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ACLOCAL_AMFLAGS = -I m4
EXTRA_DIST = m4/gnulib-cache.m4 doc/jellyfish.pdf doc/jellyfish.man \
README LICENSE HalfLICENSE 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 jellyfish/randomc.h \
jellyfish/generate_sequence_cmdline.hpp $(TESTS) $(GTEST_SRC)
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lib_LTLIBRARIES = libjellyfish.la
########################################
# Build Jellyfish the exec
########################################
bin_jellyfish_SOURCES = jellyfish/jellyfish.cc jellyfish/stats_main.cc \
jellyfish/hash_merge.cc jellyfish/storage.cc jellyfish/misc.cc \
jellyfish/err.cc jellyfish/mer_counter.cc jellyfish/histo_main.cc \
jellyfish/dump_main.cc jellyfish/time.cc jellyfish/thread_exec.cc \
jellyfish/query_main.cc jellyfish/square_binary_matrix.cc \
jellyfish/dump_fastq_main.cc jellyfish/histo_fastq_main.cc \
jellyfish/cite.cc jellyfish/parse_dna.cc jellyfish/file_parser.cc \
jellyfish/parse_quake.cc jellyfish/parse_qual_dna.cc \
jellyfish/sequence_parser.cc jellyfish/seq_qual_parser.cc \
jellyfish/half.cpp jellyfish/hash_fastq_merge.cc jellyfish/dbg.cc \
jellyfish/mapped_file.cc jellyfish/backtrace.cc jellyfish/floats.cc \
jellyfish/uniqueness_main.cc \
jellyfish/allocators_mmap.cc jellyfish/yaggo.cpp
########################################
# Build Jellyfish the shared library
########################################
libjellyfish_la_LDFLAGS = -version-info 1:0:0
libjellyfish_la_SOURCES = 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
libjellyfish_la_CPPFLAGS = $(AM_CPPFLAGS)
library_includedir = $(includedir)/jellyfish-1.1.4/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
########################################
# Build tests
########################################
bin_generate_sequence_SOURCES = jellyfish/generate_sequence.cc jellyfish/misc.cc \
jellyfish/mersenne.cpp \
jellyfish/square_binary_matrix.cc \
jellyfish/backtrace.cc jellyfish/dbg.cc jellyfish/time.cc
bin_test_double_fifo_input_SOURCES = jellyfish/test_double_fifo_input.cc \
jellyfish/parse_dna.cc jellyfish/file_parser.cc \
jellyfish/sequence_parser.cc \
jellyfish/backtrace.cc jellyfish/thread_exec.cc \
jellyfish/dbg.cc jellyfish/time.cc \
jellyfish/allocators_mmap.cc
bin_test_read_parser_SOURCES = jellyfish/test_read_parser.cc jellyfish/file_parser.cc \
jellyfish/read_parser.cc jellyfish/parse_read.cc \
jellyfish/dbg.cc jellyfish/backtrace.cc jellyfish/time.cc
########################################
# Tests
########################################
TEST_EXTENSIONS = .sh
SH_LOG_COMPILER = /bin/sh
AM_SH_LOG_FLAGS =
########################################
# Unit tests
########################################
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 unit_tests/unit_tests.sh
bin_test_offsets_key_value_SOURCES = unit_tests/test_offsets_key_value.cc
bin_test_offsets_key_value_CXXFLAGS = -I$(top_srcdir)/unit_tests/gtest/include -I$(top_srcdir)/unit_tests/gtest
bin_test_offsets_key_value_LDADD = libgtest_main.la
##############################
# Gtest build.
##############################
# Build rules for libraries.
check_LTLIBRARIES = libgtest.la libgtest_main.la
libgtest_la_SOURCES = unit_tests/gtest/src/gtest-all.cc
libgtest_main_la_SOURCES = unit_tests/gtest/src/gtest_main.cc
libgtest_main_la_LIBADD = libgtest.la
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libgtest_main_la_CXXFLAGS = -I$(top_srcdir)/unit_tests/gtest \
