changes while testing

[mothur.git] / getoturepcommand.cpp

diff --git a/getoturepcommand.cpp b/getoturepcommand.cpp
index a041b38aadac3c3cc28bf7313eeb4e8bde6e4535..d476cc3499844c88014bcef9e1a005459fab3dda 100644 (file)
--- a/getoturepcommand.cpp
+++ b/getoturepcommand.cpp
@@ -261,11 +261,15 @@ GetOTURepCommand::GetOTURepCommand(string option)  {
                        else if (countfile == "not open") { abort = true; countfile =  ""; }    
                        else {   
                 m->setCountTableFile(countfile); 
-                ct.readTable(countfile);
+                ct.readTable(countfile, true);
                 if (ct.hasGroupInfo()) { hasGroups = true; }
             }
             
-                               
+            groupfile = validParameter.validFile(parameters, "group", true);
+                       if (groupfile == "not open") { groupfile = ""; abort = true; }
+                       else if (groupfile == "not found") { groupfile = ""; }
+                       else { m->setGroupFile(groupfile); }
+                       
             method = validParameter.validFile(parameters, "method", false);            if (method == "not found"){     method = "distance";    }
                        if ((method != "distance") && (method != "abundance")) {
                                m->mothurOut(method + " is not a valid option for the method parameter. The only options are: distance and abundance, aborting."); m->mothurOutEndLine(); abort = true;
@@ -337,11 +341,7 @@ GetOTURepCommand::GetOTURepCommand(string option)  {
                                else { allLines = 1;  }
                        }
                        
-                       groupfile = validParameter.validFile(parameters, "group", true);
-                       if (groupfile == "not open") { groupfile = ""; abort = true; }
-                       else if (groupfile == "not found") { groupfile = ""; }
-                       else { m->setGroupFile(groupfile); }
-                       
+                                               
                        sorted = validParameter.validFile(parameters, "sorted", false);         if (sorted == "not found"){     sorted = "";    }
                        if (sorted == "none") { sorted=""; }
                        if ((sorted != "") && (sorted != "name") && (sorted != "bin") && (sorted != "size") && (sorted != "group")) {
@@ -1106,7 +1106,7 @@ int GetOTURepCommand::processFastaNames(string filename, string label, FastaMap*
         
         CountTable thisCt;
         if (countfile != "") {
-            thisCt.readTable(countfile);
+            thisCt.readTable(countfile, true);
             if (tempGroup != "noGroup") { out2 << "Representative_Sequence\ttotal\t" << tempGroup << endl; }
         }
     
@@ -1253,7 +1253,7 @@ int GetOTURepCommand::processNames(string filename, string label) {
         
         CountTable thisCt;
         if (countfile != "") {
-            thisCt.readTable(countfile);
+            thisCt.readTable(countfile, true);
             if (tempGroup != "noGroup") { out2 << "Representative_Sequence\ttotal\t" << tempGroup << endl; }
         }