c_cpp/etc/jellyfish/Makefile.am

   1 ACLOCAL_AMFLAGS = -I m4
   2 EXTRA_DIST = m4/gnulib-cache.m4 doc/jellyfish.pdf doc/jellyfish.man README LICENSE HalfLICENSE
   3 man1_MANS = doc/jellyfish.man
   4
   5 pkgconfigdir = $(libdir)/pkgconfig
   6 pkgconfig_DATA = jellyfish-1.1.pc
   7
   8 AM_LDFLAGS = -lpthread
   9 AM_CPPFLAGS = -Wall -Werror -Wnon-virtual-dtor -I$(top_srcdir)
  10 AM_CXXFLAGS = -g -O3
  11
  12 # What to build
  13 bin_PROGRAMS = bin/jellyfish
  14 lib_LTLIBRARIES = libjellyfish.la
  15 check_PROGRAMS = bin/generate_sequence bin/test_double_fifo_input       \
  16                  bin/test_read_parser
  17
  18 ########################################
  19 # Build Jellyfish the exec
  20 ########################################
  21 bin_jellyfish_SOURCES = jellyfish/jellyfish.cc jellyfish/stats_main.cc                  \
  22                     jellyfish/hash_merge.cc jellyfish/storage.cc jellyfish/misc.cc      \
  23                     jellyfish/err.cc jellyfish/mer_counter.cc jellyfish/histo_main.cc   \
  24                     jellyfish/dump_main.cc jellyfish/time.cc jellyfish/thread_exec.cc   \
  25                     jellyfish/query_main.cc jellyfish/square_binary_matrix.cc   \
  26                     jellyfish/dump_fastq_main.cc jellyfish/histo_fastq_main.cc  \
  27                     jellyfish/cite.cc jellyfish/parse_dna.cc jellyfish/file_parser.cc   \
  28                     jellyfish/parse_quake.cc jellyfish/parse_qual_dna.cc                \
  29                     jellyfish/sequence_parser.cc jellyfish/seq_qual_parser.cc   \
  30                     jellyfish/half.cpp jellyfish/hash_fastq_merge.cc jellyfish/dbg.cc   \
  31                     jellyfish/mapped_file.cc jellyfish/backtrace.cc jellyfish/floats.cc \
  32                     jellyfish/allocators_mmap.cc jellyfish/yaggo.cpp
  33
  34 EXTRA_DIST += jellyfish/cite_cmdline.hpp jellyfish/query_cmdline.hpp            \
  35               jellyfish/hash_merge_cmdline.hpp jellyfish/histo_main_cmdline.hpp \
  36               jellyfish/stats_main_cmdline.hpp                          \
  37               jellyfish/histo_fastq_main_cmdline.hpp                            \
  38               jellyfish/dump_fastq_main_cmdline.hpp                             \
  39               jellyfish/count_main_cmdline.hpp                          \
  40               jellyfish/hash_fastq_merge_cmdline.hpp                            \
  41               jellyfish/dump_main_cmdline.hpp jellyfish/double_fifo_input.hpp   \
  42               jellyfish/simple_growing_array.hpp jellyfish/backtrace.hpp                \
  43               jellyfish/noop_dumper.hpp jellyfish/yaggo.hpp                             \
  44               jellyfish/fstream_default.hpp
  45
  46 ########################################
  47 # Build Jellyfish the shared library
  48 ########################################
  49 libjellyfish_la_LDFLAGS = -version-info 1:0:0
  50 libjellyfish_la_SOURCES = jellyfish/square_binary_matrix.cc             \
  51                           jellyfish/err.cc jellyfish/misc.cc            \
  52                           jellyfish/storage.cc                          \
  53                           jellyfish/thread_exec.cc jellyfish/time.cc    \
  54                           jellyfish/file_parser.cc                      \
  55                           jellyfish/read_parser.cc                      \
  56                           jellyfish/parse_read.cc jellyfish/half.cpp    \
  57                           jellyfish/mapped_file.cc                      \
  58                           jellyfish/parse_dna.cc                        \
  59                           jellyfish/parse_quake.cc                      \
  60                           jellyfish/parse_qual_dna.cc                   \
  61                           jellyfish/sequence_parser.cc                  \
  62                           jellyfish/seq_qual_parser.cc                  \
  63                           jellyfish/backtrace.cc jellyfish/floats.cc    \
  64                           jellyfish/dbg.cc                              \
  65                           jellyfish/allocators_mmap.cc
  66 libjellyfish_la_CPPFLAGS = $(AM_CPPFLAGS)
  67 library_includedir=$(includedir)/jellyfish-@PACKAGE_VERSION@/jellyfish
  68 library_include_HEADERS = jellyfish/allocators_malloc.hpp                       \
  69                           jellyfish/allocators_mmap.hpp                 \
  70                           jellyfish/allocators_shm.hpp jellyfish/atomic_gcc.hpp \
  71                           jellyfish/compacted_dumper.hpp                        \
  72                           jellyfish/compacted_hash.hpp                  \
  73                           jellyfish/concurrent_queues.hpp                       \
  74                           jellyfish/direct_indexing_array.hpp                   \
  75                           jellyfish/direct_sorted_dumper.hpp jellyfish/divisor.hpp      \
  76                           jellyfish/dumper.hpp jellyfish/hash_function.hpp              \
  77                           jellyfish/hash.hpp jellyfish/heap.hpp                 \
  78                           jellyfish/invertible_hash_array.hpp                   \
  79                           jellyfish/locking_hash_counters.hpp                   \
  80                           jellyfish/locks_pthread.hpp jellyfish/mapped_file.hpp \
  81                           jellyfish/mer_counting.hpp jellyfish/err.hpp          \
