added checks to make sure windows processes completed their tasks.

[mothur.git] / chimerauchimecommand.h

diff --git a/chimerauchimecommand.h b/chimerauchimecommand.h
index 39c3141a1bf95e6b4506887771c2bfaa85834327..6d9d001a142aaa6357cc81614c5f50af23f2bf76 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;
@@ -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);
@@ -535,12 +546,13 @@ static DWORD WINAPI MyUchimeSeqsThreadFunction(LPVOID lpParam){
         ofstream out23;
         pDataArray->m->openOutputFile(outputFileName, out23);
         
+        int fcount = 0;
         while (!in23.eof()) {
             if (pDataArray->m->control_pressed) { break;  }
             
             Sequence seq(in23); pDataArray->m->gobble(in23);
             
-            if (seq.getName() != "") { seq.printSequence(out23); }
+            if (seq.getName() != "") { seq.printSequence(out23); fcount++; }
         }
         in23.close();
         out23.close();
@@ -588,6 +600,15 @@ 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 +779,8 @@ 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"); }
@@ -799,12 +822,15 @@ static DWORD WINAPI MyUchimeSeqsThreadFunction(LPVOID lpParam){
                in.close();
                out.close();
                
+        if (fcount != totalSeqs) { pDataArray->m->mothurOut("[ERROR]: process " + toString(pDataArray->threadID) + " only processed " + toString(pDataArray->count) + " of " + toString(pDataArray->end) + " sequences assigned to it, quitting. \n"); pDataArray->m->control_pressed = true; }
+        
                if (pDataArray->m->control_pressed) { return 0; }
                
                pDataArray->m->mothurOutEndLine(); pDataArray->m->mothurOut("It took " + toString(time(NULL) - start) + " secs to check " + toString(totalSeqs) + " sequences.");       pDataArray->m->mothurOutEndLine();                                      
        
                pDataArray->count = totalSeqs;
                pDataArray->numChimeras = numChimeras;
+        
                return totalSeqs;
                
        }