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......@@ -19,3 +19,9 @@
[submodule "filevercmp"]
path = filevercmp
url = https://github.com/ekg/filevercmp.git
[submodule "googletest"]
path = googletest
url = https://github.com/google/googletest.git
[submodule "libVCFH"]
path = libVCFH
url = https://github.com/edawson/libVCFH.git
language: cpp
sudo: required
compiler:
- gcc
- gcc
before_install:
- sudo apt-get install g++
- sudo apt-get install build-essential
- git submodule update --init --recursive
- sudo add-apt-repository ppa:ubuntu-toolchain-r/test -y
- ls /etc/apt/sources.list.d
- sudo apt-get update
- sudo apt-get install -qq gcc-4.9 g++-4.9
- sudo update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-4.9 60 --slave /usr/bin/g++ g++ /usr/bin/g++-4.9
- gcc --version && g++ --version
- sudo apt-get install build-essential
- git submodule update --init --recursive
os:
- linux
script: make
\ No newline at end of file
- linux
script: make
......@@ -25,8 +25,10 @@ OBJ_DIR:=obj
#vcfstats.cpp
BIN_SOURCES = src/vcfecho.cpp \
src/vcfnormalizesvs.cpp \
src/dumpContigsFromHeader.cpp \
src/bFst.cpp \
src/pVst.cpp \
src/hapLrt.cpp \
src/popStats.cpp \
src/wcFst.cpp \
......@@ -37,7 +39,7 @@ BIN_SOURCES = src/vcfecho.cpp \
src/sequenceDiversity.cpp \
src/pFst.cpp \
src/smoother.cpp \
src/LD.cpp \
src/vcfld.cpp \
src/plotHaps.cpp \
src/abba-baba.cpp \
src/permuteGPAT++.cpp \
......@@ -105,6 +107,8 @@ BIN_SOURCES = src/vcfecho.cpp \
src/vcfqual2info.cpp \
src/vcfinfo2qual.cpp \
src/vcfglbound.cpp \
src/vcfunphase.cpp \
src/vcfnull2ref.cpp \
src/vcfinfosummarize.cpp
# when we can figure out how to build on mac
......@@ -125,23 +129,24 @@ FSOM = fsom/fsom.o
FILEVERCMP = filevercmp/filevercmp.o
INCLUDES = -Itabixpp/htslib -I$(INC_DIR) -L. -Ltabixpp/htslib
LDFLAGS = -L$(LIB_DIR) -lvcflib -lhts -lpthread -lz -lm -fopenmp
LDFLAGS = -L$(LIB_DIR) -lvcflib -lhts -lpthread -lz -lm -llzma -lbz2
all: $(OBJECTS) $(BINS)
all: $(OBJECTS) $(BINS) scriptToBin
scriptToBin: $(BINS)
cp scripts/* bin
GIT_VERSION := $(shell git describe --abbrev=4 --dirty --always)
CXX = g++
CXXFLAGS = -O3 -D_FILE_OFFSET_BITS=64 -std=c++0x -DVERSION=\"$(GIT_VERSION)\"
CXXFLAGS = -O3 -D_FILE_OFFSET_BITS=64 -std=c++0x
#CXXFLAGS = -O2
#CXXFLAGS = -pedantic -Wall -Wshadow -Wpointer-arith -Wcast-qual
SSW = src/ssw.o src/ssw_cpp.o
ssw.o: src/ssw.h
ssw_cpp.o:src/ssw_cpp.h
ssw.o: src/ssw.hpp
ssw_cpp.o:src/ssw_cpp.hpp
openmp:
$(MAKE) CXXFLAGS="$(CXXFLAGS) -fopenmp -D HAS_OPENMP"
......@@ -152,7 +157,7 @@ profiling:
gprof:
$(MAKE) CXXFLAGS="$(CXXFLAGS) -pg" all
$(OBJECTS): $(SOURCES) $(HEADERS) $(TABIX) multichoose pre $(SMITHWATERMAN) $(FILEVERCMP)
$(OBJECTS): $(SOURCES) $(HEADERS) $(TABIX) multichoose pre $(SMITHWATERMAN) $(FILEVERCMP) $(FASTAHACK)
$(CXX) -c -o $@ src/$(*F).cpp $(INCLUDES) $(LDFLAGS) $(CXXFLAGS) && cp src/*.h* $(VCF_LIB_LOCAL)/$(INC_DIR)/
multichoose: pre
......@@ -188,7 +193,7 @@ $(SHORTBINS): pre
$(MAKE) bin/$@
$(BINS): $(BIN_SOURCES) libvcflib.a $(OBJECTS) $(SMITHWATERMAN) $(FASTAHACK) $(DISORDER) $(LEFTALIGN) $(INDELALLELE) $(SSW) $(FILEVERCMP) pre intervaltree
$(CXX) src/$(notdir $@).cpp -o $@ $(INCLUDES) $(LDFLAGS) $(CXXFLAGS)
$(CXX) src/$(notdir $@).cpp -o $@ $(INCLUDES) $(LDFLAGS) $(CXXFLAGS) -DVERSION=\"$(GIT_VERSION)\"
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)
......
