[med-svn] [libvcflib] 02/03: Use debian packaged libsmithwaterman
Andreas Tille
tille at debian.org
Thu Jun 23 12:28:57 UTC 2016
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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