added end of file character to some type type reads. fixes while testing.

[mothur.git] / sequence.cpp

diff --git a/sequence.cpp b/sequence.cpp
index 224ecb10cb1529db7d6bdb10c268be047dae5834..d1cf7299a46c522255eb725dccb058673f6b1c78 100644 (file)
--- a/sequence.cpp
+++ b/sequence.cpp
@@ -220,7 +220,7 @@ Sequence::Sequence(ifstream& fastaFile, string& extraInfo, bool getInfo){
                        //read info after sequence name
                        while (!fastaFile.eof())        {       
                 char c = fastaFile.get(); 
-                if (c == 10 || c == 13){  break;       }       
+                if (c == 10 || c == 13 || c == -1){  break;    }
                 extraInfo += c;
             } 
                        
@@ -772,6 +772,8 @@ void Sequence::trim(int length){
        if(numBases > length){
                unaligned = unaligned.substr(0,length);
                numBases = length;
+        aligned = "";
+        isAligned = 0;
        }
        
 }