[med-svn] [libvcflib] 02/03: Use debian packaged libsmithwaterman

[Andreas Tille]

This is an automated email from the git hooks/post-receive script.

tille pushed a commit to branch master
in repository libvcflib.

commit 03900d4b00208e6bbde06a53d8cf085f86d8f703
Author: Andreas Tille <tille at debian.org>
Date:   Thu Jun 23 14:23:22 2016 +0200

    Use debian packaged libsmithwaterman
---
 debian/patches/series                                |  2 +-
 ...patch => use_debian_packaged_smithwaterman.patch} | 11 ++++++++++-
 debian/patches/use_debian_packaged_tabixpp.patch     | 20 ++++++++++++++++++++
 3 files changed, 31 insertions(+), 2 deletions(-)

diff --git a/debian/patches/series b/debian/patches/series
index f649203..59f906d 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,5 +1,5 @@
 use_debian_packaged_tabixpp.patch
-ignore_smith_watermann.patch
+use_debian_packaged_smithwaterman.patch
 multichoose.h.patch
 filevercmp.h.patch
 use_debian_packaged_fastahack.patch
diff --git a/debian/patches/ignore_smith_watermann.patch b/debian/patches/use_debian_packaged_smithwaterman.patch
similarity index 75%
rename from debian/patches/ignore_smith_watermann.patch
rename to debian/patches/use_debian_packaged_smithwaterman.patch
index f1fb2ad..3dfa590 100644
--- a/debian/patches/ignore_smith_watermann.patch
+++ b/debian/patches/use_debian_packaged_smithwaterman.patch
@@ -9,7 +9,7 @@
  LDFLAGS = -L$(LIB_DIR) -lvcflib -lhts -lpthread -lz -lm -fopenmp
  
  
-@@ -156,17 +156,20 @@ $(OBJECTS): $(SOURCES) $(HEADERS) $(TABI
+@@ -156,17 +156,20 @@ $(OBJECTS): $(SOURCES) $(HEADERS) multic
  	$(CXX) -c -o $@ src/$(*F).cpp $(INCLUDES) $(LDFLAGS) $(CXXFLAGS) && cp src/*.h* $(VCF_LIB_LOCAL)/$(INC_DIR)/
  
  multichoose: pre
@@ -33,6 +33,15 @@
  
  $(DISORDER): $(SMITHWATERMAN)
  
+@@ -192,7 +195,7 @@ $(BINS): $(BIN_SOURCES) libvcflib.a $(OB
+ 	$(CXX) src/$(notdir $@).cpp -o $@ $(INCLUDES) $(LDFLAGS) $(CXXFLAGS)
+ 
+ libvcflib.a: $(OBJECTS) $(SMITHWATERMAN) $(REPEATS) $(FASTAHACK) $(DISORDER) $(LEFTALIGN) $(INDELALLELE) $(SSW) $(FILEVERCMP) pre
+-	ar rs libvcflib.a $(OBJECTS) smithwaterman/sw.o $(FASTAHACK) $(SSW) $(FILEVERCMP)
++	ar rs libvcflib.a $(OBJECTS) $(FASTAHACK) $(SSW) $(FILEVERCMP)
+ 	cp libvcflib.a $(LIB_DIR)
+ 
+ 
 @@ -220,7 +223,7 @@ clean:
  	rm -rf $(INC_DIR)
  	rm -rf $(OBJ_DIR)
diff --git a/debian/patches/use_debian_packaged_tabixpp.patch b/debian/patches/use_debian_packaged_tabixpp.patch
index a9167e0..1bc601a 100644
--- a/debian/patches/use_debian_packaged_tabixpp.patch
+++ b/debian/patches/use_debian_packaged_tabixpp.patch
@@ -9,6 +9,15 @@
  FASTAHACK = fastahack/Fasta.o
  SMITHWATERMAN = smithwaterman/SmithWatermanGotoh.o
  REPEATS = smithwaterman/Repeats.o
+@@ -152,7 +152,7 @@ profiling:
+ gprof:
+ 	$(MAKE) CXXFLAGS="$(CXXFLAGS) -pg" all
+ 
+-$(OBJECTS): $(SOURCES) $(HEADERS) $(TABIX) multichoose pre $(SMITHWATERMAN) $(FILEVERCMP)
++$(OBJECTS): $(SOURCES) $(HEADERS) multichoose pre $(SMITHWATERMAN) $(FILEVERCMP)
+ 	$(CXX) -c -o $@ src/$(*F).cpp $(INCLUDES) $(LDFLAGS) $(CXXFLAGS) && cp src/*.h* $(VCF_LIB_LOCAL)/$(INC_DIR)/
+ 
+ multichoose: pre
 @@ -162,7 +162,8 @@ intervaltree: pre
  	cd intervaltree && $(MAKE) && cp *.h* $(VCF_LIB_LOCAL)/$(INC_DIR)/
  
@@ -19,6 +28,17 @@
  
  $(SMITHWATERMAN): pre
  	cd smithwaterman && $(MAKE) && cp *.h* $(VCF_LIB_LOCAL)/$(INC_DIR)/ && cp *.o $(VCF_LIB_LOCAL)/$(OBJ_DIR)/
+@@ -190,8 +191,8 @@ $(SHORTBINS): pre
+ $(BINS): $(BIN_SOURCES) libvcflib.a $(OBJECTS) $(SMITHWATERMAN) $(FASTAHACK) $(DISORDER) $(LEFTALIGN) $(INDELALLELE) $(SSW) $(FILEVERCMP) pre intervaltree
+ 	$(CXX) src/$(notdir $@).cpp -o $@ $(INCLUDES) $(LDFLAGS) $(CXXFLAGS)
+ 
+-libvcflib.a: $(OBJECTS) $(SMITHWATERMAN) $(REPEATS) $(FASTAHACK) $(DISORDER) $(LEFTALIGN) $(INDELALLELE) $(SSW) $(FILEVERCMP) $(TABIX) pre
+-	ar rs libvcflib.a $(OBJECTS) smithwaterman/sw.o $(FASTAHACK) $(SSW) $(FILEVERCMP) $(TABIX)
++libvcflib.a: $(OBJECTS) $(SMITHWATERMAN) $(REPEATS) $(FASTAHACK) $(DISORDER) $(LEFTALIGN) $(INDELALLELE) $(SSW) $(FILEVERCMP) pre
++	ar rs libvcflib.a $(OBJECTS) smithwaterman/sw.o $(FASTAHACK) $(SSW) $(FILEVERCMP)
+ 	cp libvcflib.a $(LIB_DIR)
+ 
+ 
 @@ -218,7 +219,7 @@ clean:
  	rm -rf $(LIB_DIR)
  	rm -rf $(INC_DIR)

-- 
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