#OBJ_DIR = ./
HEADERS = src/Variant.h \
src/split.h \
src/join.h
SOURCES = src/Variant.cpp \
src/split.cpp
OBJECTS= $(SOURCES:.cpp=.o)
# TODO
#vcfstats.cpp
BIN_SOURCES = src/vcfecho.cpp \
src/vcfaltcount.cpp \
src/vcfhetcount.cpp \
src/vcfhethomratio.cpp \
src/vcffilter.cpp \
src/vcf2tsv.cpp \
src/vcfgenotypes.cpp \
src/vcfannotategenotypes.cpp \
src/vcfcommonsamples.cpp \
src/vcfremovesamples.cpp \
src/vcfkeepsamples.cpp \
src/vcfsamplenames.cpp \
src/vcfgenotypecompare.cpp \
src/vcffixup.cpp \
src/vcfclassify.cpp \
src/vcfsamplediff.cpp \
src/vcfremoveaberrantgenotypes.cpp \
src/vcfrandom.cpp \
src/vcfparsealts.cpp \
src/vcfstats.cpp \
src/vcfflatten.cpp \
src/vcfprimers.cpp \
src/vcfnumalt.cpp \
src/vcfcleancomplex.cpp \
src/vcfintersect.cpp \
src/vcfannotate.cpp \
src/vcfallelicprimitives.cpp \
src/vcfoverlay.cpp \
src/vcfaddinfo.cpp \
src/vcfkeepinfo.cpp \
src/vcfkeepgeno.cpp \
src/vcfafpath.cpp \
src/vcfcountalleles.cpp \
src/vcflength.cpp \
src/vcfdistance.cpp \
src/vcfrandomsample.cpp \
src/vcfentropy.cpp \
src/vcfglxgt.cpp \
src/vcfroc.cpp \
src/vcfcheck.cpp \
src/vcfstreamsort.cpp \
src/vcfuniq.cpp \
src/vcfuniqalleles.cpp \
src/vcfremap.cpp \
src/vcf2fasta.cpp \
src/vcfsitesummarize.cpp \
src/vcfbreakmulti.cpp \
src/vcfcreatemulti.cpp \
src/vcfevenregions.cpp \
src/vcfcat.cpp \
src/vcfgenosummarize.cpp \
src/vcfgenosamplenames.cpp \
src/vcfgeno2haplo.cpp \
src/vcfleftalign.cpp \
src/vcfcombine.cpp \
src/vcfgeno2alleles.cpp \
src/vcfindex.cpp \
src/vcf2dag.cpp \
src/vcfsample2info.cpp \
src/vcfqual2info.cpp \
src/vcfinfo2qual.cpp \
src/vcfglbound.cpp \
src/vcfinfosummarize.cpp
# when we can figure out how to build on mac
# src/vcfsom.cpp
#BINS = $(BIN_SOURCES:.cpp=)
BINS = $(addprefix bin/,$(notdir $(BIN_SOURCES:.cpp=)))
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
DISORDER = smithwaterman/disorder.o
LEFTALIGN = smithwaterman/LeftAlign.o
FSOM = fsom/fsom.o
FILEVERCMP = filevercmp/filevercmp.o
INCLUDES = -I. -Itabixpp/htslib/ -L. -Ltabixpp/ -Ltabixpp/htslib/
LDFLAGS = -lvcflib -lhts -lpthread -lz -lm
all: $(OBJECTS) $(BINS)
CXX = g++
CXXFLAGS = -O3 -D_FILE_OFFSET_BITS=64
#CXXFLAGS = -O2
#CXXFLAGS = -pedantic -Wall -Wshadow -Wpointer-arith -Wcast-qual
SSW = src/ssw.o src/ssw_cpp.o
ssw.o: src/ssw.h
ssw_cpp.o:src/ssw_cpp.h
openmp:
$(MAKE) CXXFLAGS="$(CXXFLAGS) -fopenmp -D HAS_OPENMP"
profiling:
$(MAKE) CXXFLAGS="$(CXXFLAGS) -g" all
gprof:
$(MAKE) CXXFLAGS="$(CXXFLAGS) -pg" all
$(OBJECTS): $(SOURCES) $(HEADERS) $(TABIX)
$(CXX) -c -o $@ src/$(*F).cpp $(INCLUDES) $(LDFLAGS) $(CXXFLAGS)
$(TABIX):
cd tabixpp && $(MAKE)
$(SMITHWATERMAN):
cd smithwaterman && $(MAKE)
$(DISORDER): $(SMITHWATERMAN)
$(REPEATS): $(SMITHWATERMAN)
$(LEFTALIGN): $(SMITHWATERMAN)
$(INDELALLELE): $(SMITHWATERMAN)
$(FASTAHACK):
cd fastahack && $(MAKE)
#$(FSOM):
# cd fsom && $(CXX) $(CXXFLAGS) -c fsom.c -lm
$(FILEVERCMP):
