Index: bowtie/sam.cpp
===================================================================
--- bowtie.orig/sam.cpp	2012-12-06 12:06:23.118153141 -0800
+++ bowtie/sam.cpp	2012-12-06 12:07:16.122153504 -0800
@@ -51,6 +51,14 @@
 	os.writeString(ss.str());
 }
 
+static inline int iseol(int c)
+{
+  if (c == '\n' || c == '\r') {
+    return true;
+  } 
+  return false;
+}
+ 
 /**
  * Append a SAM output record for an unaligned read.
  */
@@ -68,12 +76,12 @@
 	if(h.mate > 0) {
 		// truncate final 2 chars
 		for(int i = 0; i < (int)seqan::length(h.patName)-2; i++) {
-			if(isspace(h.patName[i])) break;
+			if(iseol(h.patName[i])) break;
 			ss << h.patName[i];
 		}
 	} else {
 		for(int i = 0; i < (int)seqan::length(h.patName); i++) {
-			if(isspace(h.patName[i])) break;
+			if(iseol(h.patName[i])) break;
 			ss << h.patName[i];
 		}
 	}