added check to make sure shhh.flows child processes finish properly. added subsamplin...

[mothur.git] / chimeraperseuscommand.cpp

diff --git a/chimeraperseuscommand.cpp b/chimeraperseuscommand.cpp
index 61970d53ac38a3f9877e5a010e48bc0b336dc669..e7294a854ec4134ccad5e17aa0ed8abb51876d09 100644 (file)
--- a/chimeraperseuscommand.cpp
+++ b/chimeraperseuscommand.cpp
@@ -345,16 +345,16 @@ ChimeraPerseusCommand::ChimeraPerseusCommand(string option)  {
                        
                        string temp = validParameter.validFile(parameters, "processors", false);        if (temp == "not found"){       temp = m->getProcessors();      }
                        m->setProcessors(temp);
-                       convert(temp, processors);
+                       m->mothurConvert(temp, processors);
                        
                        temp = validParameter.validFile(parameters, "cutoff", false);   if (temp == "not found"){       temp = "0.50";  }
-                       convert(temp, cutoff);
+                       m->mothurConvert(temp, cutoff);
                        
                        temp = validParameter.validFile(parameters, "alpha", false);    if (temp == "not found"){       temp = "-5.54"; }
-                       convert(temp, alpha);
+                       m->mothurConvert(temp, alpha);
                        
                        temp = validParameter.validFile(parameters, "cutoff", false);   if (temp == "not found"){       temp = "0.33";  }
-                       convert(temp, beta);
+                       m->mothurConvert(temp, beta);
                }
        }
        catch(exception& e) {
@@ -466,14 +466,15 @@ string ChimeraPerseusCommand::getNamesFile(string& inputFile){
                string inputString = "fasta=" + inputFile;
                m->mothurOut("/******************************************/"); m->mothurOutEndLine(); 
                m->mothurOut("Running command: unique.seqs(" + inputString + ")"); m->mothurOutEndLine(); 
-               
+               m->mothurCalling = true;
+        
                Command* uniqueCommand = new DeconvoluteCommand(inputString);
                uniqueCommand->execute();
                
                map<string, vector<string> > filenames = uniqueCommand->getOutputFiles();
                
                delete uniqueCommand;
-               
+               m->mothurCalling = false;
                m->mothurOut("/******************************************/"); m->mothurOutEndLine(); 
                
                nameFile = filenames["name"][0];
@@ -533,6 +534,7 @@ vector<seqData> ChimeraPerseusCommand::loadSequences(SequenceParser& parser, str
                
                vector<seqData> sequences;
                bool error = false;
+        alignLength = 0;
                
                for (int i = 0; i < thisGroupsSeqs.size(); i++) {
                
@@ -543,6 +545,7 @@ vector<seqData> ChimeraPerseusCommand::loadSequences(SequenceParser& parser, str
                        else {
                                int num = m->getNumNames(it->second);
                                sequences.push_back(seqData(thisGroupsSeqs[i].getName(), thisGroupsSeqs[i].getUnaligned(), num));
+                if (thisGroupsSeqs[i].getUnaligned().length() > alignLength) { alignLength = thisGroupsSeqs[i].getUnaligned().length(); }
                        }
                }
                
@@ -570,7 +573,8 @@ vector<seqData> ChimeraPerseusCommand::readFiles(string inputFile, string name){
                bool error = false;
                ifstream in;
                m->openInputFile(inputFile, in);
-               
+               alignLength = 0;
+        
                while (!in.eof()) {
                        
                        if (m->control_pressed) { in.close(); return sequences; }
@@ -581,6 +585,7 @@ vector<seqData> ChimeraPerseusCommand::readFiles(string inputFile, string name){
                        if (it == nameMap.end()) { error = true; m->mothurOut("[ERROR]: " + temp.getName() + " is in your fasta file and not in your namefile, please correct."); m->mothurOutEndLine(); }
                        else {
                                sequences.push_back(seqData(temp.getName(), temp.getUnaligned(), it->second));
+                if (temp.getUnaligned().length() > alignLength) { alignLength = temp.getUnaligned().length(); }
                        }
                }
                in.close();
@@ -625,7 +630,7 @@ int ChimeraPerseusCommand::driver(string chimeraFileName, vector<seqData>& seque
                }
                
                int numSeqs = sequences.size();
-               int alignLength = sequences[0].sequence.size();
+               //int alignLength = sequences[0].sequence.size();
                
                ofstream chimeraFile;
                ofstream accnosFile;
@@ -641,7 +646,7 @@ int ChimeraPerseusCommand::driver(string chimeraFileName, vector<seqData>& seque
                
                for(int i=0;i<numSeqs;i++){     
                        if (m->control_pressed) { chimeraFile.close(); m->mothurRemove(chimeraFileName); accnosFile.close(); m->mothurRemove(accnosFileName); return 0; }
-                       
+    
                        vector<bool> restricted = chimeras;
                        
                        vector<vector<int> > leftDiffs(numSeqs);
@@ -662,7 +667,9 @@ int ChimeraPerseusCommand::driver(string chimeraFileName, vector<seqData>& seque
                        
                        string dummyA, dummyB;
                        
-                       if(comparisons >= 2){   
+            if (sequences[i].sequence.size() < 3) { 
+                chimeraFile << i << '\t' << sequences[i].seqName << "\t0\t0\tNull\t0\t0\t0\tNull\tNull\t0.0\t0.0\t0.0\t0\t0\t0\t0.0\t0.0\tgood" << endl;
+            }else if(comparisons >= 2){        
                                minMismatchToChimera = myPerseus.getChimera(sequences, leftDiffs, rightDiffs, leftParentBi, rightParentBi, breakPointBi, singleLeft, bestLeft, singleRight, bestRight, restricted);
                                if (m->control_pressed) { chimeraFile.close(); m->mothurRemove(chimeraFileName); accnosFile.close(); m->mothurRemove(accnosFileName); return 0; }
 
@@ -762,7 +769,7 @@ int ChimeraPerseusCommand::createProcessesGroups(SequenceParser& parser, string
                        lines.push_back(linePair(startIndex, endIndex));
                }
                
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)          
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)         
                
                //loop through and create all the processes you want
                while (process != processors) {