cd filevercmp && make
$(SHORTBINS):
$(MAKE) bin/$@
$(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)
test: $(BINS)
@prove -Itests/lib -w tests/*.t
clean:
rm -f $(BINS) $(OBJECTS)
rm -f ssw_cpp.o ssw.o
rm -f libvcflib.a
cd tabixpp && make clean
cd smithwaterman && make clean
cd fastahack && make clean
.PHONY: clean all test
......@@ -5,7 +5,7 @@
#### license: MIT
[![Gitter](https://badges.gitter.im/Join Chat.svg)](https://gitter.im/ekg/vcflib?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge) [![Build Status](https://travis-ci.org/vcflib/vcflib.svg?branch=master)](https://travis-ci.org/vcflib/vcflib)
[![Gitter](https://badges.gitter.im/ekg/vcflib.svg)](https://gitter.im/ekg/vcflib?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge) [![Build Status](https://travis-ci.org/vcflib/vcflib.svg?branch=master)](https://travis-ci.org/vcflib/vcflib)
---
## overview
......@@ -25,6 +25,19 @@ It is both:
The API itself provides a quick and extremely permissive method to read and write VCF files.
Extensions and applications of the library provided in the included utilities (*.cpp) comprise the vast bulk of the library's utility for most users.
## download and install
1. Under the repository name, click to copy the clone URL for the repository. ![](https://help.github.com/assets/images/help/repository/clone-repo-clone-url-button.png)
2. Go to the location where you want the cloned directory to be made: `cd <PathWhereIWantToCloneVcflib>`
3. Type `git clone --recursive`, and then paste the URL you copied in Step 1.
4. Enter the cloned directory and type `make` to compile the programs. If you want to use threading type `make openmp` instead of `make`. Only a few VCFLIB tools are threaded.
5. Once make is finished the executables are ready in the folder `<PathWhereIWantToCloneVcflib>/vcflib/bin/`. Set this path as an environment variable in the .bashrc file to access executables form everywhere on your proile OR call the executables from the path where they are.
## usage
vcflib provides a variety of functions for VCF manipulation:
......
libvcflib (1.0.0~rc1+dfsg1-7) UNRELEASED; urgency=medium
libvcflib (1.0.0~rc2+dfsg-1) UNRELEASED; urgency=medium
[ Steffen Moeller ]
* Created debian/upstream/metadata for references to
registries.
-- Steffen Moeller <moeller@debian.org> Mon, 30 Oct 2017 16:12:34 +0100
[ Andreas Tille ]
* New upstream version
* debhelper 11
* Point Vcs fields to salsa.debian.org
* Standards-Version: 4.2.1
* Versioned Build-Depends: libfastahack-dev (>= 0.0+git20160702.bbc645f+dfsg-5~)
* Fix header file name
* Build-Depends: libbz2-dev
* Fix installation target dir
-- Andreas Tille <tille@debian.org> Thu, 13 Sep 2018 16:06:09 +0200
libvcflib (1.0.0~rc1+dfsg1-6) unstable; urgency=medium
......
......@@ -3,19 +3,20 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.
