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################################################################################
# Makefile for FreeBayes
# Erik Garrison, 2010
# Boston College
################################################################################
# Compiler
CXX=g++ ${CXXFLAGS}
C=gcc
export CXXFLAGS
export C
export CC
export CXX
export LDFLAGS
export LIBFLAGS
# Compiler flags
CFLAGS=-O3 -D_FILE_OFFSET_BITS=64 -g -std=gnu++11
#CFLAGS=-O3 -static -D VERBOSE_DEBUG # enables verbose debugging via --debug2
LIBS = -lbamtools -ltabixpp -lz -lm -lpthread `pkg-config --libs libvcflib` `pkg-config --libs htslib` `pkg-config --libs libseqlib` `pkg-config --libs jsoncpp`
INCLUDE = -I../ttmath -I/usr/include/bamtools `pkg-config --cflags libvcflib` `pkg-config --cflags libseqlib` `pkg-config --cflags htslib` `pkg-config --cflags jsoncpp`
all: autoversion ../bin/freebayes ../bin/bamleftalign
static:
$(MAKE) CXXFLAGS="$(CXXFLAGS) -static" all
debug:
$(MAKE) CXXFLAGS="$(CXXFLAGS) -D VERBOSE_DEBUG -g -rdynamic" all
profiling:
$(MAKE) CFLAGS="$(CFLAGS) -g" all
gprof:
$(MAKE) CXXFLAGS="$(CXXFLAGS) -pg" all
.PHONY: all static debug profiling gprof
OBJECTS=BedReader.o \
CNV.o \
fastlz.o \
Fasta.o \
Parameters.o \
Allele.o \
Sample.o \
Result.o \
AlleleParser.o \
Utility.o \
Genotype.o \
DataLikelihood.o \
Multinomial.o \
Ewens.o \
ResultData.o \
Dirichlet.o \
Marginals.o \
split.o \
LeftAlign.o \
IndelAllele.o \
Bias.o \
Contamination.o \
NonCall.o \
SegfaultHandler.o
HEADERS=multichoose.h version_git.h
# executables
freebayes ../bin/freebayes: freebayes.o $(OBJECTS) $(HEADERS) $(seqlib)
$(CXX) $(CXXFLAGS) $(INCLUDE) freebayes.o $(OBJECTS) -o ../bin/freebayes $(LIBS)
alleles ../bin/alleles: alleles.o $(OBJECTS) $(HEADERS) $(seqlib)
$(CXX) $(CXXFLAGS) $(INCLUDE) alleles.o $(OBJECTS) -o ../bin/alleles $(LIBS)
dummy ../bin/dummy: dummy.o $(OBJECTS) $(HEADERS) $(seqlib)
$(CXX) $(CXXFLAGS) $(INCLUDE) dummy.o $(OBJECTS) -o ../bin/dummy $(LIBS)
bamleftalign ../bin/bamleftalign: bamleftalign.o Fasta.o LeftAlign.o IndelAllele.o split.o
$(CXX) $(CXXFLAGS) $(INCLUDE) bamleftalign.o $(OBJECTS) -o ../bin/bamleftalign $(LIBS)
bamfiltertech ../bin/bamfiltertech: bamfiltertech.o $(OBJECTS) $(HEADERS)
$(CXX) $(CXXFLAGS) $(INCLUDE) bamfiltertech.o $(OBJECTS) -o ../bin/bamfiltertech $(LIBS)
# objects
Fasta.o: Fasta.cpp Utility.o
$(CXX) $(CXXFLAGS) $(INCLUDE) -c Fasta.cpp
alleles.o: alleles.cpp AlleleParser.o Allele.o
$(CXX) $(CXXFLAGS) $(INCLUDE) -c alleles.cpp
dummy.o: dummy.cpp AlleleParser.o Allele.o
$(CXX) $(CXXFLAGS) $(INCLUDE) -c dummy.cpp
freebayes.o: freebayes.cpp TryCatch.h
$(CXX) $(CXXFLAGS) $(INCLUDE) -c freebayes.cpp
fastlz.o: fastlz.c fastlz.h
$(C) $(CFLAGS) $(INCLUDE) -c fastlz.c
Parameters.o: Parameters.cpp Parameters.h Version.h
$(CXX) $(CXXFLAGS) $(INCLUDE) -c Parameters.cpp
Allele.o: Allele.cpp Allele.h multichoose.h Genotype.h
$(CXX) $(CXXFLAGS) $(INCLUDE) -c Allele.cpp
Sample.o: Sample.cpp Sample.h
$(CXX) $(CXXFLAGS) $(INCLUDE) -c Sample.cpp
Genotype.o: Genotype.cpp Genotype.h Allele.h multipermute.h
$(CXX) $(CXXFLAGS) $(INCLUDE) -c Genotype.cpp
Ewens.o: Ewens.cpp Ewens.h
$(CXX) $(CXXFLAGS) $(INCLUDE) -c Ewens.cpp
AlleleParser.o: AlleleParser.cpp AlleleParser.h multichoose.h Parameters.h
$(CXX) $(CXXFLAGS) $(INCLUDE) -c AlleleParser.cpp
Utility.o: Utility.cpp Utility.h Sum.h Product.h
$(CXX) $(CXXFLAGS) $(INCLUDE) -c Utility.cpp
SegfaultHandler.o: SegfaultHandler.cpp SegfaultHandler.h
$(CXX) $(CXXFLAGS) $(INCLUDE) -c SegfaultHandler.cpp
Dirichlet.o: Dirichlet.h Dirichlet.cpp Sum.h Product.h
$(CXX) $(CXXFLAGS) $(INCLUDE) -c Dirichlet.cpp
Multinomial.o: Multinomial.h Multinomial.cpp Sum.h Product.h Utility.h
$(CXX) $(CXXFLAGS) $(INCLUDE) -c Multinomial.cpp
DataLikelihood.o: DataLikelihood.cpp DataLikelihood.h Sum.h Product.h
