fixed bug with normalize.shared, printed out numbins twice. fixed bug with summary...

[mothur.git] / trimseqscommand.cpp

diff --git a/trimseqscommand.cpp b/trimseqscommand.cpp
index 56fd8c54b53aaff9f4e43e8e694fc71f6987fd7c..4e7a12994f4854c487d036dd422aa1f3130e288c 100644 (file)
--- a/trimseqscommand.cpp
+++ b/trimseqscommand.cpp
@@ -26,6 +26,7 @@ vector<string> TrimSeqsCommand::getValidParameters(){
 //**********************************************************************************************************************
 TrimSeqsCommand::TrimSeqsCommand(){    
        try {
+               abort = true;
                //initialize outputTypes
                vector<string> tempOutNames;
                outputTypes["fasta"] = tempOutNames;
@@ -757,7 +758,7 @@ int TrimSeqsCommand::setLines(string filename, string qfilename, vector<unsigned
                //seach for filePos of each first name in the qfile and save in qfileFilePos
                ifstream inQual;
                m->openInputFile(qfilename, inQual);
-                       
+               
                string input;
                while(!inQual.eof()){   
                        input = m->getline(inQual);
@@ -783,6 +784,7 @@ int TrimSeqsCommand::setLines(string filename, string qfilename, vector<unsigned
                }
                inQual.close();
                
+               
                if (firstSeqNames.size() != 0) { 
                        for (map<string, int>::iterator it = firstSeqNames.begin(); it != firstSeqNames.end(); it++) {
                                m->mothurOut(it->first + " is in your fasta file and not in your quality file, not using quality file."); m->mothurOutEndLine();