Uploaders: Andreas Tille <tille@debian.org>
Section: science
Priority: optional
Build-Depends: debhelper (>= 10),
Build-Depends: debhelper (>= 11~),
dh-exec,
python-markdown,
libtabixpp-dev,
libbz2-dev,
libdisorder-dev,
libsmithwaterman-dev (>= 0.0+20160702-2),
libssw-dev,
libfastahack-dev,
libfastahack-dev (>= 0.0+git20160702.bbc645f+dfsg-5~),
pkg-config,
libipc-run3-perl
Standards-Version: 4.1.0
Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/libvcflib.git
Vcs-Git: https://anonscm.debian.org/git/debian-med/libvcflib.git
Standards-Version: 4.2.1
Vcs-Browser: https://salsa.debian.org/med-team/libvcflib
Vcs-Git: https://salsa.debian.org/med-team/libvcflib.git
Homepage: https://github.com/ekg/vcflib
Package: libvcflib1
......
bin/*.R usr/lib/R/site-library/vcflib
binaries/*.R usr/lib/R/site-library/vcflib
binaries usr/lib/vcflib
debian/wrapper/* usr/bin
......@@ -12,7 +12,7 @@ Description: Inject two files via quilt patch
--- a/Makefile
+++ b/Makefile
@@ -186,7 +186,12 @@
@@ -191,7 +191,12 @@ $(FASTAHACK): pre
# cd fsom && $(CXX) $(CXXFLAGS) -c fsom.c -lm
$(FILEVERCMP): pre
......
Author: Andreas Tille <tille@debian.org>
Last-Update: Thu, 13 Sep 2018 19:35:33 +0200
Description: Upstream should use consistent installation target dir
--- a/Makefile
+++ b/Makefile
@@ -133,7 +133,7 @@ LDFLAGS = -L$(LIB_DIR) -lvcflib -lhts -l
all: $(OBJECTS) $(BINS) scriptToBin
scriptToBin: $(BINS)
- cp scripts/* bin
+ cp scripts/* $(BIN_DIR)
GIT_VERSION := $(shell git describe --abbrev=4 --dirty --always)
Author: Andreas Tille <tille@debian.org>
Last-Update: Thu, 13 Sep 2018 19:35:33 +0200
Description: The header file is named ssw_cpp.h
--- a/src/Variant.h
+++ b/src/Variant.h
@@ -20,7 +20,7 @@
#include "tabix.hpp"
#include "SmithWatermanGotoh.h"
#include "disorder.h"
-#include "ssw_cpp.hpp"
+#include <ssw_cpp.h>
#include "convert.h"
#include "multichoose.h"
#include "Fasta.h"
......@@ -5,7 +5,7 @@ Description: We provide a local copy of intervaltree in debian/include and
--- a/Makefile
+++ b/Makefile
@@ -160,6 +160,7 @@ multichoose: pre
@@ -166,6 +166,7 @@ multichoose: pre
intervaltree: pre
echo "Source does not contain dir intervaltree"
# cd intervaltree && $(MAKE) && cp *.h* $(VCF_LIB_LOCAL)/$(INC_DIR)/
......
......@@ -15,7 +15,7 @@ Description: There is a dir bin/ containing some R files which
LIB_DIR:=lib
SRC_DIR=src
INC_DIR:=include
@@ -111,7 +111,7 @@ BIN_SOURCES = src/vcfecho.cpp \
@@ -115,7 +115,7 @@ BIN_SOURCES = src/vcfecho.cpp \
# src/vcfsom.cpp
#BINS = $(BIN_SOURCES:.cpp=)
......@@ -24,7 +24,7 @@ Description: There is a dir bin/ containing some R files which
SHORTBINS = $(notdir $(BIN_SOURCES:.cpp=))
# TABIX = tabixpp/tabix.o
@@ -177,7 +177,7 @@ $(FILEVERCMP): pre
@@ -183,7 +183,7 @@ $(FILEVERCMP): pre
ln -sf ../filevercmp/filevercmp.h $(VCF_LIB_LOCAL)/$(INC_DIR)/filevercmp.h
$(SHORTBINS): pre
......@@ -32,4 +32,4 @@ Description: There is a dir bin/ containing some R files which
+ $(MAKE) $(BIN_DIR)/$@
$(BINS): $(BIN_SOURCES) libvcflib.so $(OBJECTS) $(SMITHWATERMAN) $(DISORDER) $(LEFTALIGN) $(INDELALLELE) $(SSW) $(FILEVERCMP) pre intervaltree
$(CXX) src/$(notdir $@).cpp -o $@ $(INCLUDES) $(LDFLAGS) $(CXXFLAGS)
$(CXX) src/$(notdir $@).cpp -o $@ $(INCLUDES) $(LDFLAGS) $(CXXFLAGS) -DVERSION=\"$(GIT_VERSION)\"
