# Makefile.in generated by automake 1.15 from Makefile.am.
# Makefile.  Generated from Makefile.in by configure.

# Copyright (C) 1994-2014 Free Software Foundation, Inc.

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YAGGO = false
abs_builddir = /home/psgendb/BIRCHDEV/pkg/Rcorrector-master/jellyfish
abs_srcdir = /home/psgendb/BIRCHDEV/pkg/Rcorrector-master/jellyfish
abs_top_builddir = /home/psgendb/BIRCHDEV/pkg/Rcorrector-master/jellyfish
abs_top_srcdir = /home/psgendb/BIRCHDEV/pkg/Rcorrector-master/jellyfish
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ACLOCAL_AMFLAGS = -I m4
EXTRA_DIST = doc/jellyfish.pdf doc/jellyfish.man README LICENSE \
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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
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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_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 \
	jellyfish/generate_sequence_cmdline.hpp \
	unit_tests/test_main_cmdline.hpp
lib_LTLIBRARIES = libjellyfish-2.0.la
LDADD = libjellyfish-2.0.la # $(VALGRIND_LIBS)

############################
# 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)

######################################
# 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-2.2.4/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


###############
# Build tests #
###############
bin_generate_sequence_SOURCES = jellyfish/generate_sequence.cc		\
                                jellyfish/mersenne.cpp			\
                                jellyfish/backtrace.cc			\
                                jellyfish/dbg.cc


#########
# Tests #
#########
TEST_EXTENSIONS = .sh
SH_LOG_COMPILER = $(SHELL)
AM_SH_LOG_FLAGS = 

# SWIG tests

##############
# Unit tests #
##############
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 tests/swig_python.sh \
	tests/swig_ruby.sh tests/swig_perl.sh unit_tests/unit_tests.sh
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 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)

# SWIG
SWIG_SRC = swig/jellyfish.i swig/hash_counter.i swig/hash_set.i	\
           swig/mer_dna.i swig/mer_file.i swig/string_mers.i

#SWIG_V_GEN = $(swig_v_GEN_$(V))
#swig_v_GEN_ = $(swig_v_GEN_$(AM_DEFAULT_VERBOSITY))
#swig_v_GEN_0 = @echo "  SWIG    " $@;

# Python support
#PYTHON_BUILT = swig/python/swig_wrap.cpp swig/python/jellyfish.py
#pythonextdir = $(PYTHON_SITE_PKG)/jellyfish
#pythonext_SCRIPTS = swig/python/__init__.pyc
#pythonext_LTLIBRARIES = swig/python/_jellyfish.la
#swig_python__jellyfish_la_SOURCES = swig/python/swig_wrap.cpp $(SWIG_SRC)
#swig_python__jellyfish_la_CPPFLAGS = $(PYTHON_CPPFLAGS) -I$(srcdir)/include
#swig_python__jellyfish_la_LDFLAGS = -module
#swig_python__jellyfish_la_LIBADD = libjellyfish-2.0.la
#PYTHONC_V_GEN = $(pythonc_v_GEN_$(V))
#pythonc_v_GEN_ = $(pythonc_v_GEN_$(AM_DEFAULT_VERBOSITY))
#pythonc_v_GEN_0 = @echo "  PYTHONC " $@;

# Ruby support
#RUBY_BUILT = swig/ruby/swig_wrap.cpp
#rubyextdir = $(RUBY_EXT_LIB)
#rubyext_LTLIBRARIES = swig/ruby/jellyfish.la
#swig_ruby_jellyfish_la_SOURCES = swig/ruby/swig_wrap.cpp $(SWIG_SRC)
#swig_ruby_jellyfish_la_CPPFLAGS = $(RUBY_EXT_CFLAGS) -I$(srcdir)/include
#swig_ruby_jellyfish_la_LDFLAGS = -module
#swig_ruby_jellyfish_la_LIBADD = libjellyfish-2.0.la