$(CXX) $(CXXFLAGS) $(INCLUDE) -c DataLikelihood.cpp
Marginals.o: Marginals.cpp Marginals.h
$(CXX) $(CXXFLAGS) $(INCLUDE) -c Marginals.cpp
ResultData.o: ResultData.cpp ResultData.h Result.h Result.cpp Allele.h Utility.h Genotype.h AlleleParser.h Version.h
$(CXX) $(CXXFLAGS) $(INCLUDE) -c ResultData.cpp
Result.o: Result.cpp Result.h
$(CXX) $(CXXFLAGS) $(INCLUDE) -c Result.cpp
NonCall.o: NonCall.cpp NonCall.h
$(CXX) $(CXXFLAGS) $(INCLUDE) -c NonCall.cpp
BedReader.o: BedReader.cpp BedReader.h
$(CXX) $(CXXFLAGS) $(INCLUDE) -c BedReader.cpp
CNV.o: CNV.cpp CNV.h
$(CXX) $(CXXFLAGS) $(INCLUDE) -c CNV.cpp
Bias.o: Bias.cpp Bias.h
$(CXX) $(CXXFLAGS) $(INCLUDE) -c Bias.cpp
split.o: split.h split.cpp
$(CXX) $(CXXFLAGS) $(INCLUDE) -c split.cpp
bamleftalign.o: bamleftalign.cpp LeftAlign.cpp
$(CXX) $(CXXFLAGS) $(INCLUDE) -c bamleftalign.cpp
bamfiltertech.o: bamfiltertech.cpp
$(CXX) $(CXXFLAGS) $(INCLUDE) -c bamfiltertech.cpp
LeftAlign.o: LeftAlign.h LeftAlign.cpp
$(CXX) $(CXXFLAGS) $(INCLUDE) -c LeftAlign.cpp
IndelAllele.o: IndelAllele.cpp IndelAllele.h
$(CXX) $(CXXFLAGS) $(INCLUDE) -c IndelAllele.cpp
VERSION_FILE=./version_git.h
RELEASED_VERSION_FILE=./version_release.txt
## versioning system from BedTools
##
## For freebayes developers (not users):
## When you want to release (and tag) a new version, run:
## $ make setversion VERSION=v2.17.2
## This will:
## 1. Update the "/src/utils/version/version_release.txt" file
## 2. Commit the file
## 3. Git-Tag the commit with the latest version
##
.PHONY: setversion
setversion:
ifeq "$(VERSION)" ""
$(error please set VERSION variable to the new version (e.g "make setversion VERSION=v2.17.2"))
endif
@echo "# This file was auto-generated by running \"make setversion VERSION=$(VERSION)\"" > "$(RELEASED_VERSION_FILE)"
@echo "# on $$(date) ." >> "$(RELEASED_VERSION_FILE)"
@echo "# Please do not edit or commit this file manually." >> "$(RELEASED_VERSION_FILE)"
@echo "#" >> "$(RELEASED_VERSION_FILE)"
@echo "$(VERSION)" >> $(RELEASED_VERSION_FILE)
@git add $(RELEASED_VERSION_FILE)
@git commit -q -m "Setting Release-Version $(VERSION)"
@git tag "$(VERSION)"
@echo "Version updated to $(VERSION)."
@echo ""
@echo "Don't forget to push the commits AND the tags:"
@echo " git push --all --tags"
@echo ""
## Automatic version detection
##
## What's going on here?
## 1. If there's a ".git" repository - use the version from the repository.
## ignore any released-version file. git repository is authorative.
##
## 2, If there's no ".git" repository,
## get the "released" version number from the release-version file.
##
## 3. Compare the detected version (from steps 1,2) to the current string
## in ./src/utils/version/version_git.h .
## If they differ, update the header file - will cause a recompilation
## of version.o .
##
.PHONY: autoversion
autoversion:
@( \
if [ -d "../.git" ] && which git > /dev/null ; then \
DETECTED_VERSION=$$(git describe --always --tags --dirty) ; \
else \
DETECTED_VERSION=$$(grep -v "^#" "$(RELEASED_VERSION_FILE)") ; \
fi ; \
\
CURRENT_VERSION="" ; \
[ -e "$(VERSION_FILE)" ] && CURRENT_VERSION=$$(grep "define VERSION_GIT " "$(VERSION_FILE)" | cut -f3 -d" " | sed 's/"//g') ; \
\
echo "DETECTED_VERSION = $$DETECTED_VERSION" ; \
echo "CURRENT_VERSION = $$CURRENT_VERSION" ; \
if [ "$${DETECTED_VERSION}" != "$${CURRENT_VERSION}" ] ; then \
echo "Updating version file." ; \
echo "#ifndef VERSION_GIT_H" > $(VERSION_FILE) ; \
echo "#define VERSION_GIT_H" >> $(VERSION_FILE) ; \
echo "#define VERSION_GIT \"$${DETECTED_VERSION}\"" >> $(VERSION_FILE) ; \
echo "#endif /* VERSION_GIT_H */" >> $(VERSION_FILE) ; \
fi )
clean:
rm -rf *.o *.cgh *~ freebayes alleles ../bin/freebayes ../bin/alleles ../vcflib/*.o ../vcflib/tabixpp/*.{o,a} tabix.hpp
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