added oldfasta and column parameter to dist.seqs so you can append distances to an...

[mothur.git] / splitabundcommand.cpp

diff --git a/splitabundcommand.cpp b/splitabundcommand.cpp
index 287086a28a3b0b1ecc18b3988f68ef41ec1909dc..891fb979e3aa533a53453628f2701e790161fbcc 100644 (file)
--- a/splitabundcommand.cpp
+++ b/splitabundcommand.cpp
@@ -176,6 +176,7 @@ int SplitAbundCommand::execute(){
                if (abort == true) {    return 0;       }
                
                if (listfile != "") { //you are using a listfile to determine abundance
+                       if (outputDir == "") { outputDir = hasPath(listfile); }
                
                        //remove old files so you can append later....
                        string fileroot = outputDir + getRootName(getSimpleName(listfile));
@@ -292,7 +293,8 @@ int SplitAbundCommand::execute(){
 
                                                                        
                }else { //you are using the namefile to determine abundance
-
+                       if (outputDir == "") { outputDir = hasPath(namefile); }
+                       
                        splitNames(); 
                        writeNames();
                        
@@ -802,7 +804,7 @@ int SplitAbundCommand::parseGroup(string tag) { //namefile
                                                if (rareNames.count(itName->first) != 0) { //you are a rare name
                                                        rout << names[i] << '\t' << group << endl;
                                                }else{ //you are a abund name
-                                                       rout << names[i] << '\t' << group << endl;
+                                                       aout << names[i] << '\t' << group << endl;
                                                }
                                        }
                                }