added cutoff change to mgcluster

[mothur.git] / seqerrorcommand.cpp

diff --git a/seqerrorcommand.cpp b/seqerrorcommand.cpp
index 5efb1ce78c659577c520defc124c48e60b848dc8..564e412ea95f1421b1d3cc72761c2ac98fe61c44 100644 (file)
--- a/seqerrorcommand.cpp
+++ b/seqerrorcommand.cpp
@@ -24,7 +24,6 @@ vector<string> SeqErrorCommand::setParameters(){
                CommandParameter pignorechimeras("ignorechimeras", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pignorechimeras);
                CommandParameter pthreshold("threshold", "Number", "", "1.0", "", "", "",false,false); parameters.push_back(pthreshold);
                CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
-               CommandParameter pfilter("filter", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pfilter);
                CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
                CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
                
@@ -165,6 +164,7 @@ SeqErrorCommand::SeqErrorCommand(string option)  {
                                else {  m->mothurOut("You have no current fasta file and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
                        }
                        else if (queryFileName == "not open") { abort = true; } 
+                       else { m->setFastaFile(queryFileName); }
                        
                        referenceFileName = validParameter.validFile(parameters, "reference", true);
                        if (referenceFileName == "not found") { m->mothurOut("reference is a required parameter for the seq.error command."); m->mothurOutEndLine(); abort = true; }
@@ -175,11 +175,13 @@ SeqErrorCommand::SeqErrorCommand(string option)  {
                        namesFileName = validParameter.validFile(parameters, "name", true);
                        if(namesFileName == "not found"){       namesFileName = "";     }
                        else if (namesFileName == "not open") { namesFileName = ""; abort = true; }     
+                       else { m->setNameFile(namesFileName); }
                        
                        qualFileName = validParameter.validFile(parameters, "qfile", true);
                        if(qualFileName == "not found"){        qualFileName = "";      }
                        else if (qualFileName == "not open") { qualFileName = ""; abort = true; }       
-
+                       else { m->setQualFile(qualFileName); }
+                       
                        reportFileName = validParameter.validFile(parameters, "report", true);
                        if(reportFileName == "not found"){      reportFileName = "";    }
                        else if (reportFileName == "not open") { reportFileName = ""; abort = true; }   
@@ -204,9 +206,6 @@ SeqErrorCommand::SeqErrorCommand(string option)  {
                        temp = validParameter.validFile(parameters, "ignorechimeras", false);   if (temp == "not found") { temp = "T"; }
                        ignoreChimeras = m->isTrue(temp);
                        
-                       temp = validParameter.validFile(parameters, "filter", false);   if (temp == "not found") { temp = "T"; }
-                       filter = m->isTrue(temp);  
-                       
                        temp = validParameter.validFile(parameters, "processors", false);       if (temp == "not found"){       temp = m->getProcessors();      }
                        m->setProcessors(temp);
                        convert(temp, processors); 
@@ -230,25 +229,6 @@ int SeqErrorCommand::execute(){
                maxLength = 2000;
                totalBases = 0;
                totalMatches = 0;
-
-               //run vertical filter on query and reference files.
-               if (filter) {
-                       string inputString = "fasta=" + queryFileName + "-" + referenceFileName;
-                       m->mothurOut("/******************************************/"); m->mothurOutEndLine(); 
-                       m->mothurOut("Running command: filter.seqs(" + inputString + ") to improve processing time."); m->mothurOutEndLine(); 
-                       
-                       Command* filterCommand = new FilterSeqsCommand(inputString);
-                       filterCommand->execute();
-                       
-                       map<string, vector<string> > filenames = filterCommand->getOutputFiles();
-                       
-                       delete filterCommand;
-                       
-                       m->mothurOut("/******************************************/"); m->mothurOutEndLine(); 
-                       
-                       queryFileName = filenames["fasta"][0];
-                       referenceFileName = filenames["fasta"][1];
-               }
                
                string errorSummaryFileName = queryFileName.substr(0,queryFileName.find_last_of('.')) + ".error.summary";
                outputNames.push_back(errorSummaryFileName); outputTypes["error.summary"].push_back(errorSummaryFileName);