added primer.design command. fixed bug with linux unifrac subsampling, metastats...

[mothur.git] / screenseqscommand.cpp

diff --git a/screenseqscommand.cpp b/screenseqscommand.cpp
index 5a9c0c8320b7305834cdf4bb544effd515728417..2524e652667bcacf8c76e89635e3c4e3f89ccc51 100644 (file)
--- a/screenseqscommand.cpp
+++ b/screenseqscommand.cpp
@@ -588,7 +588,7 @@ int ScreenSeqsCommand::screenNameGroupFile(set<string> badSeqNames){
                while(!inputNames.eof()){
                        if (m->control_pressed) { goodNameOut.close();  inputNames.close(); m->mothurRemove(goodNameFile);  return 0; }
 
-                       inputNames >> seqName >> seqList;
+                       inputNames >> seqName; m->gobble(inputNames); inputNames >> seqList;
                        it = badSeqNames.find(seqName);
                                
                        if(it != badSeqNames.end()){
@@ -636,7 +636,7 @@ int ScreenSeqsCommand::screenNameGroupFile(set<string> badSeqNames){
                        while(!inputGroups.eof()){
                                if (m->control_pressed) { goodGroupOut.close(); inputGroups.close(); m->mothurRemove(goodNameFile);  m->mothurRemove(goodGroupFile); return 0; }
 
-                               inputGroups >> seqName >> group;
+                               inputGroups >> seqName; m->gobble(inputGroups); inputGroups >> group;
                                
                                it = badSeqGroups.find(seqName);
                                
@@ -970,7 +970,7 @@ int ScreenSeqsCommand::screenGroupFile(set<string> badSeqNames){
                while(!inputGroups.eof()){
                        if (m->control_pressed) { goodGroupOut.close(); inputGroups.close(); m->mothurRemove(goodGroupFile); return 0; }
 
-                       inputGroups >> seqName >> group;
+                       inputGroups >> seqName; m->gobble(inputGroups); inputGroups >> group;
                        it = badSeqNames.find(seqName);
                        
                        if(it != badSeqNames.end()){
@@ -1157,7 +1157,7 @@ int ScreenSeqsCommand::screenTaxonomy(set<string> badSeqNames){
                while(!input.eof()){
                        if (m->control_pressed) { goodTaxOut.close(); input.close(); m->mothurRemove(goodTaxFile); return 0; }
                        
-                       input >> seqName >> tax;
+                       input >> seqName; m->gobble(input); input >> tax;
                        it = badSeqNames.find(seqName);
                        
                        if(it != badSeqNames.end()){ badSeqNames.erase(it); }