......@@ -8,3 +8,5 @@ shared_lib.patch
keep_R_files.patch
use_debian_packaged_libssw.patch
pkg-config.patch
fix_ssw_cpp_header_name.patch
fix_installation.patch
......@@ -4,7 +4,7 @@ Description: Create shared lib instead of static
--- a/Makefile
+++ b/Makefile
@@ -115,11 +115,11 @@ BINS = $(addprefix bin/,$(notdir $(BIN_S
@@ -119,11 +119,11 @@ BINS = $(addprefix bin/,$(notdir $(BIN_S
SHORTBINS = $(notdir $(BIN_SOURCES:.cpp=))
# TABIX = tabixpp/tabix.o
......@@ -21,12 +21,12 @@ Description: Create shared lib instead of static
FSOM = fsom/fsom.o
FILEVERCMP = filevercmp/filevercmp.o
@@ -138,8 +138,11 @@ CXXFLAGS = -O3 -D_FILE_OFFSET_BITS=64 -s
@@ -143,8 +143,11 @@ CXXFLAGS = -O3 -D_FILE_OFFSET_BITS=64 -s
SSW = src/ssw.o src/ssw_cpp.o
-ssw.o: src/ssw.h
-ssw_cpp.o:src/ssw_cpp.h
-ssw.o: src/ssw.hpp
-ssw_cpp.o:src/ssw_cpp.hpp
+src/ssw.o: src/ssw.h src/ssw.c
+ $(CXX) -c $(CFLAGS) -fPIC -o $@ src/$(*F).c
+
......@@ -35,16 +35,16 @@ Description: Create shared lib instead of static
openmp:
$(MAKE) CXXFLAGS="$(CXXFLAGS) -fopenmp -D HAS_OPENMP"
@@ -151,7 +154,7 @@ gprof:
$(MAKE) CXXFLAGS="$(CXXFLAGS) -pg" all
@@ -157,7 +160,7 @@ gprof:
$(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)/
+ $(CXX) -c $(CFLAGS) -fPIC -o $@ src/$(*F).cpp $(INCLUDES) $(LDFLAGS) $(CXXFLAGS) && cp src/*.h* $(VCF_LIB_LOCAL)/$(INC_DIR)/
multichoose: pre
echo "Source does not contain dir multichoose"
@@ -162,22 +165,6 @@ intervaltree: pre
@@ -168,22 +171,6 @@ intervaltree: pre
# cd intervaltree && $(MAKE) && cp *.h* $(VCF_LIB_LOCAL)/$(INC_DIR)/
mkdir -p $(VCF_LIB_LOCAL)/$(INC_DIR)/ && cp -a debian/include/* $(VCF_LIB_LOCAL)/$(INC_DIR)/
......@@ -67,7 +67,7 @@ Description: Create shared lib instead of static
#$(FSOM):
# cd fsom && $(CXX) $(CXXFLAGS) -c fsom.c -lm
@@ -186,19 +173,20 @@ $(FILEVERCMP): pre
@@ -192,18 +179,20 @@ $(FILEVERCMP): pre
#cp /usr/share/gnulib/lib/filevercmp.* filevercmp
#echo 'Proper use of filevercmp would be: `gnulib-tool --import filevercmp` - but it needs ./configure.ac'
#We here go with quilt patches from upstream files
......@@ -80,21 +80,20 @@ Description: Create shared lib instead of static
-$(BINS): $(BIN_SOURCES) libvcflib.a $(OBJECTS) $(SMITHWATERMAN) $(DISORDER) $(LEFTALIGN) $(INDELALLELE) $(SSW) $(FILEVERCMP) pre intervaltree
+$(BINS): $(BIN_SOURCES) libvcflib.so $(OBJECTS) $(SMITHWATERMAN) $(DISORDER) $(LEFTALIGN) $(INDELALLELE) $(SSW) $(FILEVERCMP) pre intervaltree
$(CXX) src/$(notdir $@).cpp -o $@ $(INCLUDES) $(LDFLAGS) $(CXXFLAGS)
$(CXX) src/$(notdir $@).cpp -o $@ $(INCLUDES) $(LDFLAGS) $(CXXFLAGS) -DVERSION=\"$(GIT_VERSION)\"
-libvcflib.a: $(OBJECTS) $(SMITHWATERMAN) $(REPEATS) $(DISORDER) $(LEFTALIGN) $(INDELALLELE) $(SSW) $(FILEVERCMP) pre
- ar rs libvcflib.a $(OBJECTS) $(SSW) $(FILEVERCMP)
- cp libvcflib.a $(LIB_DIR)
-
+libvcflib.so: $(OBJECTS) $(SMITHWATERMAN) $(REPEATS) $(DISORDER) $(LEFTALIGN) $(INDELALLELE) $(SSW) $(FILEVERCMP) pre
+ # ar rs libvcflib.a $(OBJECTS) $(SSW) $(FILEVERCMP)
+ gcc -shared -Wl,-soname -Wl,libvcflib.so.1 -o libvcflib.so.1 $(OBJECTS) $(SSW) $(FILEVERCMP)
+ ln -s libvcflib.so.1 libvcflib.so
+ cp -a libvcflib.so* $(LIB_DIR)
test: $(BINS)
@prove -Itests/lib -w tests/*.t
@@ -218,7 +206,7 @@ update: pull all
@@ -224,7 +213,7 @@ update: pull all
clean:
rm -f $(BINS) $(OBJECTS)
rm -f ssw_cpp.o ssw.o
......
