added adjustDots function to pcr.seqs, keeps sequences aligned in case where primers...

[mothur.git] / splitmatrix.cpp

diff --git a/splitmatrix.cpp b/splitmatrix.cpp
index 28bc5d4cec4fc4ec409bca26359ed103951c8701..a5ae3cbda79fd52a9358464eab1941c96a69bd63 100644 (file)
--- a/splitmatrix.cpp
+++ b/splitmatrix.cpp
@@ -191,8 +191,12 @@ int SplitMatrix::createDistanceFilesFromTax(map<string, int>& seqGroup, int numG
             else { options = "fasta=" + (fastafile + "." + toString(i) + ".temp") + ", processors=" + toString(processors) + ", cutoff=" + toString(distCutoff); }
                        if (outputDir != "") { options += ", outputdir=" + outputDir; }
                        
+            m->mothurOut("/******************************************/"); m->mothurOutEndLine(); 
+            
                        Command* command = new DistanceCommand(options);
                        
+            m->mothurOut("/******************************************/"); m->mothurOutEndLine(); 
+            
                        command->execute();
                        delete command;
                        
@@ -637,7 +641,7 @@ int SplitMatrix::splitNames(map<string, int>& seqGroup, int numGroups, vector<st
                     ofstream out;
                     string newtempNameFile = tempNameFile + "2";
                     m->openOutputFile(newtempNameFile, out);
-                    out << headers << endl;
+                    out << "Representative_Sequence\ttotal" << endl;
                     out.close();
                     m->appendFiles(tempNameFile, newtempNameFile);
                     m->mothurRemove(tempNameFile);
@@ -671,7 +675,7 @@ int SplitMatrix::splitNames(map<string, int>& seqGroup, int numGroups, vector<st
             ofstream out;
             string newtempNameFile = singleton + "2";
             m->openOutputFile(newtempNameFile, out);
-            out << headers << endl;
+            out << "Representative_Sequence\ttotal" << endl; 
             out.close();
             m->appendFiles(singleton, newtempNameFile);
             m->mothurRemove(singleton);