# Perl5 support
#PERL_BUILT = swig/perl5/swig_wrap.cpp swig/perl5/jellyfish.pm
#perlextdir = $(PERL_EXT_LIB)
#perlext_SCRIPTS = swig/perl5/jellyfish.pm
#perlext_LTLIBRARIES = swig/perl5/jellyfish.la
#swig_perl5_jellyfish_la_SOURCES = swig/perl5/swig_wrap.cpp $(SWIG_SRC)
#swig_perl5_jellyfish_la_CPPFLAGS = $(PERL_EXT_CPPFLAGS) -I$(PERL_EXT_INC) -I$(srcdir)/include
#swig_perl5_jellyfish_la_LDFLAGS = -module
#swig_perl5_jellyfish_la_LIBADD = libjellyfish-2.0.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
libgtest_la_CXXFLAGS = -I$(srcdir)/unit_tests
libgtest_main_la_CXXFLAGS = -I$(srcdir)/unit_tests
GTEST_SRC = unit_tests/gtest/src/gtest-all.cc	\
	    unit_tests/gtest/src/gtest_main.cc	\
	    unit_tests/gtest/gtest.h

all: $(BUILT_SOURCES) config.h
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config.h: stamp-h1
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stamp-h1: $(srcdir)/config.h.in $(top_builddir)/config.status
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distclean-hdr:
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tests/compat.sh: $(top_builddir)/config.status $(top_srcdir)/tests/compat.sh.in
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jellyfish-2.0.pc: $(top_builddir)/config.status $(srcdir)/jellyfish-2.0.pc.in
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clean-checkLTLIBRARIES:
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jellyfish/bin_test_all-backtrace.$(OBJEXT): jellyfish/$(am__dirstamp) \
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bin/test_all$(EXEEXT): $(bin_test_all_OBJECTS) $(bin_test_all_DEPENDENCIES) $(EXTRA_bin_test_all_DEPENDENCIES) bin/$(am__dirstamp)
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install-pythonextSCRIPTS: $(pythonext_SCRIPTS)
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mostlyclean-compile:
	-rm -f *.$(OBJEXT)
	-rm -f jellyfish/*.$(OBJEXT)
	-rm -f lib/*.$(OBJEXT)
	-rm -f lib/*.lo
	-rm -f sub_commands/*.$(OBJEXT)
	-rm -f swig/perl5/*.$(OBJEXT)
	-rm -f swig/perl5/*.lo
	-rm -f swig/python/*.$(OBJEXT)
	-rm -f swig/python/*.lo
	-rm -f swig/ruby/*.$(OBJEXT)
	-rm -f swig/ruby/*.lo
	-rm -f unit_tests/*.$(OBJEXT)
	-rm -f unit_tests/gtest/src/*.$(OBJEXT)
	-rm -f unit_tests/gtest/src/*.lo