......@@ -4,27 +4,37 @@ Description: Use Debian packaged libfastahack (and libdisorder)
--- a/Makefile
+++ b/Makefile
@@ -115,7 +115,6 @@ BINS = $(addprefix bin/,$(notdir $(BIN_S
@@ -119,7 +119,6 @@ BINS = $(addprefix bin/,$(notdir $(BIN_S
SHORTBINS = $(notdir $(BIN_SOURCES:.cpp=))
# TABIX = tabixpp/tabix.o
-FASTAHACK = fastahack/Fasta.o
-# FASTAHACK = fastahack/Fasta.o
SMITHWATERMAN = smithwaterman/SmithWatermanGotoh.o
REPEATS = smithwaterman/Repeats.o
INDELALLELE = smithwaterman/IndelAllele.o
@@ -124,9 +123,8 @@ LEFTALIGN = smithwaterman/LeftAlign.o
@@ -128,8 +127,8 @@ LEFTALIGN = smithwaterman/LeftAlign.o
FSOM = fsom/fsom.o
FILEVERCMP = filevercmp/filevercmp.o
-INCLUDES = `pkg-config --cflags libsmithwaterman` -I$(INC_DIR)
-LDFLAGS += -L$(LIB_DIR) -lvcflib -lhts -lpthread -lz -lm -fopenmp -ltabixpp `pkg-config --libs libsmithwaterman`
-
-LDFLAGS = -L$(LIB_DIR) -lvcflib -lhts -lpthread -lz -lm -llzma -lbz2 -ltabixpp `pkg-config --libs libsmithwaterman`
+INCLUDES = `pkg-config --cflags libsmithwaterman` `pkg-config --cflags libfastahack` -I$(INC_DIR)
+LDFLAGS += -L$(LIB_DIR) -lvcflib -lhts -lpthread -lz -lm -fopenmp -ltabixpp `pkg-config --libs libsmithwaterman` `pkg-config --libs libfastahack` -ldisorder
+LDFLAGS = -L$(LIB_DIR) -lvcflib -lhts -lpthread -lz -lm -llzma -lbz2 -ltabixpp `pkg-config --libs libsmithwaterman` `pkg-config --libs libfastahack` -ldisorder
all: $(OBJECTS) $(BINS) scriptToBin
@@ -156,8 +155,8 @@ profiling:
gprof:
$(MAKE) CXXFLAGS="$(CXXFLAGS) -pg" all
all: $(OBJECTS) $(BINS)
-$(OBJECTS): $(SOURCES) $(HEADERS) $(TABIX) multichoose pre $(SMITHWATERMAN) $(FILEVERCMP) $(FASTAHACK)
-$(OBJECTS): $(SOURCES) $(HEADERS) multichoose pre $(SMITHWATERMAN) $(FILEVERCMP) $(FASTAHACK)
+$(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)/
@@ -179,9 +177,6 @@ $(LEFTALIGN): $(SMITHWATERMAN)
multichoose: pre
@@ -184,9 +183,6 @@ $(LEFTALIGN): $(SMITHWATERMAN)
$(INDELALLELE): $(SMITHWATERMAN)
......@@ -34,13 +44,13 @@ Description: Use Debian packaged libfastahack (and libdisorder)
#$(FSOM):
# cd fsom && $(CXX) $(CXXFLAGS) -c fsom.c -lm
@@ -196,11 +191,11 @@ $(FILEVERCMP): pre
@@ -201,11 +197,11 @@ $(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)
$(CXX) src/$(notdir $@).cpp -o $@ $(INCLUDES) $(LDFLAGS) $(CXXFLAGS) -DVERSION=\"$(GIT_VERSION)\"
-libvcflib.a: $(OBJECTS) $(SMITHWATERMAN) $(REPEATS) $(FASTAHACK) $(DISORDER) $(LEFTALIGN) $(INDELALLELE) $(SSW) $(FILEVERCMP) pre
- ar rs libvcflib.a $(OBJECTS) $(FASTAHACK) $(SSW) $(FILEVERCMP)
......@@ -49,7 +59,7 @@ Description: Use Debian packaged libfastahack (and libdisorder)
cp libvcflib.a $(LIB_DIR)
@@ -229,6 +224,6 @@ clean:
@@ -234,6 +230,6 @@ clean:
rm -rf $(OBJ_DIR)
# cd tabixpp && make clean
# cd smithwaterman && make clean
......
