bowtie2: Import new patch from FreeBSD

[Jason Bacon <bacon@centosdev.local>]

Module Name:	pkgsrc-wip
Committed By:	Jason Bacon <bacon@centosdev.local>
Pushed By:	outpaddling
Date:		Mon Feb 20 16:37:00 2017 -0600
Changeset:	8b7b3c3d601cd9d901b1b50ef202cb3835fa4d95

Modified Files:
	bowtie2/distinfo
Added Files:
	bowtie2/patches/patch-aligner__result.cpp

Log Message:
bowtie2: Import new patch from FreeBSD

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=8b7b3c3d601cd9d901b1b50ef202cb3835fa4d95

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.

diffstat:
 bowtie2/distinfo                          |  1 +
 bowtie2/patches/patch-aligner__result.cpp | 11 +++++++++++
 2 files changed, 12 insertions(+)

diffs:
diff --git a/bowtie2/distinfo b/bowtie2/distinfo
index 4341bff5fe..e505473cd8 100644
--- a/bowtie2/distinfo
+++ b/bowtie2/distinfo
@@ -5,3 +5,4 @@ RMD160 (bowtie2-2.2.7.tar.gz) = bf7af50df878a98ea84df70f3b1196d9b7ed5948
 SHA512 (bowtie2-2.2.7.tar.gz) = 5dc34d7fc9f31af0a648d2b6ec16e4a45679cf40569fdb69ba2f909aeed0b99b9cd364cbc8cfff8a7d011726fc53e7e7665f466cffaa27dd74ba5acd41b17d8d
 Size (bowtie2-2.2.7.tar.gz) = 5813850 bytes
 SHA1 (patch-Makefile) = de7328796af0997784e6ba37d3770aa57a149076
+SHA1 (patch-aligner__result.cpp) = 1c7ed81fdd4ac2decb27eac898286fc2284ddbae
diff --git a/bowtie2/patches/patch-aligner__result.cpp b/bowtie2/patches/patch-aligner__result.cpp
new file mode 100644
index 0000000000..70e515da16
--- /dev/null
+++ b/bowtie2/patches/patch-aligner__result.cpp
@@ -0,0 +1,11 @@
+--- aligner_result.cpp.orig	2017-02-19 18:40:54.398991000 -0600
++++ aligner_result.cpp	2017-02-19 18:41:14.093250000 -0600
+@@ -1130,7 +1130,7 @@ bool AlnFlags::printYF(BTString& o, bool
+ 	else if(!nfilt_  ) flag = "NS";
+ 	else if(!scfilt_ ) flag = "SC";
+ 	else if(!qcfilt_ ) flag = "QC";
+-	if(flag > 0) {
++	if(*flag != '\0') {
+ 		if(!first) o.append('\t');
+ 		o.append("YF:Z:");
+ 		o.append(flag);