fixed bug with aligner in database class, worked on chimeras

[mothur.git] / chimeraseqscommand.cpp

diff --git a/chimeraseqscommand.cpp b/chimeraseqscommand.cpp
index aaed3bab7b56b14460d06de90c9551df70c4351d..ba980a50e46405dfc3087f5ba7c02d0b25cab1ff 100644 (file)
--- a/chimeraseqscommand.cpp
+++ b/chimeraseqscommand.cpp
@@ -22,7 +22,7 @@ ChimeraSeqsCommand::ChimeraSeqsCommand(string option){
                
                else {
                        //valid paramters for this command
-                       string Array[] =  {"fasta", "filter", "correction", "processors", "method", "window", "increment", "template", "conservation", "quantile" };
+                       string Array[] =  {"fasta", "filter", "correction", "processors", "method", "window", "increment", "template", "conservation", "quantile", "mask" };
                        vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
                        
                        OptionParser parser(option);
@@ -50,7 +50,12 @@ ChimeraSeqsCommand::ChimeraSeqsCommand(string option){
                        
                        quanfile = validParameter.validFile(parameters, "quantile", true);
                        if (quanfile == "not open") { abort = true; }
-                       else if (quanfile == "not found") { quanfile = "";  }   
+                       else if (quanfile == "not found") { quanfile = "";  }
+                               
+                       maskfile = validParameter.validFile(parameters, "mask", true);
+                       if (maskfile == "not open") { abort = true; }
+                       else if (maskfile == "not found") { maskfile = "";  }   
+
                        
 
                        string temp;
@@ -86,11 +91,12 @@ ChimeraSeqsCommand::ChimeraSeqsCommand(string option){
 void ChimeraSeqsCommand::help(){
        try {
                mothurOut("The chimera.seqs command reads a fastafile and creates a sorted priority score list of potentially chimeric sequences (ideally, the sequences should already be aligned).\n");
-               mothurOut("The chimera.seqs command parameters are fasta, filter, correction, processors and method.  fasta is required.\n");
+               mothurOut("The chimera.seqs command parameters are fasta, filter, correction, processors, mask and method.  fasta is required.\n");
                mothurOut("The filter parameter allows you to specify if you would like to apply a 50% soft filter.  The default is false. \n");
                mothurOut("The correction parameter allows you to put more emphasis on the distance between highly similar sequences and less emphasis on the differences between remote homologs.   The default is true. \n");
                mothurOut("The processors parameter allows you to specify how many processors you would like to use.  The default is 1. \n");
                mothurOut("The method parameter allows you to specify the method for finding chimeric sequences.  The default is pintail. \n");
+               mothurOut("The mask parameter allows you to specify a file containing one sequence you wish to use as a mask for the pintail and mallard method.  The default is 236627 EU009184.1 Shigella dysenteriae str. FBD013. \n");
                mothurOut("The chimera.seqs command should be in the following format: \n");
                mothurOut("chimera.seqs(fasta=yourFastaFile, filter=yourFilter, correction=yourCorrection, processors=yourProcessors, method=bellerophon) \n");
                mothurOut("Example: chimera.seqs(fasta=AD.align, filter=True, correction=true, processors=2, method=yourMethod) \n");
@@ -122,6 +128,10 @@ int ChimeraSeqsCommand::execute(){
                        //saves time to avoid generating it
                        if (quanfile != "")                     {               chimera->setQuantiles(quanfile);                                }
                        else                                            {               chimera->setQuantiles("");                                              }
+                       
+                       if (maskfile == "") { mothurOut("You have not provided a mask, so I am using the default 236627 EU009184.1 Shigella dysenteriae str. FBD013."); mothurOutEndLine();  }
+                       chimera->setMask(maskfile);
+                                               
                }else { mothurOut("Not a valid method."); mothurOutEndLine(); return 0;         }
                
                //set user options