......@@ -6,7 +6,7 @@ Description: Use Debian packaged libssw (while its not clear
--- a/Makefile
+++ b/Makefile
@@ -136,13 +136,7 @@ CXXFLAGS = -O3 -D_FILE_OFFSET_BITS=64 -s
@@ -141,13 +141,7 @@ CXXFLAGS = -O3 -D_FILE_OFFSET_BITS=64 -s
#CXXFLAGS = -O2
#CXXFLAGS = -pedantic -Wall -Wshadow -Wpointer-arith -Wcast-qual
......
......@@ -4,18 +4,18 @@ Description: Use Debian packaged libsmithwaterman
--- a/Makefile
+++ b/Makefile
@@ -124,8 +124,8 @@ LEFTALIGN = smithwaterman/LeftAlign.o
@@ -128,8 +128,8 @@ LEFTALIGN = smithwaterman/LeftAlign.o
FSOM = fsom/fsom.o
FILEVERCMP = filevercmp/filevercmp.o
-INCLUDES = -I$(INC_DIR)
-LDFLAGS = -L$(LIB_DIR) -lvcflib -lhts -lpthread -lz -lm -fopenmp -ltabixpp
-LDFLAGS = -L$(LIB_DIR) -lvcflib -lhts -lpthread -lz -lm -llzma -lbz2 -ltabixpp
+INCLUDES = `pkg-config --cflags libsmithwaterman` -I$(INC_DIR)
+LDFLAGS += -L$(LIB_DIR) -lvcflib -lhts -lpthread -lz -lm -fopenmp -ltabixpp `pkg-config --libs libsmithwaterman`
+LDFLAGS = -L$(LIB_DIR) -lvcflib -lhts -lpthread -lz -lm -llzma -lbz2 -ltabixpp `pkg-config --libs libsmithwaterman`
all: $(OBJECTS) $(BINS) scriptToBin
all: $(OBJECTS) $(BINS)
@@ -156,17 +156,20 @@ $(OBJECTS): $(SOURCES) $(HEADERS) multic
@@ -161,17 +161,20 @@ $(OBJECTS): $(SOURCES) $(HEADERS) multic
$(CXX) -c -o $@ src/$(*F).cpp $(INCLUDES) $(LDFLAGS) $(CXXFLAGS) && cp src/*.h* $(VCF_LIB_LOCAL)/$(INC_DIR)/
multichoose: pre
......@@ -39,8 +39,8 @@ Description: Use Debian packaged libsmithwaterman
$(DISORDER): $(SMITHWATERMAN)
@@ -192,7 +195,7 @@ $(BINS): $(BIN_SOURCES) libvcflib.a $(OB
$(CXX) src/$(notdir $@).cpp -o $@ $(INCLUDES) $(LDFLAGS) $(CXXFLAGS)
@@ -197,7 +200,7 @@ $(BINS): $(BIN_SOURCES) libvcflib.a $(OB
$(CXX) src/$(notdir $@).cpp -o $@ $(INCLUDES) $(LDFLAGS) $(CXXFLAGS) -DVERSION=\"$(GIT_VERSION)\"
libvcflib.a: $(OBJECTS) $(SMITHWATERMAN) $(REPEATS) $(FASTAHACK) $(DISORDER) $(LEFTALIGN) $(INDELALLELE) $(SSW) $(FILEVERCMP) pre
- ar rs libvcflib.a $(OBJECTS) smithwaterman/sw.o $(FASTAHACK) $(SSW) $(FILEVERCMP)
......@@ -48,7 +48,7 @@ Description: Use Debian packaged libsmithwaterman
cp libvcflib.a $(LIB_DIR)
@@ -220,7 +223,7 @@ clean:
@@ -225,7 +228,7 @@ clean:
rm -rf $(INC_DIR)
rm -rf $(OBJ_DIR)
# cd tabixpp && make clean
......