-I$(top_srcdir)/unit_tests/gtest/include
# gtest source files that we don't compile directly. They are
# #included by gtest-all.cc.
GTEST_SRC = unit_tests/gtest/src/gtest-death-test.cc \
unit_tests/gtest/src/gtest-filepath.cc \
unit_tests/gtest/src/gtest-internal-inl.h \
unit_tests/gtest/src/gtest-port.cc \
unit_tests/gtest/src/gtest-printers.cc \
unit_tests/gtest/src/gtest-test-part.cc \
unit_tests/gtest/src/gtest-typed-test.cc \
unit_tests/gtest/src/gtest.cc
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$(GTEST_I)/internal/gtest-string.h \
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jellyfish/$(DEPDIR)/$(am__dirstamp)
jellyfish/libjellyfish_la-storage.lo: jellyfish/$(am__dirstamp) \
jellyfish/$(DEPDIR)/$(am__dirstamp)
jellyfish/libjellyfish_la-thread_exec.lo: jellyfish/$(am__dirstamp) \
jellyfish/$(DEPDIR)/$(am__dirstamp)
jellyfish/libjellyfish_la-time.lo: jellyfish/$(am__dirstamp) \
jellyfish/$(DEPDIR)/$(am__dirstamp)
jellyfish/libjellyfish_la-file_parser.lo: jellyfish/$(am__dirstamp) \
jellyfish/$(DEPDIR)/$(am__dirstamp)
jellyfish/libjellyfish_la-read_parser.lo: jellyfish/$(am__dirstamp) \
jellyfish/$(DEPDIR)/$(am__dirstamp)
jellyfish/libjellyfish_la-parse_read.lo: jellyfish/$(am__dirstamp) \
jellyfish/$(DEPDIR)/$(am__dirstamp)
jellyfish/libjellyfish_la-half.lo: jellyfish/$(am__dirstamp) \
jellyfish/$(DEPDIR)/$(am__dirstamp)
jellyfish/libjellyfish_la-mapped_file.lo: jellyfish/$(am__dirstamp) \
jellyfish/$(DEPDIR)/$(am__dirstamp)
jellyfish/libjellyfish_la-parse_dna.lo: jellyfish/$(am__dirstamp) \
jellyfish/$(DEPDIR)/$(am__dirstamp)
jellyfish/libjellyfish_la-parse_quake.lo: jellyfish/$(am__dirstamp) \
jellyfish/$(DEPDIR)/$(am__dirstamp)
jellyfish/libjellyfish_la-parse_qual_dna.lo: \
jellyfish/$(am__dirstamp) jellyfish/$(DEPDIR)/$(am__dirstamp)
jellyfish/libjellyfish_la-sequence_parser.lo: \
jellyfish/$(am__dirstamp) jellyfish/$(DEPDIR)/$(am__dirstamp)
jellyfish/libjellyfish_la-seq_qual_parser.lo: \
jellyfish/$(am__dirstamp) jellyfish/$(DEPDIR)/$(am__dirstamp)
jellyfish/libjellyfish_la-backtrace.lo: jellyfish/$(am__dirstamp) \
jellyfish/$(DEPDIR)/$(am__dirstamp)
jellyfish/libjellyfish_la-floats.lo: jellyfish/$(am__dirstamp) \
jellyfish/$(DEPDIR)/$(am__dirstamp)
jellyfish/libjellyfish_la-dbg.lo: jellyfish/$(am__dirstamp) \
jellyfish/$(DEPDIR)/$(am__dirstamp)
jellyfish/libjellyfish_la-allocators_mmap.lo: \
jellyfish/$(am__dirstamp) jellyfish/$(DEPDIR)/$(am__dirstamp)
libjellyfish.la: $(libjellyfish_la_OBJECTS) $(libjellyfish_la_DEPENDENCIES) $(EXTRA_libjellyfish_la_DEPENDENCIES)
