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ACLOCAL_AMFLAGS = -I m4
EXTRA_DIST = doc/jellyfish.pdf doc/jellyfish.man README LICENSE HalfLICENSE
man1_MANS = doc/jellyfish.man
pkgconfigdir = $(libdir)/pkgconfig
pkgconfig_DATA = jellyfish-1.1.pc
AM_LDFLAGS = -lpthread
AM_CPPFLAGS = -Wall -Wnon-virtual-dtor -I$(top_srcdir)
AM_CXXFLAGS = -g -O3
LDADD = libjellyfish-1.1.la
# What to build
lib_LTLIBRARIES = libjellyfish-1.1.la
bin_PROGRAMS = bin/jellyfish
check_PROGRAMS = bin/generate_sequence bin/test_double_fifo_input \
bin/test_read_parser
########################################
# Build Jellyfish the exec
########################################
bin_jellyfish_SOURCES = jellyfish/jellyfish.cc \
jellyfish/stats_main.cc \
jellyfish/hash_merge.cc \
jellyfish/mer_counter.cc \
jellyfish/histo_main.cc \
jellyfish/dump_main.cc \
jellyfish/query_main.cc \
jellyfish/dump_fastq_main.cc \
jellyfish/histo_fastq_main.cc \
jellyfish/cite.cc \
jellyfish/hash_fastq_merge.cc \
jellyfish/yaggo.cpp
# bin_jellyfish_LDADD = libjellyfish-1.1.la
bin_jellyfish_LDFLAGS = $(AM_LDFLAGS) $(STATIC_FLAGS) -Wl,--as-needed -latomic
EXTRA_DIST += jellyfish/cite_cmdline.hpp jellyfish/query_cmdline.hpp \
jellyfish/hash_merge_cmdline.hpp \
jellyfish/histo_main_cmdline.hpp \
jellyfish/stats_main_cmdline.hpp \
jellyfish/histo_fastq_main_cmdline.hpp \
jellyfish/dump_fastq_main_cmdline.hpp \
jellyfish/count_main_cmdline.hpp \
jellyfish/hash_fastq_merge_cmdline.hpp \
jellyfish/dump_main_cmdline.hpp \
jellyfish/double_fifo_input.hpp \
jellyfish/simple_growing_array.hpp \
jellyfish/backtrace.hpp jellyfish/noop_dumper.hpp \
jellyfish/yaggo.hpp jellyfish/fstream_default.hpp
########################################
# Build Jellyfish the shared library
########################################
libjellyfish_srcs = jellyfish/square_binary_matrix.cc \
jellyfish/err.cc jellyfish/misc.cc \
jellyfish/storage.cc jellyfish/thread_exec.cc \
jellyfish/time.cc jellyfish/file_parser.cc \
jellyfish/read_parser.cc \
jellyfish/parse_read.cc jellyfish/half.cpp \
jellyfish/mapped_file.cc \
jellyfish/parse_dna.cc \
jellyfish/parse_quake.cc \
jellyfish/parse_qual_dna.cc \
jellyfish/sequence_parser.cc \
jellyfish/seq_qual_parser.cc \
jellyfish/backtrace.cc jellyfish/floats.cc \
jellyfish/dbg.cc jellyfish/allocators_mmap.cc \
jellyfish/dna_codes.cc
libjellyfish_1_1_la_SOURCES = $(libjellyfish_srcs)
libjellyfish_1_1_la_LDFLAGS = -version-info 1:1:0
library_includedir=$(includedir)/jellyfish-@PACKAGE_VERSION@/jellyfish
library_include_HEADERS = jellyfish/allocators_malloc.hpp \
jellyfish/allocators_mmap.hpp \
jellyfish/allocators_shm.hpp \
jellyfish/atomic_gcc.hpp \
jellyfish/compacted_dumper.hpp \
jellyfish/compacted_hash.hpp \
jellyfish/concurrent_queues.hpp \
jellyfish/direct_indexing_array.hpp \
jellyfish/direct_sorted_dumper.hpp \
jellyfish/divisor.hpp jellyfish/dumper.hpp \
jellyfish/hash_function.hpp \
jellyfish/hash.hpp jellyfish/heap.hpp \
jellyfish/invertible_hash_array.hpp \
jellyfish/locking_hash_counters.hpp \
jellyfish/locks_pthread.hpp \
jellyfish/mapped_file.hpp \
jellyfish/mer_counting.hpp \
jellyfish/err.hpp jellyfish/misc.hpp \
jellyfish/offsets_key_value.hpp \
jellyfish/reversible_hash_function.hpp \
jellyfish/sorted_dumper.hpp \
jellyfish/square_binary_matrix.hpp \
jellyfish/storage.hpp \
jellyfish/thread_exec.hpp \
jellyfish/time.hpp jellyfish/token_ring.hpp \
