[med-svn] [libvcflib] 07/09: Remove code copy of libssw

[Andreas Tille]

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tille pushed a commit to branch master
in repository libvcflib.

commit 47e2b72a6db1fb37e58c76ca7a0a3d43745c4bac
Author: Andreas Tille <tille at debian.org>
Date:   Tue Nov 22 13:09:20 2016 +0100

    Remove code copy of libssw
---
 debian/changelog                                |  1 +
 debian/control                                  |  4 +++-
 debian/patches/series                           |  1 +
 debian/patches/use_debian_packaged_libssw.patch | 23 +++++++++++++++++++++++
 4 files changed, 28 insertions(+), 1 deletion(-)

diff --git a/debian/changelog b/debian/changelog
index b43c46c..dfcb963 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -6,6 +6,7 @@ libvcflib (1.0.0~rc1+dfsg1-1) UNRELEASED; urgency=medium
   * d/watch: version=4
   * debhelper 10
   * Remove code copy of libssw
+    Closes: #838513
 
  -- Andreas Tille <tille at debian.org>  Tue, 22 Nov 2016 10:56:09 +0100
 
diff --git a/debian/control b/debian/control
index 727c986..a2dfa99 100644
--- a/debian/control
+++ b/debian/control
@@ -9,6 +9,7 @@ Build-Depends: debhelper (>= 10),
                libtabixpp-dev,
                libdisorder-dev,
                libsmithwaterman-dev,
+               libssw-dev,
                libfastahack-dev,
                pkg-config,
                libipc-run3-perl
@@ -45,7 +46,8 @@ Depends: ${shlibs:Depends},
          libvcflib1 (= ${binary:Version}),
          libdisorder-dev,
          libtabixpp-dev,
-         libsmithwaterman-dev
+         libsmithwaterman-dev,
+         libssw-dev
 Description: C++ library for parsing and manipulating VCF files (development)
  The Variant Call Format (VCF) is a flat-file, tab-delimited textual format
  intended to concisely describe reference-indexed variations between
diff --git a/debian/patches/series b/debian/patches/series
index d178342..58cb293 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -6,3 +6,4 @@ use_debian_packaged_fastahack.patch
 intervaltree.patch
 shared_lib.patch
 keep_R_files.patch
+use_debian_packaged_libssw.patch
diff --git a/debian/patches/use_debian_packaged_libssw.patch b/debian/patches/use_debian_packaged_libssw.patch
new file mode 100644
index 0000000..61c6049
--- /dev/null
+++ b/debian/patches/use_debian_packaged_libssw.patch
@@ -0,0 +1,23 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Tue, 22 Nov 2016 10:56:09 +0100
+Bug-Debian: https://bugs.debian.org/838513
+Description: Use Debian packaged libssw (while its not clear
+ why two implementations of Smith-Waterman are needed at all)
+
+--- a/Makefile
++++ b/Makefile
+@@ -136,13 +136,7 @@ CXXFLAGS = -O3 -D_FILE_OFFSET_BITS=64 -s
+ #CXXFLAGS = -O2
+ #CXXFLAGS = -pedantic -Wall -Wshadow -Wpointer-arith -Wcast-qual
+ 
+-SSW = src/ssw.o src/ssw_cpp.o
+-
+-src/ssw.o: src/ssw.h src/ssw.c
+-	$(CXX) -c $(CFLAGS) -fPIC -o $@ src/$(*F).c
+-
+-src/ssw_cpp.o: src/ssw_cpp.cpp src/ssw_cpp.h
+-	$(CXX) -c $(CFLAGS) -fPIC -o $@ src/$(*F).cpp
++SSW = 
+ 
+ openmp:
+ 	$(MAKE) CXXFLAGS="$(CXXFLAGS) -fopenmp -D HAS_OPENMP"

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