distclean-compile:
	-rm -f *.tab.c

include jellyfish/$(DEPDIR)/backtrace.Po
include jellyfish/$(DEPDIR)/bin_test_all-backtrace.Po
include jellyfish/$(DEPDIR)/dbg.Po
include jellyfish/$(DEPDIR)/generate_sequence.Po
include jellyfish/$(DEPDIR)/merge_files.Po
include jellyfish/$(DEPDIR)/mersenne.Po
include lib/$(DEPDIR)/allocators_mmap.Plo
include lib/$(DEPDIR)/generator_manager.Plo
include lib/$(DEPDIR)/int128.Plo
include lib/$(DEPDIR)/jsoncpp.Plo
include lib/$(DEPDIR)/mer_dna.Plo
include lib/$(DEPDIR)/misc.Plo
include lib/$(DEPDIR)/rectangular_binary_matrix.Plo
include lib/$(DEPDIR)/storage.Plo
include lib/$(DEPDIR)/thread_exec.Plo
include lib/$(DEPDIR)/time.Plo
include sub_commands/$(DEPDIR)/bc_main.Po
include sub_commands/$(DEPDIR)/cite_main.Po
include sub_commands/$(DEPDIR)/count_main.Po
include sub_commands/$(DEPDIR)/dump_main.Po
include sub_commands/$(DEPDIR)/histo_main.Po
include sub_commands/$(DEPDIR)/info_main.Po
include sub_commands/$(DEPDIR)/jellyfish.Po
include sub_commands/$(DEPDIR)/mem_main.Po
include sub_commands/$(DEPDIR)/merge_main.Po
include sub_commands/$(DEPDIR)/query_main.Po
include sub_commands/$(DEPDIR)/stats_main.Po
include swig/perl5/$(DEPDIR)/swig_perl5_jellyfish_la-swig_wrap.Plo
include swig/python/$(DEPDIR)/swig_python__jellyfish_la-swig_wrap.Plo
include swig/ruby/$(DEPDIR)/swig_ruby_jellyfish_la-swig_wrap.Plo
include unit_tests/$(DEPDIR)/bin_test_all-test_allocators_mmap.Po
include unit_tests/$(DEPDIR)/bin_test_all-test_atomic_bits_array.Po
include unit_tests/$(DEPDIR)/bin_test_all-test_cooperative_pool2.Po
include unit_tests/$(DEPDIR)/bin_test_all-test_dumpers.Po
include unit_tests/$(DEPDIR)/bin_test_all-test_file_header.Po
include unit_tests/$(DEPDIR)/bin_test_all-test_generator_manager.Po
include unit_tests/$(DEPDIR)/bin_test_all-test_hash_counter.Po
include unit_tests/$(DEPDIR)/bin_test_all-test_int128.Po
include unit_tests/$(DEPDIR)/bin_test_all-test_large_hash_array.Po
include unit_tests/$(DEPDIR)/bin_test_all-test_main.Po
include unit_tests/$(DEPDIR)/bin_test_all-test_mapped_file.Po
include unit_tests/$(DEPDIR)/bin_test_all-test_mer_dna.Po
include unit_tests/$(DEPDIR)/bin_test_all-test_mer_dna_bloom_counter.Po
include unit_tests/$(DEPDIR)/bin_test_all-test_mer_heap.Po
include unit_tests/$(DEPDIR)/bin_test_all-test_mer_iterator.Po
include unit_tests/$(DEPDIR)/bin_test_all-test_mer_overlap_sequence_parser.Po
include unit_tests/$(DEPDIR)/bin_test_all-test_misc.Po
include unit_tests/$(DEPDIR)/bin_test_all-test_offsets_key_value.Po
include unit_tests/$(DEPDIR)/bin_test_all-test_rectangular_binary_matrix.Po
include unit_tests/$(DEPDIR)/bin_test_all-test_simple_circular_buffer.Po
include unit_tests/$(DEPDIR)/bin_test_all-test_stdio_filebuf.Po
include unit_tests/$(DEPDIR)/bin_test_all-test_stream_iterator.Po
include unit_tests/$(DEPDIR)/bin_test_all-test_text_dumper.Po
include unit_tests/$(DEPDIR)/bin_test_all-test_token_ring.Po
include unit_tests/$(DEPDIR)/bin_test_all-test_whole_sequence_parser.Po
include unit_tests/gtest/src/$(DEPDIR)/libgtest_la-gtest-all.Plo
include unit_tests/gtest/src/$(DEPDIR)/libgtest_main_la-gtest_main.Plo

.cc.o:
	$(AM_V_CXX)depbase=`echo $@ | sed 's|[^/]*$$|$(DEPDIR)/&|;s|\.o$$||'`;\
	$(CXXCOMPILE) -MT $@ -MD -MP -MF $$depbase.Tpo -c -o $@ $< &&\
	$(am__mv) $$depbase.Tpo $$depbase.Po
#	$(AM_V_CXX)source='$<' object='$@' libtool=no \
#	DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) \
#	$(AM_V_CXX_no)$(CXXCOMPILE) -c -o $@ $<

