From: Diane Trout <diane@caltech.edu>
Date: Thu, 6 Dec 2012 20:09:20 +0000 (-0800)
Subject: Commit patch to not break on spaces.
X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=bowtie.git;a=commitdiff_plain;h=refs%2Fheads%2Fmaster

Commit patch to not break on spaces.
---

diff --git a/debian/changelog b/debian/changelog
index 8c0543a..84dc9c8 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,9 @@
+bowtie (0.12.7-3~ppa1) UNRELEASED; urgency=low
+
+  * Patch sam.cpp to not stop writing the header on the first space.
+
+ -- Diane Trout <diane@caltech.edu>  Thu, 06 Dec 2012 12:08:23 -0800
+
 bowtie (0.12.7-3) unstable; urgency=low
 
   * debian/patches/use-dpkg-buildflags.patch: Regard LDFLAGS/CPPFLAGS
diff --git a/debian/patches/series b/debian/patches/series
index 9982159..89efa8e 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,2 +1,3 @@
+spaces-in-sam
 gcc-4.7.patch
 use-dpkg-buildflags.patch
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];
+ 		}
+ 	}