......@@ -4,36 +4,38 @@ Description: Use Debian packaged libtabixpp
--- a/Makefile
+++ b/Makefile
@@ -114,7 +114,7 @@ BIN_SOURCES = src/vcfecho.cpp \
@@ -118,8 +118,8 @@ BIN_SOURCES = src/vcfecho.cpp \
BINS = $(addprefix bin/,$(notdir $(BIN_SOURCES:.cpp=)))
SHORTBINS = $(notdir $(BIN_SOURCES:.cpp=))
-TABIX = tabixpp/tabix.o
-FASTAHACK = fastahack/Fasta.o
+# TABIX = tabixpp/tabix.o
FASTAHACK = fastahack/Fasta.o
+# FASTAHACK = fastahack/Fasta.o
SMITHWATERMAN = smithwaterman/SmithWatermanGotoh.o
REPEATS = smithwaterman/Repeats.o
@@ -124,8 +124,8 @@ LEFTALIGN = smithwaterman/LeftAlign.o
INDELALLELE = smithwaterman/IndelAllele.o
@@ -128,9 +128,8 @@ LEFTALIGN = smithwaterman/LeftAlign.o
FSOM = fsom/fsom.o
FILEVERCMP = filevercmp/filevercmp.o
-INCLUDES = -Itabixpp/htslib -I$(INC_DIR) -L. -Ltabixpp/htslib
-LDFLAGS = -L$(LIB_DIR) -lvcflib -lhts -lpthread -lz -lm -fopenmp
-LDFLAGS = -L$(LIB_DIR) -lvcflib -lhts -lpthread -lz -lm -llzma -lbz2
-
+INCLUDES = -I$(INC_DIR)
+LDFLAGS = -L$(LIB_DIR) -lvcflib -lhts -lpthread -lz -lm -fopenmp -ltabixpp
+LDFLAGS = -L$(LIB_DIR) -lvcflib -lhts -lpthread -lz -lm -llzma -lbz2 -ltabixpp
all: $(OBJECTS) $(BINS) scriptToBin
all: $(OBJECTS) $(BINS)
@@ -152,7 +152,7 @@ profiling:
gprof:
@@ -158,6 +157,7 @@ gprof:
$(MAKE) CXXFLAGS="$(CXXFLAGS) -pg" all
-$(OBJECTS): $(SOURCES) $(HEADERS) $(TABIX) multichoose pre $(SMITHWATERMAN) $(FILEVERCMP)
+$(OBJECTS): $(SOURCES) $(HEADERS) multichoose pre $(SMITHWATERMAN) $(FILEVERCMP)
$(OBJECTS): $(SOURCES) $(HEADERS) $(TABIX) multichoose pre $(SMITHWATERMAN) $(FILEVERCMP) $(FASTAHACK)
+$(OBJECTS): $(SOURCES) $(HEADERS) multichoose pre $(SMITHWATERMAN) $(FILEVERCMP) $(FASTAHACK)
$(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
@@ -167,7 +167,8 @@ intervaltree: pre
cd intervaltree && $(MAKE) && cp *.h* $(VCF_LIB_LOCAL)/$(INC_DIR)/
$(TABIX): pre
......@@ -43,9 +45,9 @@ Description: Use Debian packaged libtabixpp
$(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
@@ -195,8 +196,8 @@ $(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)
$(CXX) src/$(notdir $@).cpp -o $@ $(INCLUDES) $(LDFLAGS) $(CXXFLAGS) -DVERSION=\"$(GIT_VERSION)\"
-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)
......@@ -54,7 +56,7 @@ Description: Use Debian packaged libtabixpp
cp libvcflib.a $(LIB_DIR)
@@ -218,7 +219,7 @@ clean:
@@ -223,7 +224,7 @@ clean:
rm -rf $(LIB_DIR)
rm -rf $(INC_DIR)
rm -rf $(OBJ_DIR)
......