[med-svn] [libvcflib] 01/01: Libtabixpp is now available but some other things (smithwaterman) are missing

[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 9fa4de42130bec6da08894c96f4b594c19353454
Author: Andreas Tille <tille at debian.org>
Date:   Sun Dec 20 08:54:18 2015 +0100

    Libtabixpp is now available but some other things (smithwaterman) are missing
---
 debian/changelog                                 |  3 +-
 debian/control                                   |  3 +-
 debian/patches/series                            |  1 +
 debian/patches/use_debian_packaged_tabixpp.patch | 49 ++++++++++++++++++++++++
 4 files changed, 53 insertions(+), 3 deletions(-)

diff --git a/debian/changelog b/debian/changelog
index 41b0910..b0e1184 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,7 +1,6 @@
 libvcflib (1.0.0~rc0-1) UNRELEASED; urgency=low
 
-  TODO: Needs https://github.com/ekg/tabixpp
-     git://anonscm.debian.org/debian-med/libtabixpp.git
   * Initial release (Closes: #<bug>)
+  TODO: tabixpp is available but smithwaterman (??) is missing
 
  -- Andreas Tille <tille at debian.org>  Sun, 01 Feb 2015 14:58:21 +0100
diff --git a/debian/control b/debian/control
index 8f95c85..9bbb354 100644
--- a/debian/control
+++ b/debian/control
@@ -4,7 +4,8 @@ Priority: optional
 Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
 Uploaders: Andreas Tille <tille at debian.org>
 Build-Depends: debhelper (>= 9),
-               python-markdown
+               python-markdown,
+               libtabixpp-dev
 Standards-Version: 3.9.6
 Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/libvcflib.git
 Vcs-Git: git://anonscm.debian.org/debian-med/libvcflib.git
diff --git a/debian/patches/series b/debian/patches/series
new file mode 100644
index 0000000..37e6a7c
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1 @@
+use_debian_packaged_tabixpp.patch
diff --git a/debian/patches/use_debian_packaged_tabixpp.patch b/debian/patches/use_debian_packaged_tabixpp.patch
new file mode 100644
index 0000000..3e19ae6
--- /dev/null
+++ b/debian/patches/use_debian_packaged_tabixpp.patch
@@ -0,0 +1,49 @@
+--- a/Makefile
++++ b/Makefile
+@@ -80,7 +80,7 @@ BIN_SOURCES = src/vcfecho.cpp \
+ BINS = $(addprefix bin/,$(notdir $(BIN_SOURCES:.cpp=)))
+ SHORTBINS = $(notdir $(BIN_SOURCES:.cpp=))
+ 
+-TABIX = tabixpp/tabix.o
++# TABIX = tabixpp/tabix.o
+ FASTAHACK = fastahack/Fasta.o
+ SMITHWATERMAN = smithwaterman/SmithWatermanGotoh.o 
+ REPEATS = smithwaterman/Repeats.o
+@@ -90,7 +90,7 @@ LEFTALIGN = smithwaterman/LeftAlign.o
+ FSOM = fsom/fsom.o
+ FILEVERCMP = filevercmp/filevercmp.o
+ 
+-INCLUDES = -I. -Itabixpp/htslib/ -L. -Ltabixpp/ -Ltabixpp/htslib/
++INCLUDES = -I. -Itabixpp/htslib/ #-L. -Ltabixpp/ -Ltabixpp/htslib/
+ LDFLAGS = -lvcflib -ltabix -lhts -lpthread -lz -lm
+ 
+ 
+@@ -115,7 +115,7 @@ profiling:
+ gprof:
+ 	$(MAKE) CXXFLAGS="$(CXXFLAGS) -pg" all
+ 
+-$(OBJECTS): $(SOURCES) $(HEADERS) $(TABIX)
++$(OBJECTS): $(SOURCES) $(HEADERS) # $(TABIX)
+ 	$(CXX) -c -o $@ src/$(*F).cpp $(INCLUDES) $(LDFLAGS) $(CXXFLAGS)
+ 
+ $(TABIX):
+@@ -147,8 +147,8 @@ $(SHORTBINS):
+ $(BINS): $(BIN_SOURCES) libvcflib.a $(OBJECTS) $(SMITHWATERMAN) $(FASTAHACK) $(DISORDER) $(LEFTALIGN) $(INDELALLELE) $(SSW) $(FILEVERCMP)
+ 	$(CXX) src/$(notdir $@).cpp -o $@ $(INCLUDES) $(LDFLAGS) $(CXXFLAGS)
+ 
+-libvcflib.a: $(OBJECTS) $(SMITHWATERMAN) $(REPEATS) $(FASTAHACK) $(DISORDER) $(LEFTALIGN) $(INDELALLELE) $(SSW) $(FILEVERCMP) $(TABIX)
+-	ar rs libvcflib.a $(OBJECTS) smithwaterman/sw.o $(FASTAHACK) $(SSW) $(FILEVERCMP) $(TABIX)
++libvcflib.a: $(OBJECTS) $(SMITHWATERMAN) $(REPEATS) $(FASTAHACK) $(DISORDER) $(LEFTALIGN) $(INDELALLELE) $(SSW) $(FILEVERCMP) # $(TABIX)
++	ar rs libvcflib.a $(OBJECTS) smithwaterman/sw.o $(FASTAHACK) $(SSW) $(FILEVERCMP) # $(TABIX)
+ 
+ 
+ test: $(BINS)
+@@ -158,7 +158,7 @@ clean:
+ 	rm -f $(BINS) $(OBJECTS)
+ 	rm -f ssw_cpp.o ssw.o
+ 	rm -f libvcflib.a
+-	cd tabixpp && make clean
++	# cd tabixpp && make clean
+ 	cd smithwaterman && make clean
+ 	cd fastahack && make clean
+ 

-- 
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