changes while testing

[mothur.git] / getseqscommand.cpp

diff --git a/getseqscommand.cpp b/getseqscommand.cpp
index 9538698a3fea181430056d11f16835f66186452e..83fdf73e9af36fd9826f5a8c2efcc11655ac938e 100644 (file)
--- a/getseqscommand.cpp
+++ b/getseqscommand.cpp
@@ -430,9 +430,11 @@ int GetSeqsCommand::readFasta(){
             
             if (!dups) {//adjust name if needed
                 map<string, string>::iterator it = uniqueMap.find(name);
-                if (it != uniqueMap.end()) { name = it->second; }
+                if (it != uniqueMap.end()) { currSeq.setName(it->second); }
             }
                        
+            name = currSeq.getName();
+            
                        if (name != "") {
                                //if this name is in the accnos file
                                if (names.count(name) != 0) {
@@ -710,7 +712,7 @@ int GetSeqsCommand::readName(){
                
                        if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName);  return 0; }
 
-                       in >> firstCol;                         
+                       in >> firstCol;                 m->gobble(in);
                        in >> secondCol;
                        
                        string hold = "";
@@ -734,6 +736,7 @@ int GetSeqsCommand::readName(){
                                selectedCount += parsedNames.size();
                 if (m->debug) { sanity["name"].insert(firstCol); }
                        }else {
+                
                                selectedCount += validSecond.size();
                                
                                //if the name in the first column is in the set then print it and any other names in second column also in set
@@ -752,6 +755,7 @@ int GetSeqsCommand::readName(){
                                
                                //make first name in set you come to first column and then add the remaining names to second column
                                }else {
+                    
                                        //you want part of this row
                                        if (validSecond.size() != 0) {