$(AM_V_CXXLD)$(libjellyfish_la_LINK) -rpath $(libdir) $(libjellyfish_la_OBJECTS) $(libjellyfish_la_LIBADD) $(LIBS)
install-binPROGRAMS: $(bin_PROGRAMS)
@$(NORMAL_INSTALL)
@list='$(bin_PROGRAMS)'; test -n "$(bindir)" || list=; \
if test -n "$$list"; then \
echo " $(MKDIR_P) '$(DESTDIR)$(bindir)'"; \
$(MKDIR_P) "$(DESTDIR)$(bindir)" || exit 1; \
fi; \
for p in $$list; do echo "$$p $$p"; done | \
sed 's/$(EXEEXT)$$//' | \
while read p p1; do if test -f $$p || test -f $$p1; \
then echo "$$p"; echo "$$p"; else :; fi; \
done | \
sed -e 'p;s,.*/,,;n;h' -e 's|.*|.|' \
-e 'p;x;s,.*/,,;s/$(EXEEXT)$$//;$(transform);s/$$/$(EXEEXT)/' | \
sed 'N;N;N;s,\n, ,g' | \
$(AWK) 'BEGIN { files["."] = ""; dirs["."] = 1 } \
{ d=$$3; if (dirs[d] != 1) { print "d", d; dirs[d] = 1 } \
if ($$2 == $$4) files[d] = files[d] " " $$1; \
else { print "f", $$3 "/" $$4, $$1; } } \
END { for (d in files) print "f", d, files[d] }' | \
while read type dir files; do \
if test "$$dir" = .; then dir=; else dir=/$$dir; fi; \
test -z "$$files" || { \
echo " $(INSTALL_PROGRAM_ENV) $(LIBTOOL) $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) --mode=install $(INSTALL_PROGRAM) $$files '$(DESTDIR)$(bindir)$$dir'"; \
$(INSTALL_PROGRAM_ENV) $(LIBTOOL) $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) --mode=install $(INSTALL_PROGRAM) $$files "$(DESTDIR)$(bindir)$$dir" || exit $$?; \
} \
; done
uninstall-binPROGRAMS:
@$(NORMAL_UNINSTALL)
@list='$(bin_PROGRAMS)'; test -n "$(bindir)" || list=; \
files=`for p in $$list; do echo "$$p"; done | \
sed -e 'h;s,^.*/,,;s/$(EXEEXT)$$//;$(transform)' \
-e 's/$$/$(EXEEXT)/' `; \
test -n "$$list" || exit 0; \
echo " ( cd '$(DESTDIR)$(bindir)' && rm -f" $$files ")"; \
cd "$(DESTDIR)$(bindir)" && rm -f $$files
clean-binPROGRAMS:
@list='$(bin_PROGRAMS)'; test -n "$$list" || exit 0; \
echo " rm -f" $$list; \
rm -f $$list || exit $$?; \
test -n "$(EXEEXT)" || exit 0; \
list=`for p in $$list; do echo "$$p"; done | sed 's/$(EXEEXT)$$//'`; \
echo " rm -f" $$list; \
rm -f $$list
clean-checkPROGRAMS:
@list='$(check_PROGRAMS)'; test -n "$$list" || exit 0; \
echo " rm -f" $$list; \
rm -f $$list || exit $$?; \
test -n "$(EXEEXT)" || exit 0; \
list=`for p in $$list; do echo "$$p"; done | sed 's/$(EXEEXT)$$//'`; \
echo " rm -f" $$list; \
rm -f $$list
jellyfish/generate_sequence.$(OBJEXT): jellyfish/$(am__dirstamp) \
jellyfish/$(DEPDIR)/$(am__dirstamp)
jellyfish/misc.$(OBJEXT): jellyfish/$(am__dirstamp) \
jellyfish/$(DEPDIR)/$(am__dirstamp)
