X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=seqerrorcommand.cpp;h=41ddf35a7705264445749caf8868d80049ae61ac;hb=250e3b11b1c9c1e1ad458ab6c7e71ac2e67e11d9;hp=54d3dcc5c9b6c93f267478e6491126b3aedff772;hpb=af0a94ea8f02421b2b73e77e68753a2b4c37768e;p=mothur.git

diff --git a/seqerrorcommand.cpp b/seqerrorcommand.cpp
index 54d3dcc..41ddf35 100644
--- a/seqerrorcommand.cpp
+++ b/seqerrorcommand.cpp
@@ -358,7 +358,7 @@ int SeqErrorCommand::execute(){
 		if(namesFileName != "")     {	weights = getWeights();         }
         else if (countfile != "")   {
             CountTable ct;
-            ct.readTable(countfile, false);
+            ct.readTable(countfile, false, false);
             weights = ct.getNameMap();
         }
 		
@@ -1412,9 +1412,7 @@ int SeqErrorCommand::setLines(string filename, string qfilename, string rfilenam
 					string sname = "";  nameStream >> sname;
 					sname = sname.substr(1);
                     
-                    for (int i = 0; i < sname.length(); i++) {
-                        if (sname[i] == ':') { sname[i] = '_'; m->changedSeqNames = true; }
-                    }
+                    m->checkName(sname);
 					
 					map<string, int>::iterator it = firstSeqNames.find(sname);
 					
@@ -1475,9 +1473,7 @@ int SeqErrorCommand::setLines(string filename, string qfilename, string rfilenam
                     istringstream nameStream(input);
                     string sname = "";  nameStream >> sname;
                     
-                    for (int i = 0; i < sname.length(); i++) {
-                        if (sname[i] == ':') { sname[i] = '_'; m->changedSeqNames = true; }
-                    }
+                    m->checkName(sname);
                     
                     map<string, int>::iterator it = firstSeqNamesReport.find(sname);