  82                           jellyfish/misc.hpp jellyfish/offsets_key_value.hpp    \
  83                           jellyfish/reversible_hash_function.hpp                \
  84                           jellyfish/sorted_dumper.hpp                           \
  85                           jellyfish/square_binary_matrix.hpp jellyfish/storage.hpp      \
  86                           jellyfish/thread_exec.hpp jellyfish/time.hpp          \
  87                           jellyfish/token_ring.hpp jellyfish/raw_dumper.hpp             \
  88                           jellyfish/capped_integer.hpp                  \
  89                           jellyfish/aligned_values_array.hpp                    \
  90                           jellyfish/fastq_dumper.hpp jellyfish/floats.hpp               \
  91                           jellyfish/circular_buffer.hpp jellyfish/counter.hpp   \
  92                           jellyfish/parse_quake.hpp jellyfish/parse_dna.hpp             \
  93                           jellyfish/parse_qual_dna.hpp jellyfish/file_parser.hpp        \
  94                           jellyfish/sequence_parser.hpp                 \
  95                           jellyfish/seq_qual_parser.hpp                 \
  96                           jellyfish/double_fifo_input.hpp                       \
  97                           jellyfish/read_parser.hpp jellyfish/parse_read.hpp    \
  98                           jellyfish/simple_growing_array.hpp jellyfish/toFloat.h        \
  99                           jellyfish/eLut.h jellyfish/dbg.hpp jellyfish/half.h           \
 100                           jellyfish/backtrace.hpp
 101
 102 ########################################
 103 # Build tests
 104 ########################################
 105 bin_generate_sequence_SOURCES = jellyfish/generate_sequence.cc jellyfish/misc.cc        \
 106                             jellyfish/mersenne.cpp                              \
 107                             jellyfish/square_binary_matrix.cc                   \
 108                             jellyfish/backtrace.cc jellyfish/dbg.cc jellyfish/time.cc
 109 bin_test_double_fifo_input_SOURCES = jellyfish/test_double_fifo_input.cc                \
 110                                  jellyfish/parse_dna.cc jellyfish/file_parser.cc        \
 111                                  jellyfish/sequence_parser.cc                   \
 112                                  jellyfish/backtrace.cc jellyfish/thread_exec.cc        \
 113                                  jellyfish/dbg.cc jellyfish/time.cc                     \
 114                                  jellyfish/allocators_mmap.cc
 115 bin_test_read_parser_SOURCES = jellyfish/test_read_parser.cc jellyfish/file_parser.cc   \
 116                            jellyfish/read_parser.cc jellyfish/parse_read.cc             \
 117                            jellyfish/dbg.cc jellyfish/backtrace.cc jellyfish/time.cc
 118 EXTRA_DIST += jellyfish/randomc.h jellyfish/generate_sequence_cmdline.hpp
 119
 120 ########################################
 121 # Tests
 122 ########################################
 123 TEST_EXTENSIONS = .sh
 124 SH_LOG_COMPILER = /bin/sh
 125 AM_SH_LOG_FLAGS =
 126
 127 TESTS = tests/generate_sequence.sh tests/serial_hashing.sh              \
 128         tests/parallel_hashing.sh tests/serial_direct_indexing.sh       \
 129         tests/parallel_direct_indexing.sh tests/raw_hash.sh             \
 130         tests/generate_fastq_sequence.sh                                \
 131         tests/parallel_fastq_hashing.sh tests/multi_file.sh             \
 132         tests/multi_file_fastq.sh tests/from_stream.sh                  \
 133         tests/parallel_fastq_sequence_hashing.sh                        \
 134         tests/from_stream_fastq.sh tests/merge.sh tests/min_qual.sh     \
 135         tests/big.sh tests/parsers.sh
 136
 137 EXTRA_DIST += $(TESTS)
 138 clean-local: clean-local-check
 139 .PHONY: clean-local-check
 140 clean-local-check:
 141         -cd tests; rm -f seq10m* seq1m* *_0 *_1 *_2 *.md5sum *.histo *.stats *.timing *.query *.dump *.fa
 142
 143 tests/serial_hashing.log: tests/generate_sequence.log
 144 tests/parallel_hashing.log: tests/generate_sequence.log
 145 tests/serial_direct_indexing.log: tests/generate_sequence.log
 146 tests/parallel_direct_indexing.log: tests/generate_sequence.log
 147 tests/multi_file.log: tests/generate_sequence.log
 148 tests/raw_hash.log: tests/generate_sequence.log
 149 tests/from_stream.log: tests/generate_sequence.log
 150 tests/parallel_fastq_hashing.log: tests/generate_fastq_sequence.log
 151 tests/parallel_fastq_sequence_hashing.log: tests/generate_fastq_sequence.log
 152 tests/multi_file_fastq.log: tests/generate_fastq_sequence.log
 153 tests/from_stream_fastq.log: tests/generate_fastq_sequence.log
 154 tests/merge.log: tests/generate_fastq_sequence.log
 155 tests/min_qual.log: tests/generate_fastq_sequence.log
 156 tests/parsers.log: tests/generate_sequence.log
 157
 158 ########################################
 159 # Unit tests
 160 ########################################
 161 TESTS += unit_tests/unit_tests.sh
 162 check_PROGRAMS += bin/test_offsets_key_value
 163
 164 bin_test_offsets_key_value_SOURCES = unit_tests/test_offsets_key_value.cc
 165 bin_test_offsets_key_value_CXXFLAGS = -I$(top_srcdir)/unit_tests/gtest/include -I$(top_srcdir)/unit_tests/gtest
 166 bin_test_offsets_key_value_LDADD = libgtest_main.la
 167
 168 include gtest.mk