+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];
+ }
+ }