fixed bug in chimera.uchime

[mothur.git] / chimeraslayercommand.cpp

diff --git a/chimeraslayercommand.cpp b/chimeraslayercommand.cpp
index cf219951f08e314f57ebb2e6c27985d3f5409167..a422c8883ea9f172fe076961fa7705cb548e767e 100644 (file)
--- a/chimeraslayercommand.cpp
+++ b/chimeraslayercommand.cpp
@@ -23,15 +23,15 @@ vector<string> ChimeraSlayerCommand::setParameters(){
                CommandParameter pmismatch("mismatch", "Number", "", "-4.0", "", "", "",false,false); parameters.push_back(pmismatch);
                CommandParameter pminsim("minsim", "Number", "", "90", "", "", "",false,false); parameters.push_back(pminsim);
                CommandParameter pmincov("mincov", "Number", "", "70", "", "", "",false,false); parameters.push_back(pmincov);
-               CommandParameter pminsnp("minsnp", "Number", "", "100", "", "", "",false,false); parameters.push_back(pminsnp);
+               CommandParameter pminsnp("minsnp", "Number", "", "10", "", "", "",false,false); parameters.push_back(pminsnp);
                CommandParameter pminbs("minbs", "Number", "", "90", "", "", "",false,false); parameters.push_back(pminbs);
-               CommandParameter psearch("search", "Multiple", "kmer-blast-distance", "distance", "", "", "",false,false); parameters.push_back(psearch);
+               CommandParameter psearch("search", "Multiple", "kmer-blast", "blast", "", "", "",false,false); parameters.push_back(psearch);
                CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
                CommandParameter prealign("realign", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(prealign);
                CommandParameter ptrim("trim", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(ptrim);
                CommandParameter psplit("split", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(psplit);
                CommandParameter pnumwanted("numwanted", "Number", "", "15", "", "", "",false,false); parameters.push_back(pnumwanted);
-               CommandParameter piters("iters", "Number", "", "100", "", "", "",false,false); parameters.push_back(piters);
+               CommandParameter piters("iters", "Number", "", "1000", "", "", "",false,false); parameters.push_back(piters);
                CommandParameter pdivergence("divergence", "Number", "", "1.007", "", "", "",false,false); parameters.push_back(pdivergence);
                CommandParameter pparents("parents", "Number", "", "3", "", "", "",false,false); parameters.push_back(pparents);
                CommandParameter pincrement("increment", "Number", "", "5", "", "", "",false,false); parameters.push_back(pincrement);
@@ -72,12 +72,12 @@ string ChimeraSlayerCommand::getHelpString(){
                helpString += "The parents parameter allows you to select the number of potential parents to investigate from the numwanted best matches after rating them, default is 3. \n";
                helpString += "The mismatch parameter allows you to penalize mismatched bases in blast search, default is -4. \n";
                helpString += "The divergence parameter allows you to set a cutoff for chimera determination, default is 1.007. \n";
-               helpString += "The iters parameter allows you to specify the number of bootstrap iters to do with the chimeraslayer method, default=100.\n";
+               helpString += "The iters parameter allows you to specify the number of bootstrap iters to do with the chimeraslayer method, default=1000.\n";
                helpString += "The minsim parameter allows you to specify a minimum similarity with the parent fragments, default=90. \n";
                helpString += "The mincov parameter allows you to specify minimum coverage by closest matches found in template. Default is 70, meaning 70%. \n";
                helpString += "The minbs parameter allows you to specify minimum bootstrap support for calling a sequence chimeric. Default is 90, meaning 90%. \n";
-               helpString += "The minsnp parameter allows you to specify percent of SNPs to sample on each side of breakpoint for computing bootstrap support (default: 100) \n";
-               helpString += "The search parameter allows you to specify search method for finding the closest parent. Choices are distance, blast, and kmer, default distance. \n";
+               helpString += "The minsnp parameter allows you to specify percent of SNPs to sample on each side of breakpoint for computing bootstrap support (default: 10) \n";
+               helpString += "The search parameter allows you to specify search method for finding the closest parent. Choices are blast, and kmer, default blast. \n";
                helpString += "The realign parameter allows you to realign the query to the potential parents. Choices are true or false, default true.  \n";
                helpString += "The chimera.slayer command should be in the following format: \n";
                helpString += "chimera.slayer(fasta=yourFastaFile, reference=yourTemplate, search=yourSearch) \n";
@@ -112,6 +112,7 @@ ChimeraSlayerCommand::ChimeraSlayerCommand(string option)  {
                
