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Makefile.am
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ACLOCAL_AMFLAGS = -I m4
EXTRA_DIST = doc/jellyfish.pdf doc/jellyfish.man README LICENSE # jellyfish.spec
man1_MANS = doc/jellyfish.man
pkgconfigdir = $(libdir)/pkgconfig
pkgconfig_DATA = jellyfish-2.0.pc
AM_LDFLAGS = -lpthread # $(VALGRIND_LIBS)
AM_CPPFLAGS = -Wall -Wnon-virtual-dtor -I$(srcdir) -I$(srcdir)/include -g -O3 $(VALGRIND_CFLAGS)
AM_CXXFLAGS = $(ALL_CXXFLAGS) -g -O3
noinst_HEADERS = $(YAGGO_SOURCES)
bin_PROGRAMS =
dist_bin_SCRIPTS =
data_DATA =
BUILT_SOURCES = $(YAGGO_SOURCES)
CLEANFILES =
DISTCLEANFILES = $(BUILT_SOURCES)
# Yaggo automatic rules with silencing
V_YAGGO = $(V_YAGGO_$(V))
V_YAGGO_ = $(V_YAGGO_$(AM_DEFAULT_VERBOSITY))
V_YAGGO_0 = @echo " YAGGO " $@;
.yaggo.hpp:
$(V_YAGGO)$(YAGGO) --license $(srcdir)/header-license -o $@ $<
YAGGO_SOURCES = # Append all file to be built by yaggo
# What to build
bin_PROGRAMS += bin/jellyfish
lib_LTLIBRARIES = libjellyfish-2.0.la
LDADD = libjellyfish-2.0.la # $(VALGRIND_LIBS)
check_PROGRAMS = bin/generate_sequence
############################
# Build Jellyfish the exec #
############################
bin_jellyfish_SOURCES = sub_commands/jellyfish.cc \
sub_commands/count_main.cc \
sub_commands/info_main.cc \
sub_commands/dump_main.cc \
sub_commands/histo_main.cc \
sub_commands/stats_main.cc \
sub_commands/merge_main.cc \
sub_commands/bc_main.cc \
sub_commands/query_main.cc \
sub_commands/cite_main.cc \
sub_commands/mem_main.cc \
jellyfish/merge_files.cc
bin_jellyfish_LDFLAGS = $(AM_LDFLAGS) $(STATIC_FLAGS)
YAGGO_SOURCES += sub_commands/count_main_cmdline.hpp \
sub_commands/info_main_cmdline.hpp \
sub_commands/dump_main_cmdline.hpp \
sub_commands/histo_main_cmdline.hpp \
sub_commands/stats_main_cmdline.hpp \
sub_commands/merge_main_cmdline.hpp \
sub_commands/bc_main_cmdline.hpp \
sub_commands/query_main_cmdline.hpp \
sub_commands/cite_main_cmdline.hpp \
sub_commands/mem_main_cmdline.hpp
######################################
# Build Jellyfish the shared library #
######################################
libjellyfish_2_0_la_LDFLAGS = -version-info 2:0:0
libjellyfish_2_0_la_SOURCES = lib/rectangular_binary_matrix.cc \
lib/mer_dna.cc lib/storage.cc \
lib/allocators_mmap.cc lib/misc.cc \
lib/int128.cc lib/thread_exec.cc \
lib/jsoncpp.cpp lib/time.cc \
lib/generator_manager.cc
library_includedir=$(includedir)/jellyfish-@PACKAGE_VERSION@/jellyfish
JFI = include/jellyfish
library_include_HEADERS = $(JFI)/allocators_mmap.hpp \
$(JFI)/backtrace.hpp $(JFI)/atomic_gcc.hpp \
$(JFI)/large_hash_array.hpp $(JFI)/err.hpp \
$(JFI)/misc.hpp \
$(JFI)/offsets_key_value.hpp \
$(JFI)/int128.hpp \
$(JFI)/rectangular_binary_matrix.hpp \
$(JFI)/mer_dna.hpp $(JFI)/storage.hpp \
$(JFI)/simple_circular_buffer.hpp \
$(JFI)/circular_buffer.hpp \
$(JFI)/atomic_field.hpp \
$(JFI)/compare_and_swap.hpp \
$(JFI)/divisor.hpp \
$(JFI)/large_hash_iterator.hpp \
$(JFI)/jellyfish.hpp $(JFI)/thread_exec.hpp \
$(JFI)/stream_iterator.hpp \
$(JFI)/mer_overlap_sequence_parser.hpp \
$(JFI)/whole_sequence_parser.hpp \
$(JFI)/binary_dumper.hpp \
$(JFI)/sorted_dumper.hpp \
$(JFI)/text_dumper.hpp $(JFI)/dumper.hpp \
$(JFI)/time.hpp $(JFI)/mer_heap.hpp \
$(JFI)/token_ring.hpp \
$(JFI)/locks_pthread.hpp \
$(JFI)/file_header.hpp \
$(JFI)/generic_file_header.hpp \
$(JFI)/json.h $(JFI)/hash_counter.hpp \
$(JFI)/mapped_file.hpp \
$(JFI)/mer_dna_bloom_counter.hpp \
$(JFI)/bloom_common.hpp \
$(JFI)/bloom_counter2.hpp \
$(JFI)/bloom_filter.hpp \
$(JFI)/cooperative_pool.hpp \
