[med-svn] [libvcflib] 01/03: Use Debian packaged fastahack

[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 7b192b8ce39e40ec3f5324ee7da52b7dfc2834ca
Author: Andreas Tille <tille at debian.org>
Date:   Thu Jun 23 14:18:56 2016 +0200

    Use Debian packaged fastahack
---
 debian/control                                     |  1 +
 debian/patches/ignore_smith_watermann.patch        |  5 +--
 debian/patches/series                              |  1 +
 debian/patches/use_debian_packaged_fastahack.patch | 43 ++++++++++++++++++++++
 4 files changed, 47 insertions(+), 3 deletions(-)

diff --git a/debian/control b/debian/control
index 645aba3..8f2dd87 100644
--- a/debian/control
+++ b/debian/control
@@ -7,6 +7,7 @@ Build-Depends: debhelper (>= 9),
                python-markdown,
                libtabixpp-dev,
                libsmithwaterman-dev,
+               libfastahack-dev,
                pkg-config,
                gnulib
 Standards-Version: 3.9.8
diff --git a/debian/patches/ignore_smith_watermann.patch b/debian/patches/ignore_smith_watermann.patch
index f5bbcf4..f1fb2ad 100644
--- a/debian/patches/ignore_smith_watermann.patch
+++ b/debian/patches/ignore_smith_watermann.patch
@@ -33,13 +33,12 @@
  
  $(DISORDER): $(SMITHWATERMAN)
  
-@@ -220,7 +224,7 @@ clean:
+@@ -220,7 +223,7 @@ clean:
  	rm -rf $(INC_DIR)
  	rm -rf $(OBJ_DIR)
  	# cd tabixpp && make clean
 -	cd smithwaterman && make clean
--	cd fastahack && make clean
 +	# cd smithwaterman && make clean
-+	# cd fastahack && make clean
+ 	cd fastahack && make clean
  
  .PHONY: clean all test pre
diff --git a/debian/patches/series b/debian/patches/series
index 3004089..f649203 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -2,3 +2,4 @@ use_debian_packaged_tabixpp.patch
 ignore_smith_watermann.patch
 multichoose.h.patch
 filevercmp.h.patch
+use_debian_packaged_fastahack.patch
diff --git a/debian/patches/use_debian_packaged_fastahack.patch b/debian/patches/use_debian_packaged_fastahack.patch
new file mode 100644
index 0000000..98c47fb
--- /dev/null
+++ b/debian/patches/use_debian_packaged_fastahack.patch
@@ -0,0 +1,43 @@
+--- a/Makefile
++++ b/Makefile
+@@ -115,7 +115,6 @@ BINS = $(addprefix bin/,$(notdir $(BIN_S
+ SHORTBINS = $(notdir $(BIN_SOURCES:.cpp=))
+ 
+ # TABIX = tabixpp/tabix.o
+-FASTAHACK = fastahack/Fasta.o
+ SMITHWATERMAN = smithwaterman/SmithWatermanGotoh.o
+ REPEATS = smithwaterman/Repeats.o
+ INDELALLELE = smithwaterman/IndelAllele.o
+@@ -179,9 +178,6 @@ $(LEFTALIGN): $(SMITHWATERMAN)
+ 
+ $(INDELALLELE): $(SMITHWATERMAN)
+ 
+-$(FASTAHACK): pre
+-	cd fastahack && $(MAKE) && cp *.h* $(VCF_LIB_LOCAL)/$(INC_DIR)/ && cp Fasta.o $(VCF_LIB_LOCAL)/$(OBJ_DIR)/
+-
+ #$(FSOM):
+ #	cd fsom && $(CXX) $(CXXFLAGS) -c fsom.c -lm
+ 
+@@ -191,11 +187,11 @@ $(FILEVERCMP): pre
+ $(SHORTBINS): pre
+ 	$(MAKE) bin/$@
+ 
+-$(BINS): $(BIN_SOURCES) libvcflib.a $(OBJECTS) $(SMITHWATERMAN) $(FASTAHACK) $(DISORDER) $(LEFTALIGN) $(INDELALLELE) $(SSW) $(FILEVERCMP) pre intervaltree
++$(BINS): $(BIN_SOURCES) libvcflib.a $(OBJECTS) $(SMITHWATERMAN) $(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) $(DISORDER) $(LEFTALIGN) $(INDELALLELE) $(SSW) $(FILEVERCMP) $(TABIX) pre
++	ar rs libvcflib.a $(OBJECTS) smithwaterman/sw.o $(SSW) $(FILEVERCMP) $(TABIX)
+ 	cp libvcflib.a $(LIB_DIR)
+ 
+ 
+@@ -224,6 +220,6 @@ clean:
+ 	rm -rf $(OBJ_DIR)
+ 	# cd tabixpp && make clean
+ 	# cd smithwaterman && make clean
+-	cd fastahack && make clean
++	# cd fastahack && make clean
+ 
+ .PHONY: clean all test pre

-- 
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