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 93ecb70f066fd8a1da6415453347aac66c57d0dd..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;
             } 
                        
@@ -575,6 +575,15 @@ string Sequence::getUnaligned(){
 int Sequence::getNumBases(){
        return numBases;
 }
+//********************************************************************************************************************
+
+int Sequence::getNumNs(){
+    int numNs = 0;
+       for (int i = 0; i < unaligned.length(); i++) {
+        if(toupper(unaligned[i]) == 'N') { numNs++; }
+    }
+    return numNs;
+}
 
 //********************************************************************************************************************
 
@@ -763,6 +772,8 @@ void Sequence::trim(int length){
        if(numBases > length){
                unaligned = unaligned.substr(0,length);
                numBases = length;
+        aligned = "";
+        isAligned = 0;
        }
        
 }