$(JFI)/cooperative_pool2.hpp \
$(JFI)/stream_manager.hpp \
$(JFI)/generator_manager.hpp \
$(JFI)/cpp_array.hpp \
$(JFI)/mer_iterator.hpp \
$(JFI)/atomic_bits_array.hpp \
$(JFI)/stdio_filebuf.hpp \
$(JFI)/mer_qual_iterator.hpp
noinst_HEADERS += jellyfish/fstream_default.hpp jellyfish/dbg.hpp \
jellyfish/randomc.h jellyfish/merge_files.hpp
###############
# Build tests #
###############
bin_generate_sequence_SOURCES = jellyfish/generate_sequence.cc \
jellyfish/mersenne.cpp \
jellyfish/backtrace.cc \
jellyfish/dbg.cc
YAGGO_SOURCES += jellyfish/generate_sequence_cmdline.hpp
#########
# Tests #
#########
TEST_EXTENSIONS = .sh
SH_LOG_COMPILER = $(SHELL)
AM_SH_LOG_FLAGS =
TESTS = tests/generate_sequence.sh tests/parallel_hashing.sh \
tests/merge.sh tests/bloom_filter.sh tests/big.sh \
tests/subset_hashing.sh tests/multi_file.sh \
tests/bloom_counter.sh tests/large_key.sh
EXTRA_DIST += $(TESTS)
clean-local: clean-local-check
.PHONY: clean-local-check
clean-local-check:
-cd tests; rm -f *
tests/parallel_hashing.log: tests/generate_sequence.log
tests/subset_hashing.log: tests/generate_sequence.log
tests/bloom_filter.log: tests/generate_sequence.log
tests/bloom_counter.log: tests/generate_sequence.log
tests/multi_file.log: tests/generate_sequence.log
tests/merge.log: tests/generate_sequence.log
tests/min_qual.log: tests/generate_fastq_sequence.log
tests/large_key.log: tests/generate_sequence.log
tests/quality_filter.log: tests/generate_sequence.log
# SWIG tests
TESTS += tests/swig_python.sh tests/swig_ruby.sh tests/swig_perl.sh
tests/swig_python.log: tests/generate_sequence.log
tests/swig_ruby.log: tests/generate_sequence.log
tests/swig_perl.log: tests/generate_sequence.log
EXTRA_DIST += swig/python/test_mer_file.py swig/python/test_hash_counter.py swig/python/test_string_mers.py
EXTRA_DIST += swig/ruby/test_mer_file.rb swig/ruby/test_hash_counter.rb swig/ruby/test_string_mers.rb
EXTRA_DIST += swig/perl5/t/test_mer_file.t swig/perl5/t/test_hash_counter.t swig/perl5/t/test_string_mers.t
##############
# Unit tests #
##############
TESTS += unit_tests/unit_tests.sh
check_PROGRAMS += bin/test_all
bin_test_all_SOURCES = unit_tests/test_main.cc \
unit_tests/test_misc.cc \
unit_tests/test_offsets_key_value.cc \
unit_tests/test_simple_circular_buffer.cc \
unit_tests/test_rectangular_binary_matrix.cc \
unit_tests/test_mer_dna.cc \
unit_tests/test_large_hash_array.cc \
unit_tests/test_mer_overlap_sequence_parser.cc \
unit_tests/test_file_header.cc \
unit_tests/test_mer_iterator.cc \
unit_tests/test_hash_counter.cc \
unit_tests/test_mer_heap.cc \
unit_tests/test_stream_iterator.cc \
unit_tests/test_token_ring.cc \
unit_tests/test_text_dumper.cc \
unit_tests/test_dumpers.cc \
unit_tests/test_mapped_file.cc \
unit_tests/test_int128.cc \
unit_tests/test_mer_dna_bloom_counter.cc \
unit_tests/test_whole_sequence_parser.cc \
unit_tests/test_allocators_mmap.cc \
unit_tests/test_cooperative_pool2.cc \
unit_tests/test_generator_manager.cc \
unit_tests/test_atomic_bits_array.cc \
unit_tests/test_stdio_filebuf.cc
bin_test_all_SOURCES += jellyfish/backtrace.cc
bin_test_all_CPPFLAGS = -DJSON_IS_AMALGAMATION=1
bin_test_all_CXXFLAGS = $(AM_CXXFLAGS) -I$(srcdir)/unit_tests/gtest/include -I$(srcdir)/unit_tests -I$(srcdir)/include
bin_test_all_LDADD = libgtest.la $(LDADD)
YAGGO_SOURCES += unit_tests/test_main_cmdline.hpp
noinst_HEADERS += unit_tests/test_main.hpp
#################
# SWIG bindings #
#################
include swig/Makefile.am
include gtest.mk
-include $(srcdir)/development.mk
# Print the value of a variable
print-%:
@echo -n $($*)