bugs fixes while testing for 1.5 release

[mothur.git] / getseqscommand.cpp

diff --git a/getseqscommand.cpp b/getseqscommand.cpp
index 8406b813711aeb655ba786ac47eb6df16020327b..04b254599f46ef00081a3f153c0e097fea665cf4 100644 (file)
--- a/getseqscommand.cpp
+++ b/getseqscommand.cpp
@@ -155,7 +155,7 @@ void GetSeqsCommand::readFasta(){
 void GetSeqsCommand::readName(){
        try {
        
-               string outputFileName = getRootName(namefile) + "pick" +  getExtension(namefile);;
+               string outputFileName = getRootName(namefile) + "pick" +  getExtension(namefile);
                ofstream out;
                openOutputFile(outputFileName, out);
 
@@ -186,7 +186,6 @@ void GetSeqsCommand::readName(){
                        for (int i = 0; i < parsedNames.size(); i++) {
                                if (names.count(parsedNames[i]) == 1) {
                                        validSecond.push_back(parsedNames[i]);
-                                       names.erase(parsedNames[i]);
                                }
                        }
 
@@ -202,7 +201,6 @@ void GetSeqsCommand::readName(){
                                for (int i = 0; i < validSecond.size()-1; i++) {  out << validSecond[i] << ',';  }
                                out << validSecond[validSecond.size()-1] << endl;
                                
-                               names.erase(firstCol);
                        
                        //make first name in set you come to first column and then add the remaining names to second column
                        }else {
@@ -285,7 +283,7 @@ void GetSeqsCommand::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 GetSeqsCommand::readAlign(){
        try {
-               string outputFileName = getRootName(alignfile) + "pick" +  getExtension(alignfile);;
+               string outputFileName = getRootName(getRootName(alignfile)) + "pick.align.report";
                ofstream out;
                openOutputFile(outputFileName, out);