.cc.obj:
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	$(CXXCOMPILE) -MT $@ -MD -MP -MF $$depbase.Tpo -c -o $@ `$(CYGPATH_W) '$<'` &&\
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.cc.lo:
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#	DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) \
#	$(AM_V_CXX_no)$(LTCXXCOMPILE) -c -o $@ $<

unit_tests/gtest/src/libgtest_la-gtest-all.lo: unit_tests/gtest/src/gtest-all.cc
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	$(AM_V_at)$(am__mv) unit_tests/gtest/src/$(DEPDIR)/libgtest_la-gtest-all.Tpo unit_tests/gtest/src/$(DEPDIR)/libgtest_la-gtest-all.Plo
#	$(AM_V_CXX)source='unit_tests/gtest/src/gtest-all.cc' object='unit_tests/gtest/src/libgtest_la-gtest-all.lo' libtool=yes \
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unit_tests/gtest/src/libgtest_main_la-gtest_main.lo: unit_tests/gtest/src/gtest_main.cc
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	$(AM_V_at)$(am__mv) unit_tests/gtest/src/$(DEPDIR)/libgtest_main_la-gtest_main.Tpo unit_tests/gtest/src/$(DEPDIR)/libgtest_main_la-gtest_main.Plo
#	$(AM_V_CXX)source='unit_tests/gtest/src/gtest_main.cc' object='unit_tests/gtest/src/libgtest_main_la-gtest_main.lo' libtool=yes \
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swig/perl5/swig_perl5_jellyfish_la-swig_wrap.lo: swig/perl5/swig_wrap.cpp
	$(AM_V_CXX)$(LIBTOOL) $(AM_V_lt) --tag=CXX $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) --mode=compile $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(swig_perl5_jellyfish_la_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT swig/perl5/swig_perl5_jellyfish_la-swig_wrap.lo -MD -MP -MF swig/perl5/$(DEPDIR)/swig_perl5_jellyfish_la-swig_wrap.Tpo -c -o swig/perl5/swig_perl5_jellyfish_la-swig_wrap.lo `test -f 'swig/perl5/swig_wrap.cpp' || echo '$(srcdir)/'`swig/perl5/swig_wrap.cpp
	$(AM_V_at)$(am__mv) swig/perl5/$(DEPDIR)/swig_perl5_jellyfish_la-swig_wrap.Tpo swig/perl5/$(DEPDIR)/swig_perl5_jellyfish_la-swig_wrap.Plo
#	$(AM_V_CXX)source='swig/perl5/swig_wrap.cpp' object='swig/perl5/swig_perl5_jellyfish_la-swig_wrap.lo' libtool=yes \
#	DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) \
#	$(AM_V_CXX_no)$(LIBTOOL) $(AM_V_lt) --tag=CXX $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) --mode=compile $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(swig_perl5_jellyfish_la_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o swig/perl5/swig_perl5_jellyfish_la-swig_wrap.lo `test -f 'swig/perl5/swig_wrap.cpp' || echo '$(srcdir)/'`swig/perl5/swig_wrap.cpp

swig/python/swig_python__jellyfish_la-swig_wrap.lo: swig/python/swig_wrap.cpp
	$(AM_V_CXX)$(LIBTOOL) $(AM_V_lt) --tag=CXX $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) --mode=compile $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(swig_python__jellyfish_la_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT swig/python/swig_python__jellyfish_la-swig_wrap.lo -MD -MP -MF swig/python/$(DEPDIR)/swig_python__jellyfish_la-swig_wrap.Tpo -c -o swig/python/swig_python__jellyfish_la-swig_wrap.lo `test -f 'swig/python/swig_wrap.cpp' || echo '$(srcdir)/'`swig/python/swig_wrap.cpp
	$(AM_V_at)$(am__mv) swig/python/$(DEPDIR)/swig_python__jellyfish_la-swig_wrap.Tpo swig/python/$(DEPDIR)/swig_python__jellyfish_la-swig_wrap.Plo
#	$(AM_V_CXX)source='swig/python/swig_wrap.cpp' object='swig/python/swig_python__jellyfish_la-swig_wrap.lo' libtool=yes \
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#	$(AM_V_CXX_no)$(LIBTOOL) $(AM_V_lt) --tag=CXX $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) --mode=compile $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(swig_python__jellyfish_la_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o swig/python/swig_python__jellyfish_la-swig_wrap.lo `test -f 'swig/python/swig_wrap.cpp' || echo '$(srcdir)/'`swig/python/swig_wrap.cpp