jellyfish/mersenne.$(OBJEXT): jellyfish/$(am__dirstamp) \
jellyfish/$(DEPDIR)/$(am__dirstamp)
jellyfish/square_binary_matrix.$(OBJEXT): jellyfish/$(am__dirstamp) \
jellyfish/$(DEPDIR)/$(am__dirstamp)
jellyfish/backtrace.$(OBJEXT): jellyfish/$(am__dirstamp) \
jellyfish/$(DEPDIR)/$(am__dirstamp)
jellyfish/dbg.$(OBJEXT): jellyfish/$(am__dirstamp) \
jellyfish/$(DEPDIR)/$(am__dirstamp)
jellyfish/time.$(OBJEXT): jellyfish/$(am__dirstamp) \
jellyfish/$(DEPDIR)/$(am__dirstamp)
bin/$(am__dirstamp):
@$(MKDIR_P) bin
@: > bin/$(am__dirstamp)
bin/generate_sequence$(EXEEXT): $(bin_generate_sequence_OBJECTS) $(bin_generate_sequence_DEPENDENCIES) $(EXTRA_bin_generate_sequence_DEPENDENCIES) bin/$(am__dirstamp)
@rm -f bin/generate_sequence$(EXEEXT)
$(AM_V_CXXLD)$(CXXLINK) $(bin_generate_sequence_OBJECTS) $(bin_generate_sequence_LDADD) $(LIBS)
jellyfish/jellyfish.$(OBJEXT): jellyfish/$(am__dirstamp) \
jellyfish/$(DEPDIR)/$(am__dirstamp)
jellyfish/stats_main.$(OBJEXT): jellyfish/$(am__dirstamp) \
jellyfish/$(DEPDIR)/$(am__dirstamp)
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jellyfish/$(DEPDIR)/$(am__dirstamp)
jellyfish/storage.$(OBJEXT): jellyfish/$(am__dirstamp) \
jellyfish/$(DEPDIR)/$(am__dirstamp)
jellyfish/err.$(OBJEXT): jellyfish/$(am__dirstamp) \
jellyfish/$(DEPDIR)/$(am__dirstamp)
jellyfish/mer_counter.$(OBJEXT): jellyfish/$(am__dirstamp) \
jellyfish/$(DEPDIR)/$(am__dirstamp)
jellyfish/histo_main.$(OBJEXT): jellyfish/$(am__dirstamp) \
jellyfish/$(DEPDIR)/$(am__dirstamp)
jellyfish/dump_main.$(OBJEXT): jellyfish/$(am__dirstamp) \
jellyfish/$(DEPDIR)/$(am__dirstamp)
jellyfish/thread_exec.$(OBJEXT): jellyfish/$(am__dirstamp) \
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jellyfish/query_main.$(OBJEXT): jellyfish/$(am__dirstamp) \
jellyfish/$(DEPDIR)/$(am__dirstamp)
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jellyfish/$(DEPDIR)/$(am__dirstamp)
jellyfish/cite.$(OBJEXT): jellyfish/$(am__dirstamp) \
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jellyfish/$(DEPDIR)/$(am__dirstamp)
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jellyfish/$(DEPDIR)/$(am__dirstamp)
jellyfish/parse_quake.$(OBJEXT): jellyfish/$(am__dirstamp) \
jellyfish/$(DEPDIR)/$(am__dirstamp)
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jellyfish/$(DEPDIR)/$(am__dirstamp)
jellyfish/sequence_parser.$(OBJEXT): jellyfish/$(am__dirstamp) \
jellyfish/$(DEPDIR)/$(am__dirstamp)
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jellyfish/$(DEPDIR)/$(am__dirstamp)
