Merge remote-tracking branch 'origin'

[mothur.git] / seqerrorcommand.cpp

diff --git a/seqerrorcommand.cpp b/seqerrorcommand.cpp
index 99e789399e90c2b2adc429330177e7bd579e8354..2bd7054afc33c4f0600683a1b8ebe50a2fd338c4 100644 (file)
--- a/seqerrorcommand.cpp
+++ b/seqerrorcommand.cpp
@@ -23,7 +23,8 @@ vector<string> SeqErrorCommand::setParameters(){
                CommandParameter preference("reference", "InputTypes", "", "", "none", "none", "none","",false,true,true); parameters.push_back(preference);
                CommandParameter pqfile("qfile", "InputTypes", "", "", "none", "none", "QualReport","",false,false); parameters.push_back(pqfile);
                CommandParameter preport("report", "InputTypes", "", "", "none", "none", "QualReport","",false,false); parameters.push_back(preport);
-               CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(pname);
+               CommandParameter pname("name", "InputTypes", "", "", "namecount", "none", "none","",false,false,true); parameters.push_back(pname);
+        CommandParameter pcount("count", "InputTypes", "", "", "namecount", "none", "none","",false,false,true); parameters.push_back(pcount);
                CommandParameter pignorechimeras("ignorechimeras", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(pignorechimeras);
                CommandParameter pthreshold("threshold", "Number", "", "1.0", "", "", "","",false,false); parameters.push_back(pthreshold);
                CommandParameter paligned("aligned", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(paligned);
@@ -52,7 +53,8 @@ string SeqErrorCommand::getHelpString(){
                helpString += "The reference parameter...\n";
                helpString += "The qfile parameter...\n";
                helpString += "The report parameter...\n";
-               helpString += "The name parameter...\n";
+               helpString += "The name parameter allows you to provide a name file associated with the fasta file.\n";
+        helpString += "The count parameter allows you to provide a count file associated with the fasta file.\n";
                helpString += "The ignorechimeras parameter...\n";
                helpString += "The threshold parameter...\n";
                helpString += "The processors parameter...\n";
@@ -190,6 +192,14 @@ SeqErrorCommand::SeqErrorCommand(string option)  {
                                        //if the user has not given a path then, add inputdir. else leave path alone.
                                        if (path == "") {       parameters["name"] = inputDir + it->second;             }
                                }
+                
+                it = parameters.find("count");
+                               //user has given a names file
+                               if(it != parameters.end()){
+                                       path = m->hasPath(it->second);
+                                       //if the user has not given a path then, add inputdir. else leave path alone.
+                                       if (path == "") {       parameters["count"] = inputDir + it->second;            }
+                               }
 
                                it = parameters.find("qfile");
                                //user has given a quality score file
@@ -227,6 +237,12 @@ SeqErrorCommand::SeqErrorCommand(string option)  {
                        if(namesFileName == "not found"){       namesFileName = "";     }
                        else if (namesFileName == "not open") { namesFileName = ""; abort = true; }     
                        else { m->setNameFile(namesFileName); }
+            
+            //check for optional parameters
+                       countfile = validParameter.validFile(parameters, "count", true);
+                       if(countfile == "not found"){   countfile = ""; }
+                       else if (countfile == "not open") { countfile = ""; abort = true; }
+                       else { m->setCountTableFile(countfile); }
                        
                        qualFileName = validParameter.validFile(parameters, "qfile", true);
                        if(qualFileName == "not found"){        qualFileName = "";      }
@@ -243,6 +259,8 @@ SeqErrorCommand::SeqErrorCommand(string option)  {
                                outputDir += m->hasPath(queryFileName); //if user entered a file with a path then preserve it   
                        }
                        
+            if ((countfile != "") && (namesFileName != "")) { m->mothurOut("You must enter ONLY ONE of the following: count or name."); m->mothurOutEndLine(); abort = true; }
+            
                        //check for optional parameter and set defaults
                        // ...at some point should added some additional type checking...
                        temp = validParameter.validFile(parameters, "threshold", false);        if (temp == "not found") { temp = "1.00"; }
@@ -337,7 +355,12 @@ int SeqErrorCommand::execute(){
                
                getReferences();        //read in reference sequences - make sure there's no ambiguous bases
 
-               if(namesFileName != ""){        weights = getWeights(); }
+               if(namesFileName != "")     {   weights = getWeights();         }
+        else if (countfile != "")   {
+            CountTable ct;
+            ct.readTable(countfile);
+            weights = ct.getNameMap();
+        }
                
                vector<unsigned long long> fastaFilePos;
                vector<unsigned long long> qFilePos;
@@ -785,7 +808,7 @@ int SeqErrorCommand::driver(string filename, string qFileName, string rFileName,
             
             getErrors(query, reference, minCompare);
                        
-                       if(namesFileName != ""){
+                       if((namesFileName != "") || (countfile != "")){
                                it = weights.find(query.getName());
                                minCompare.weight = it->second;
                        }