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#OBJ_DIR = ./
HEADERS = src/Variant.h \
src/split.h \
src/pdflib.hpp \
src/var.hpp \
src/cdflib.hpp \
src/rnglib.hpp \
src/join.h
SOURCES = src/Variant.cpp \
src/rnglib.cpp \
src/var.cpp \
src/pdflib.cpp \
src/cdflib.cpp \
src/split.cpp
OBJECTS= $(SOURCES:.cpp=.o)
VCF_LIB_LOCAL:=$(shell pwd)
BIN_DIR:=binaries
LIB_DIR:=lib
SRC_DIR=src
INC_DIR:=include
OBJ_DIR:=obj
# TODO
#vcfstats.cpp
BIN_SOURCES = src/vcfecho.cpp \
src/dumpContigsFromHeader.cpp \
src/bFst.cpp \
src/hapLrt.cpp \
src/popStats.cpp \
src/wcFst.cpp \
src/iHS.cpp \
src/segmentFst.cpp \
src/segmentIhs.cpp \
src/genotypeSummary.cpp \
src/sequenceDiversity.cpp \
src/pFst.cpp \
src/smoother.cpp \
src/LD.cpp \
src/plotHaps.cpp \
src/abba-baba.cpp \
src/permuteGPAT++.cpp \
src/permuteSmooth.cpp \
src/normalize-iHS.cpp \
src/meltEHH.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 $(BIN_DIR)/,$(notdir $(BIN_SOURCES:.cpp=)))
SHORTBINS = $(notdir $(BIN_SOURCES:.cpp=))
# TABIX = tabixpp/tabix.o
# SMITHWATERMAN = smithwaterman/SmithWatermanGotoh.o
# REPEATS = smithwaterman/Repeats.o
# INDELALLELE = smithwaterman/IndelAllele.o
# DISORDER = smithwaterman/disorder.o
# LEFTALIGN = smithwaterman/LeftAlign.o
FSOM = fsom/fsom.o
FILEVERCMP = filevercmp/filevercmp.o
INCLUDES = `pkg-config --cflags libsmithwaterman` `pkg-config --cflags libfastahack` -I$(INC_DIR)
LDFLAGS += -L$(LIB_DIR) -lvcflib -lhts -lpthread -lz -lm -fopenmp -ltabixpp `pkg-config --libs libsmithwaterman` `pkg-config --libs libfastahack` -ldisorder
all: $(OBJECTS) $(BINS)
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 = -O2
#CXXFLAGS = -pedantic -Wall -Wshadow -Wpointer-arith -Wcast-qual
SSW =
openmp:
$(MAKE) CXXFLAGS="$(CXXFLAGS) -fopenmp -D HAS_OPENMP"
profiling:
$(MAKE) CXXFLAGS="$(CXXFLAGS) -g" all
gprof:
$(MAKE) CXXFLAGS="$(CXXFLAGS) -pg" all
$(OBJECTS): $(SOURCES) $(HEADERS) multichoose pre $(SMITHWATERMAN) $(FILEVERCMP)
$(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"
# cd multichoose && $(MAKE) && cp *.h* $(VCF_LIB_LOCAL)/$(INC_DIR)/
intervaltree: pre
echo "Source does not contain dir intervaltree"
# 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)/
#$(FSOM):
# cd fsom && $(CXX) $(CXXFLAGS) -c fsom.c -lm
$(FILEVERCMP): pre
#mkdir -p filevercmp
#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
cd filevercmp && $(CXX) $(CXXFLAGS) -fPIC -c filevercmp.c
ln -sf ../filevercmp/filevercmp.h $(VCF_LIB_LOCAL)/$(INC_DIR)/filevercmp.h
$(SHORTBINS): pre
$(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)
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
pre:
if [ ! -d $(BIN_DIR) ]; then mkdir -p $(BIN_DIR); fi
if [ ! -d $(LIB_DIR) ]; then mkdir -p $(LIB_DIR); fi
if [ ! -d $(INC_DIR) ]; then mkdir -p $(INC_DIR); fi
if [ ! -d $(OBJ_DIR) ]; then mkdir -p $(OBJ_DIR); fi
pull:
git pull
update: pull all
clean:
rm -f $(BINS) $(OBJECTS)
rm -f ssw_cpp.o ssw.o
rm -f libvcflib.so
rm -rf $(BIN_DIR)
rm -rf $(LIB_DIR)
rm -rf $(INC_DIR)
rm -rf $(OBJ_DIR)
# cd tabixpp && make clean
# cd smithwaterman && make clean
# cd fastahack && make clean
.PHONY: clean all test pre
|