jellyfish/raw_dumper.hpp \
jellyfish/capped_integer.hpp \
jellyfish/aligned_values_array.hpp \
jellyfish/fastq_dumper.hpp \
jellyfish/floats.hpp \
jellyfish/circular_buffer.hpp \
jellyfish/counter.hpp \
jellyfish/parse_quake.hpp \
jellyfish/parse_dna.hpp \
jellyfish/parse_qual_dna.hpp \
jellyfish/file_parser.hpp \
jellyfish/sequence_parser.hpp \
jellyfish/seq_qual_parser.hpp \
jellyfish/double_fifo_input.hpp \
jellyfish/read_parser.hpp \
jellyfish/parse_read.hpp \
jellyfish/simple_growing_array.hpp \
jellyfish/toFloat.h jellyfish/eLut.h \
jellyfish/dbg.hpp jellyfish/half.h \
jellyfish/backtrace.hpp \
jellyfish/dna_codes.hpp \
jellyfish/simple_circular_buffer.hpp
########################################
# Build tests
########################################
bin_generate_sequence_SOURCES = jellyfish/generate_sequence.cc \
jellyfish/mersenne.cpp
bin_test_double_fifo_input_SOURCES = jellyfish/test_double_fifo_input.cc
bin_test_read_parser_SOURCES = jellyfish/test_read_parser.cc
EXTRA_DIST += jellyfish/randomc.h jellyfish/generate_sequence_cmdline.hpp
########################################
# Tests
########################################
TEST_EXTENSIONS = .sh
SH_LOG_COMPILER = /bin/sh
AM_SH_LOG_FLAGS =
TESTS = tests/generate_sequence.sh tests/serial_hashing.sh \
tests/parallel_hashing.sh tests/serial_direct_indexing.sh \
tests/parallel_direct_indexing.sh tests/raw_hash.sh \
tests/generate_fastq_sequence.sh \
tests/parallel_fastq_hashing.sh tests/multi_file.sh \
tests/multi_file_fastq.sh tests/from_stream.sh \
tests/parallel_fastq_sequence_hashing.sh \
tests/from_stream_fastq.sh tests/merge.sh tests/min_qual.sh \
tests/big.sh tests/parsers.sh tests/small.sh \
tests/parallel_fastq_direct_indexing.sh
EXTRA_DIST += $(TESTS)
clean-local: clean-local-check
.PHONY: clean-local-check
clean-local-check:
-cd tests; rm -f seq10m* seq1m* *_0 *_1 *_2 *_S *.md5sum *.histo *.stats *.timing *.query *.dump *.fa
tests/serial_hashing.log: tests/generate_sequence.log
tests/parallel_hashing.log: tests/generate_sequence.log
tests/serial_direct_indexing.log: tests/generate_sequence.log
tests/parallel_direct_indexing.log: tests/generate_sequence.log
tests/parallel_fastq_direct_indexing.log: tests/generate_fastq_sequence.log
tests/multi_file.log: tests/generate_sequence.log
tests/raw_hash.log: tests/generate_sequence.log
tests/from_stream.log: tests/generate_sequence.log
tests/parallel_fastq_hashing.log: tests/generate_fastq_sequence.log
tests/parallel_fastq_sequence_hashing.log: tests/generate_fastq_sequence.log
tests/multi_file_fastq.log: tests/generate_fastq_sequence.log
tests/from_stream_fastq.log: tests/generate_fastq_sequence.log
tests/merge.log: tests/generate_fastq_sequence.log
tests/min_qual.log: tests/generate_fastq_sequence.log
tests/parsers.log: tests/generate_sequence.log
########################################
# Unit tests
########################################
TESTS += unit_tests/unit_tests.sh
check_PROGRAMS += bin/test_all
bin_test_all_SOURCES = unit_tests/test_offsets_key_value.cc \
unit_tests/test_simple_circular_buffer.cc \
unit_tests/test_square_binary_matrix.cc
bin_test_all_CXXFLAGS = -I$(top_srcdir)/unit_tests/gtest/include -I$(top_srcdir)/unit_tests/gtest
bin_test_all_LDADD = libgtest_main.a libgtest.a $(LDADD)
include gtest.mk
-include $(top_srcdir)/development.mk
########
# info #
########
print-%:
@echo -n $($*)
|
