Working on seq.error changes

[mothur.git] / seqerrorcommand.cpp

diff --git a/seqerrorcommand.cpp b/seqerrorcommand.cpp
index 87d45242a08c9e7ab351dbcb029c6eae9458398f..4ff1b6f07bbd782c40cfcd69d1032d16ed420956 100644 (file)
--- a/seqerrorcommand.cpp
+++ b/seqerrorcommand.cpp
@@ -24,6 +24,7 @@ vector<string> SeqErrorCommand::setParameters(){
                CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(pname);
                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);
                CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pprocessors);
                CommandParameter psave("save", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(psave);
                CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
@@ -243,6 +244,13 @@ SeqErrorCommand::SeqErrorCommand(string option)  {
                        // ...at some point should added some additional type checking...
                        temp = validParameter.validFile(parameters, "threshold", false);        if (temp == "not found") { temp = "1.00"; }
                        m->mothurConvert(temp, threshold);  
+            
+            temp = validParameter.validFile(parameters, "aligned", true);                      if (temp == "not found"){       temp = "t";                             }
+                       aligned = m->isTrue(temp); 
+//                     rdb->aligned = aligned;                     #do we need these lines for aligned?
+//                     if (aligned) { //clear out old references
+//                             rdb->clearMemory();     
+//                     }
                        
                        temp = validParameter.validFile(parameters, "save", false);                     if (temp == "not found"){       temp = "f";                             }
                        save = m->isTrue(temp); 
@@ -686,8 +694,10 @@ int SeqErrorCommand::driver(string filename, string qFileName, string rFileName,
                
                ofstream outChimeraReport;
                m->openOutputFile(chimeraOutputFileName, outChimeraReport);
-               RefChimeraTest chimeraTest(referenceSeqs);
-               if (line.start == 0) { chimeraTest.printHeader(outChimeraReport); }
+               
+        RefChimeraTest chimeraTest(referenceSeqs, aligned);
+        
+        if (line.start == 0) { chimeraTest.printHeader(outChimeraReport); }
                
                ofstream errorSummaryFile;
                m->openOutputFile(summaryFileName, errorSummaryFile);