swig/ruby/swig_ruby_jellyfish_la-swig_wrap.lo: swig/ruby/swig_wrap.cpp
	$(AM_V_CXX)$(LIBTOOL) $(AM_V_lt) --tag=CXX $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) --mode=compile $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(swig_ruby_jellyfish_la_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT swig/ruby/swig_ruby_jellyfish_la-swig_wrap.lo -MD -MP -MF swig/ruby/$(DEPDIR)/swig_ruby_jellyfish_la-swig_wrap.Tpo -c -o swig/ruby/swig_ruby_jellyfish_la-swig_wrap.lo `test -f 'swig/ruby/swig_wrap.cpp' || echo '$(srcdir)/'`swig/ruby/swig_wrap.cpp
	$(AM_V_at)$(am__mv) swig/ruby/$(DEPDIR)/swig_ruby_jellyfish_la-swig_wrap.Tpo swig/ruby/$(DEPDIR)/swig_ruby_jellyfish_la-swig_wrap.Plo
#	$(AM_V_CXX)source='swig/ruby/swig_wrap.cpp' object='swig/ruby/swig_ruby_jellyfish_la-swig_wrap.lo' libtool=yes \
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unit_tests/bin_test_all-test_main.o: unit_tests/test_main.cc
	$(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(bin_test_all_CPPFLAGS) $(CPPFLAGS) $(bin_test_all_CXXFLAGS) $(CXXFLAGS) -MT unit_tests/bin_test_all-test_main.o -MD -MP -MF unit_tests/$(DEPDIR)/bin_test_all-test_main.Tpo -c -o unit_tests/bin_test_all-test_main.o `test -f 'unit_tests/test_main.cc' || echo '$(srcdir)/'`unit_tests/test_main.cc
	$(AM_V_at)$(am__mv) unit_tests/$(DEPDIR)/bin_test_all-test_main.Tpo unit_tests/$(DEPDIR)/bin_test_all-test_main.Po
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		       "legacy program 'compress' is deprecated." >&2
	@echo WARNING: "It will be removed altogether in Automake 2.0" >&2
	tardir=$(distdir) && $(am__tar) | compress -c >$(distdir).tar.Z
	$(am__post_remove_distdir)

dist-shar: distdir
	@echo WARNING: "Support for shar distribution archives is" \
	               "deprecated." >&2
	@echo WARNING: "It will be removed altogether in Automake 2.0" >&2
	shar $(distdir) | GZIP=$(GZIP_ENV) gzip -c >$(distdir).shar.gz
	$(am__post_remove_distdir)

dist-zip: distdir
	-rm -f $(distdir).zip
	zip -rq $(distdir).zip $(distdir)
	$(am__post_remove_distdir)

dist dist-all:
	$(MAKE) $(AM_MAKEFLAGS) $(DIST_TARGETS) am__post_remove_distdir='@:'
	$(am__post_remove_distdir)

