597838f959224ceaf6bab4467ce5df..8861e19ffc4f2cca99fd50f38efd3d1f9798e2af 100644 (file)
--- 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(); 
@@ -47,8 +48,8 @@ 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;
-       string fastafile, groupfile, templatefile, outputDir, namefile, countfile, abskew, minh, mindiv, xn, dn, xa, chunks, minchunk, idsmoothwindow, minsmoothid, maxp, minlen, maxlen, queryfract, uchimeLocation;
+       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, strand;
        int processors;
        
        SequenceParser* sparser;
@@ -86,7 +87,7 @@ struct uchimeData {
        int threadID, count, numChimeras;
        vector<string> groups;
        bool useAbskew, chimealns, useMinH, useMindiv, useXn, useDn, useXa, useChunks, useMinchunk, useIdsmoothwindow, useMinsmoothid, useMaxp, skipgaps, skipgaps2, useMinlen, useMaxlen, ucl, useQueryfract, hasCount;
-       string abskew, minh, mindiv, xn, dn, xa, chunks, minchunk, idsmoothwindow, minsmoothid, maxp, minlen, maxlen, queryfract;
+       string abskew, minh, mindiv, xn, dn, xa, chunks, minchunk, idsmoothwindow, minsmoothid, maxp, minlen, maxlen, queryfract, strand;
        
        uchimeData(){}
        uchimeData(string o, string uloc, string t, string file, string f, string n, string g, string ac,  string al, vector<string> gr, MothurOut* mout, int st, int en, int tid) {
@@ -129,10 +130,11 @@ struct uchimeData {
         hasCount = hc;
        }
        
-       void setVariables(string abske, string min, string mindi, string x, string d, string xa2, string chunk, string minchun, string idsmoothwindo, string minsmoothi, string max, string minle, string maxle, string queryfrac) {
+       void setVariables(string abske, string min, string mindi, string x, string d, string xa2, string chunk, string minchun, string idsmoothwindo, string minsmoothi, string max, string minle, string maxle, string queryfrac, string stra) {
                abskew = abske;
                minh = min;
                mindiv = mindi;
+        strand = stra;
                xn = x;
                dn = d;
                xa = xa2;
@@ -190,7 +192,7 @@ static DWORD WINAPI MyUchimeThreadFunction(LPVOID lpParam){
             if (pDataArray->hasCount) { 
                 error = cparser->getSeqs(pDataArray->groups[i], pDataArray->filename, true); if ((error == 1) || pDataArray->m->control_pressed) {  delete cparser; return 0; }
             }else {
-               error = cparser->getSeqs(pDataArray->groups[i], pDataArray->filename, true); if ((error == 1) || pDataArray->m->control_pressed) {  delete parser; return 0; } 
+               error = parser->getSeqs(pDataArray->groups[i], pDataArray->filename, true); if ((error == 1) || pDataArray->m->control_pressed) {  delete parser; return 0; } 
             }
                        
                        //int numSeqs = driver((outputFName + groups[i]), filename, (accnos+ groups[i]), (alns+ groups[i]), numChimeras);
@@ -242,6 +244,15 @@ static DWORD WINAPI MyUchimeThreadFunction(LPVOID lpParam){
                                cPara.push_back(tempa);
                        }
                        
+            if (pDataArray->strand != "") {
+                char* tempA = new char[9]; 
+                *tempA = '\0'; strncat(tempA, "--strand", 8);
+                cPara.push_back(tempA);
+                char* tempa = new char[pDataArray->strand.length()+1];
+                *tempa = '\0'; strncat(tempa, pDataArray->strand.c_str(), pDataArray->strand.length());
+                cPara.push_back(tempa);
+            }
+            
                        if (pDataArray->useAbskew) {
                                char* tempskew = new char[9];
                                *tempskew = '\0'; strncat(tempskew, "--abskew", 8);
@@ -530,15 +541,15 @@ static DWORD WINAPI MyUchimeSeqsThreadFunction(LPVOID lpParam){
         //prepFile(filename, outputFileName);
         /******************************************/
         ifstream in23;
-        m->openInputFile((filename.substr(1, filename.length()-2)), in23);
+        pDataArray->m->openInputFile((filename.substr(1, filename.length()-2)), in23);
         
         ofstream out23;
-        m->openOutputFile(outputFileName, out23);
+        pDataArray->m->openOutputFile(outputFileName, out23);
         
         while (!in23.eof()) {
-            if (m->control_pressed) { break;  }
+            if (pDataArray->m->control_pressed) { break;  }
             
-            Sequence seq(in23); m->gobble(in23);
+            Sequence seq(in23); pDataArray->m->gobble(in23);
             
             if (seq.getName() != "") { seq.printSequence(out23); }
         }
@@ -588,6 +599,15 @@ static DWORD WINAPI MyUchimeSeqsThreadFunction(LPVOID lpParam){
                        cPara.push_back(tempa);
                }
                
+        if (pDataArray->strand != "") {
+            char* tempA = new char[9]; 
+            *tempA = '\0'; strncat(tempA, "--strand", 8);
+            cPara.push_back(tempA);
+            char* tempa = new char[pDataArray->strand.length()+1];
+            *tempa = '\0'; strncat(tempa, pDataArray->strand.c_str(), pDataArray->strand.length());
+            cPara.push_back(tempa);
+        }
+        
                if (pDataArray->useAbskew) {
                        char* tempskew = new char[9];
                        *tempskew = '\0'; strncat(tempskew, "--abskew", 8);
@@ -758,6 +778,8 @@ 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"); }