[med-svn] [libvcflib] 07/07: Use pkg-config to find smithwatermann header file

[Andreas Tille]

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tille pushed a commit to branch master
in repository libvcflib.

commit d56d53da8f1921c8a0f8b82b7aad62dfb0c4c810
Author: Andreas Tille <tille at debian.org>
Date:   Wed Jun 22 17:03:12 2016 +0200

    Use pkg-config to find smithwatermann header file
---
 debian/control                              | 3 ++-
 debian/patches/ignore_smith_watermann.patch | 9 +++++++++
 2 files changed, 11 insertions(+), 1 deletion(-)

diff --git a/debian/control b/debian/control
index 1418366..a9a7096 100644
--- a/debian/control
+++ b/debian/control
@@ -6,7 +6,8 @@ Priority: optional
 Build-Depends: debhelper (>= 9),
                python-markdown,
                libtabixpp-dev,
-               libsmithwaterman-dev
+               libsmithwaterman-dev,
+               pkg-config
 Standards-Version: 3.9.8
 Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/libvcflib.git
 Vcs-Git: https://anonscm.debian.org/git/debian-med/libvcflib.git
diff --git a/debian/patches/ignore_smith_watermann.patch b/debian/patches/ignore_smith_watermann.patch
index 7479d0c..9868e67 100644
--- a/debian/patches/ignore_smith_watermann.patch
+++ b/debian/patches/ignore_smith_watermann.patch
@@ -1,5 +1,14 @@
 --- a/Makefile
 +++ b/Makefile
+@@ -124,7 +124,7 @@ LEFTALIGN = smithwaterman/LeftAlign.o
+ FSOM = fsom/fsom.o
+ FILEVERCMP = filevercmp/filevercmp.o
+ 
+-INCLUDES = -Itabixpp/htslib -I$(INC_DIR) -L. -Ltabixpp/htslib
++INCLUDES = `pkg-config --cflags libsmithwaterman` -Itabixpp/htslib -I$(INC_DIR) -L. -Ltabixpp/htslib
+ LDFLAGS = -L$(LIB_DIR) -lvcflib -lhts -lpthread -lz -lm -fopenmp
+ 
+ 
 @@ -156,17 +156,20 @@ $(OBJECTS): $(SOURCES) $(HEADERS) $(TABI
  	$(CXX) -c -o $@ src/$(*F).cpp $(INCLUDES) $(LDFLAGS) $(CXXFLAGS) && cp src/*.h* $(VCF_LIB_LOCAL)/$(INC_DIR)/
  

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