bug fixes

[mothur.git] / aligncommand.cpp

diff --git a/aligncommand.cpp b/aligncommand.cpp
index 5aabeef9437bd9f5fdd90f6b785e52065afc3115..877e7c76773ece0f459142e674382fb2747bb8fb 100644 (file)
--- a/aligncommand.cpp
+++ b/aligncommand.cpp
@@ -488,7 +488,7 @@ int AlignCommand::driver(linePair* filePos, string alignFName, string reportFNam
                        if (m->control_pressed) {  return 0; }
                        
                        Sequence* candidateSeq = new Sequence(inFASTA);  m->gobble(inFASTA);
-       
+                       
                        int origNumBases = candidateSeq->getNumBases();
                        string originalUnaligned = candidateSeq->getUnaligned();
                        int numBasesNeeded = origNumBases * threshold;
@@ -565,8 +565,12 @@ int AlignCommand::driver(linePair* filePos, string alignFName, string reportFNam
                        }
                        delete candidateSeq;
                        
-                       unsigned long int pos = inFASTA.tellg();
-                       if ((pos == -1) || (pos >= filePos->end)) { break; }
+                       #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+                               unsigned long int pos = inFASTA.tellg();
+                               if ((pos == -1) || (pos >= filePos->end)) { break; }
+                       #else
+                               if (inFASTA.eof()) { break; }
+                       #endif
                        
                        //report progress
                        if((count) % 100 == 0){ m->mothurOut(toString(count)); m->mothurOutEndLine();           }