chimeras, fix to sabundvector and sharedsabundvector that caused getRabundVector...

[mothur.git] / chimeraseqscommand.cpp

diff --git a/chimeraseqscommand.cpp b/chimeraseqscommand.cpp
index 13adb52bbbbb2e18477964f7fda344fd1dc1bcf2..2ec6ea9c85e2d8034aafa6527fd53b6bf28a052d 100644 (file)
--- a/chimeraseqscommand.cpp
+++ b/chimeraseqscommand.cpp
@@ -180,7 +180,7 @@ ChimeraSeqsCommand::ChimeraSeqsCommand(string option){
                        temp = validParameter.validFile(parameters, "realign", false);                  if (temp == "not found") { temp = "f"; }
                        realign = isTrue(temp); 
                        
-                       search = validParameter.validFile(parameters, "search", false);                 if (search == "not found") { temp = "distance"; }
+                       search = validParameter.validFile(parameters, "search", false);                 if (search == "not found") { search = "distance"; }
                        
                        temp = validParameter.validFile(parameters, "iters", false);    
                        if ((temp == "not found") && (method == "chimeraslayer")) { temp = "100"; }             
@@ -198,7 +198,7 @@ ChimeraSeqsCommand::ChimeraSeqsCommand(string option){
                        else if (temp == "not found") { temp = "20"; }
                        convert(temp, numwanted);
 
-                       
+                       if ((search != "distance") && (search != "blast") && (search != "kmer")) { mothurOut(search + " is not a valid search."); mothurOutEndLine(); abort = true;  }
                        
                        if (((method != "bellerophon")) && (templatefile == "")) { mothurOut("You must provide a template file with the pintail, ccode, chimeraslayer or chimeracheck methods."); mothurOutEndLine(); abort = true;  }
                        
@@ -239,7 +239,7 @@ void ChimeraSeqsCommand::help(){
                mothurOut("The mincov parameter allows you to specify minimum coverage by closest matches found in template. Default is 70, meaning 70%. \n");
                mothurOut("The minbs parameter allows you to specify minimum bootstrap support for calling a sequence chimeric. Default is 90, meaning 90%. \n");
                mothurOut("The minsnp parameter allows you to specify percent of SNPs to sample on each side of breakpoint for computing bootstrap support (default: 10) \n");
-               mothurOut("The search parameter allows you to specify search method for finding the closest parent. Choices are distance and blast, default distance.  -used only by chimeraslayer. \n");
+               mothurOut("The search parameter allows you to specify search method for finding the closest parent. Choices are distance, blast, and kmer, default distance.  -used only by chimeraslayer. \n");
                mothurOut("The realign parameter allows you to realign the query to the potential paretns. Choices are true or false, default false.  -used only by chimeraslayer. \n");
                mothurOut("NOT ALL PARAMETERS ARE USED BY ALL METHODS. Please look below for method specifics.\n\n");
                mothurOut("Details for each method: \n"); 
@@ -282,7 +282,7 @@ int ChimeraSeqsCommand::execute(){
                else if (method == "pintail")                   {               chimera = new Pintail(fastafile, outputDir);                            }
                else if (method == "ccode")                             {               chimera = new Ccode(fastafile, outputDir);                                      }
                else if (method == "chimeracheck")              {               chimera = new ChimeraCheckRDP(fastafile, outputDir);            }
-               else if (method == "chimeraslayer")             {               chimera = new ChimeraSlayer(search, realign);                           }
+               else if (method == "chimeraslayer")             {               chimera = new ChimeraSlayer(search, realign, fastafile);        }
                else { mothurOut("Not a valid method."); mothurOutEndLine(); return 0;          }
                
                //set user options
@@ -418,7 +418,8 @@ int ChimeraSeqsCommand::execute(){
                //      else                             { fastafile = outputDir + getRootName(getSimpleName(fastafile)) + "filter.fasta"; }
                
                appendOutputFiles(tempHeader, outputFileName);
-               remove(tempHeader.c_str());
+               remove(outputFileName.c_str());
+               rename(tempHeader.c_str(), outputFileName.c_str());
 
                for (int i = 0; i < templateSeqs.size(); i++)           {   delete templateSeqs[i];     }