paralellized unifrac.weighted for windows. added get.metacommunity command. fixed...

[mothur.git] / sequence.cpp

diff --git a/sequence.cpp b/sequence.cpp
index 4c631a23451d4d9723aec3a29bed423737b243ba..ddc7d4c5a410ca99a415ee1e15d7c60b2199060f 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;
             } 
                        
@@ -683,12 +683,12 @@ int Sequence::filterToPos(int start){
     
     if (start > aligned.length()) { start = aligned.length(); m->mothurOut("[ERROR]: start to large.\n"); }
     
-       for(int j = 0; j < start-1; j++) {
+       for(int j = 0; j < start; j++) {
                aligned[j] = '.';
        }
        
     //things like ......----------AT become ................AT
-    for(int j = start-1; j < aligned.length(); j++) {
+    for(int j = start; j < aligned.length(); j++) {
         if (isalpha(aligned[j])) { break; }
         else { aligned[j] = '.'; }
     }