X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=bowtie.git;a=blobdiff_plain;f=debian%2Fpatches%2Fspaces-in-sam;fp=debian%2Fpatches%2Fspaces-in-sam;h=62bc5b954eb845967b00d9b7c9689814a0318650;hp=0000000000000000000000000000000000000000;hb=87a7281d21fdfc751212ac974a2c0ab317ee1b42;hpb=7ff6d33630733772d810e0ad76ed0a6ff60d612d

diff --git a/debian/patches/spaces-in-sam b/debian/patches/spaces-in-sam
new file mode 100644
index 0000000..62bc5b9
--- /dev/null
+++ b/debian/patches/spaces-in-sam
@@ -0,0 +1,34 @@
+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];
+ 		}
+ 	}