                //allow user to run help
                if(option == "help") { help(); abort = true; calledHelp = true; }
+               else if(option == "citation") { citation(); abort = true; calledHelp = true;}
                
                else {
                        vector<string> myArray = setParameters();
@@ -304,9 +305,10 @@ ChimeraSlayerCommand::ChimeraSlayerCommand(string option)  {
                                        
                                        templatefile = validParameter.validFile(parameters, "reference", true);
                                        if (templatefile == "not open") { abort = true; }
-                                       else if (templatefile == "not found") { templatefile = "";  m->mothurOut("reference is a required parameter for the chimera.slayer command."); m->mothurOutEndLine(); abort = true;  }  
+                                       else if (templatefile == "not found") { templatefile = "";  m->mothurOut("reference is a required parameter for the chimera.slayer command, unless and namefile is given."); m->mothurOutEndLine(); abort = true;  }    
                                }
-                       }
+                       }else if (hasName) {  templatefile = "self"; }
+                       else { templatefile = "";  m->mothurOut("reference is a required parameter for the chimera.slayer command."); m->mothurOutEndLine(); abort = true;  }   
                        
                        string temp = validParameter.validFile(parameters, "processors", false);        if (temp == "not found"){       temp = m->getProcessors();      }
                        m->setProcessors(temp);
@@ -336,13 +338,13 @@ ChimeraSlayerCommand::ChimeraSlayerCommand(string option)  {
                        temp = validParameter.validFile(parameters, "minbs", false);                    if (temp == "not found") { temp = "90"; }
                        convert(temp, minBS);
                        
-                       temp = validParameter.validFile(parameters, "minsnp", false);                   if (temp == "not found") { temp = "100"; }
+                       temp = validParameter.validFile(parameters, "minsnp", false);                   if (temp == "not found") { temp = "10"; }
                        convert(temp, minSNP);
 
                        temp = validParameter.validFile(parameters, "parents", false);                  if (temp == "not found") { temp = "3"; }
                        convert(temp, parents); 
                        
-                       temp = validParameter.validFile(parameters, "realign", true);                   if (temp == "not found") { temp = "t"; }
+                       temp = validParameter.validFile(parameters, "realign", false);                  if (temp == "not found") { temp = "t"; }
                        realign = m->isTrue(temp); 
                        
                        temp = validParameter.validFile(parameters, "trim", false);                             if (temp == "not found") { temp = "f"; }
@@ -351,9 +353,9 @@ ChimeraSlayerCommand::ChimeraSlayerCommand(string option)  {
                        temp = validParameter.validFile(parameters, "split", false);                    if (temp == "not found") { temp = "f"; }
                        trimera = m->isTrue(temp); 
                        
-                       search = validParameter.validFile(parameters, "search", false);                 if (search == "not found") { search = "distance"; }
+                       search = validParameter.validFile(parameters, "search", false);                 if (search == "not found") { search = "blast"; }
                        
-                       temp = validParameter.validFile(parameters, "iters", false);                    if (temp == "not found") { temp = "100"; }              
+                       temp = validParameter.validFile(parameters, "iters", false);                    if (temp == "not found") { temp = "1000"; }             
                        convert(temp, iters); 
                         
                        temp = validParameter.validFile(parameters, "increment", false);                if (temp == "not found") { temp = "5"; }
@@ -362,7 +364,7 @@ ChimeraSlayerCommand::ChimeraSlayerCommand(string option)  {
                        temp = validParameter.validFile(parameters, "numwanted", false);                if (temp == "not found") { temp = "15"; }               
                        convert(temp, numwanted);
 
-                       if ((search != "distance") && (search != "blast") && (search != "kmer")) { m->mothurOut(search + " is not a valid search."); m->mothurOutEndLine(); abort = true;  }
+                       if ((search != "blast") && (search != "kmer")) { m->mothurOut(search + " is not a valid search."); m->mothurOutEndLine(); abort = true;  }
                }
        }
        catch(exception& e) {
@@ -374,7 +376,6 @@ ChimeraSlayerCommand::ChimeraSlayerCommand(string option)  {
 
 int ChimeraSlayerCommand::execute(){
        try{
-               
                if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
                
                for (int s = 0; s < fastaFileNames.size(); s++) {
@@ -733,7 +734,6 @@ int ChimeraSlayerCommand::driver(linePair* filePos, string outputFName, string f
                        
                        #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
                                unsigned long int pos = inFASTA.tellg();
-                       //cout << candidateSeq->getName() << '\t' << pos << endl;
                                if ((pos == -1) || (pos >= filePos->end)) { break; }
                        #else
                                if (inFASTA.eof()) { break; }