bugs fixes while testing for 1.5 release

[mothur.git] / removeseqscommand.cpp

diff --git a/removeseqscommand.cpp b/removeseqscommand.cpp
index a49d41a9485d22b6d302164f01913d37f42802aa..1b9edb0e98e20f7752fb9b8aab3584c1c05bccc0 100644 (file)
--- a/removeseqscommand.cpp
+++ b/removeseqscommand.cpp
@@ -154,6 +154,7 @@ void RemoveSeqsCommand::readName(){
        try {
        
                string outputFileName = getRootName(namefile) + "pick" + getExtension(namefile);
+
                ofstream out;
                openOutputFile(outputFileName, out);
 
@@ -167,29 +168,29 @@ void RemoveSeqsCommand::readName(){
 
                        in >> firstCol;                         
                        in >> secondCol;                        
-                       
+
                        vector<string> parsedNames;
                        //parse second column saving each name
                        while (secondCol.find_first_of(',') != -1) { 
                                name = secondCol.substr(0,secondCol.find_first_of(','));
                                secondCol = secondCol.substr(secondCol.find_first_of(',')+1, secondCol.length());
                                parsedNames.push_back(name);
+
                        }
                        
                        //get name after last ,
                        parsedNames.push_back(secondCol);
-                       
-                       vector<string> validSecond;
+
+                       vector<string> validSecond;  validSecond.clear();
                        for (int i = 0; i < parsedNames.size(); i++) {
                                if (names.count(parsedNames[i]) == 0) {
                                        validSecond.push_back(parsedNames[i]);
-                               }else { names.erase(parsedNames[i]); }
+                               }
                        }
-
                        
                        //if the name in the first column is in the set then print it and any other names in second column also in set
                        if (names.count(firstCol) == 0) {
-                               
+                       
                                wroteSomething = true;
                                
                                out << firstCol << '\t';
@@ -200,8 +201,7 @@ void RemoveSeqsCommand::readName(){
                        
                        //make first name in set you come to first column and then add the remaining names to second column
                        }else {
-                               names.erase(firstCol);  
-                                       
+                               
                                //you want part of this row
                                if (validSecond.size() != 0) {
                                
@@ -278,7 +278,7 @@ void RemoveSeqsCommand::readGroup(){
 //alignreport file has a column header line then all other lines contain 16 columns.  we just want the first column since that contains the name
 void RemoveSeqsCommand::readAlign(){
        try {
-               string outputFileName = getRootName(alignfile) + "pick" + getExtension(alignfile);
+               string outputFileName = getRootName(getRootName(alignfile)) + "pick.align.report";
                ofstream out;
                openOutputFile(outputFileName, out);