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jellyfish/$(DEPDIR)/$(am__dirstamp)
jellyfish/hash_fastq_merge.$(OBJEXT): jellyfish/$(am__dirstamp) \
jellyfish/$(DEPDIR)/$(am__dirstamp)
jellyfish/mapped_file.$(OBJEXT): jellyfish/$(am__dirstamp) \
jellyfish/$(DEPDIR)/$(am__dirstamp)
jellyfish/floats.$(OBJEXT): jellyfish/$(am__dirstamp) \
jellyfish/$(DEPDIR)/$(am__dirstamp)
jellyfish/uniqueness_main.$(OBJEXT): jellyfish/$(am__dirstamp) \
jellyfish/$(DEPDIR)/$(am__dirstamp)
jellyfish/allocators_mmap.$(OBJEXT): jellyfish/$(am__dirstamp) \
jellyfish/$(DEPDIR)/$(am__dirstamp)
jellyfish/yaggo.$(OBJEXT): jellyfish/$(am__dirstamp) \
jellyfish/$(DEPDIR)/$(am__dirstamp)
bin/jellyfish$(EXEEXT): $(bin_jellyfish_OBJECTS) $(bin_jellyfish_DEPENDENCIES) $(EXTRA_bin_jellyfish_DEPENDENCIES) bin/$(am__dirstamp)
@rm -f bin/jellyfish$(EXEEXT)
$(AM_V_CXXLD)$(CXXLINK) $(bin_jellyfish_OBJECTS) $(bin_jellyfish_LDADD) $(LIBS)
jellyfish/test_double_fifo_input.$(OBJEXT): jellyfish/$(am__dirstamp) \
jellyfish/$(DEPDIR)/$(am__dirstamp)
bin/test_double_fifo_input$(EXEEXT): $(bin_test_double_fifo_input_OBJECTS) $(bin_test_double_fifo_input_DEPENDENCIES) $(EXTRA_bin_test_double_fifo_input_DEPENDENCIES) bin/$(am__dirstamp)
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$(AM_V_CXXLD)$(CXXLINK) $(bin_test_double_fifo_input_OBJECTS) $(bin_test_double_fifo_input_LDADD) $(LIBS)
unit_tests/$(am__dirstamp):
@$(MKDIR_P) unit_tests
@: > unit_tests/$(am__dirstamp)
unit_tests/$(DEPDIR)/$(am__dirstamp):
@$(MKDIR_P) unit_tests/$(DEPDIR)
@: > unit_tests/$(DEPDIR)/$(am__dirstamp)
unit_tests/bin_test_offsets_key_value-test_offsets_key_value.$(OBJEXT): \
unit_tests/$(am__dirstamp) \
unit_tests/$(DEPDIR)/$(am__dirstamp)
bin/test_offsets_key_value$(EXEEXT): $(bin_test_offsets_key_value_OBJECTS) $(bin_test_offsets_key_value_DEPENDENCIES) $(EXTRA_bin_test_offsets_key_value_DEPENDENCIES) bin/$(am__dirstamp)
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$(AM_V_CXXLD)$(bin_test_offsets_key_value_LINK) $(bin_test_offsets_key_value_OBJECTS) $(bin_test_offsets_key_value_LDADD) $(LIBS)
jellyfish/test_read_parser.$(OBJEXT): jellyfish/$(am__dirstamp) \
jellyfish/$(DEPDIR)/$(am__dirstamp)
jellyfish/read_parser.$(OBJEXT): jellyfish/$(am__dirstamp) \
jellyfish/$(DEPDIR)/$(am__dirstamp)
jellyfish/parse_read.$(OBJEXT): jellyfish/$(am__dirstamp) \
jellyfish/$(DEPDIR)/$(am__dirstamp)
bin/test_read_parser$(EXEEXT): $(bin_test_read_parser_OBJECTS) $(bin_test_read_parser_DEPENDENCIES) $(EXTRA_bin_test_read_parser_DEPENDENCIES) bin/$(am__dirstamp)