# This target untars the dist file and tries a VPATH configuration.  Then
# it guarantees that the distribution is self-contained by making another
# tarfile.
distcheck: dist
	case '$(DIST_ARCHIVES)' in \
	*.tar.gz*) \
	  GZIP=$(GZIP_ENV) gzip -dc $(distdir).tar.gz | $(am__untar) ;;\
	*.tar.bz2*) \
	  bzip2 -dc $(distdir).tar.bz2 | $(am__untar) ;;\
	*.tar.lz*) \
	  lzip -dc $(distdir).tar.lz | $(am__untar) ;;\
	*.tar.xz*) \
	  xz -dc $(distdir).tar.xz | $(am__untar) ;;\
	*.tar.Z*) \
	  uncompress -c $(distdir).tar.Z | $(am__untar) ;;\
	*.shar.gz*) \
	  GZIP=$(GZIP_ENV) gzip -dc $(distdir).shar.gz | unshar ;;\
	*.zip*) \
	  unzip $(distdir).zip ;;\
	esac
	chmod -R a-w $(distdir)
	chmod u+w $(distdir)
	mkdir $(distdir)/_build $(distdir)/_build/sub $(distdir)/_inst
	chmod a-w $(distdir)
	test -d $(distdir)/_build || exit 0; \
	dc_install_base=`$(am__cd) $(distdir)/_inst && pwd | sed -e 's,^[^:\\/]:[\\/],/,'` \
	  && dc_destdir="$${TMPDIR-/tmp}/am-dc-$$$$/" \
	  && am__cwd=`pwd` \
	  && $(am__cd) $(distdir)/_build/sub \
	  && ../../configure \
	    $(AM_DISTCHECK_CONFIGURE_FLAGS) \
	    $(DISTCHECK_CONFIGURE_FLAGS) \
	    --srcdir=../.. --prefix="$$dc_install_base" \
	  && $(MAKE) $(AM_MAKEFLAGS) \
	  && $(MAKE) $(AM_MAKEFLAGS) dvi \
	  && $(MAKE) $(AM_MAKEFLAGS) check \
	  && $(MAKE) $(AM_MAKEFLAGS) install \
	  && $(MAKE) $(AM_MAKEFLAGS) installcheck \
	  && $(MAKE) $(AM_MAKEFLAGS) uninstall \
	  && $(MAKE) $(AM_MAKEFLAGS) distuninstallcheck_dir="$$dc_install_base" \
	        distuninstallcheck \
	  && chmod -R a-w "$$dc_install_base" \
	  && ({ \
	       (cd ../.. && umask 077 && mkdir "$$dc_destdir") \
	       && $(MAKE) $(AM_MAKEFLAGS) DESTDIR="$$dc_destdir" install \
	       && $(MAKE) $(AM_MAKEFLAGS) DESTDIR="$$dc_destdir" uninstall \
	       && $(MAKE) $(AM_MAKEFLAGS) DESTDIR="$$dc_destdir" \
	            distuninstallcheck_dir="$$dc_destdir" distuninstallcheck; \
	      } || { rm -rf "$$dc_destdir"; exit 1; }) \
	  && rm -rf "$$dc_destdir" \
	  && $(MAKE) $(AM_MAKEFLAGS) dist \
	  && rm -rf $(DIST_ARCHIVES) \
	  && $(MAKE) $(AM_MAKEFLAGS) distcleancheck \
	  && cd "$$am__cwd" \
	  || exit 1
	$(am__post_remove_distdir)
	@(echo "$(distdir) archives ready for distribution: "; \
	  list='$(DIST_ARCHIVES)'; for i in $$list; do echo $$i; done) | \
	  sed -e 1h -e 1s/./=/g -e 1p -e 1x -e '$$p' -e '$$x'
distuninstallcheck:
	@test -n '$(distuninstallcheck_dir)' || { \
	  echo 'ERROR: trying to run $@ with an empty' \
	       '$$(distuninstallcheck_dir)' >&2; \
	  exit 1; \
	}; \
	$(am__cd) '$(distuninstallcheck_dir)' || { \
	  echo 'ERROR: cannot chdir into $(distuninstallcheck_dir)' >&2; \
	  exit 1; \
	}; \
	test `$(am__distuninstallcheck_listfiles) | wc -l` -eq 0 \
	   || { echo "ERROR: files left after uninstall:" ; \
	        if test -n "$(DESTDIR)"; then \
	          echo "  (check DESTDIR support)"; \
	        fi ; \
	        $(distuninstallcheck_listfiles) ; \
	        exit 1; } >&2
distcleancheck: distclean
	@if test '$(srcdir)' = . ; then \
	  echo "ERROR: distcleancheck can only run from a VPATH build" ; \
	  exit 1 ; \
	fi
	@test `$(distcleancheck_listfiles) | wc -l` -eq 0 \
	  || { echo "ERROR: files left in build directory after distclean:" ; \
	       $(distcleancheck_listfiles) ; \
	       exit 1; } >&2
check-am: all-am
	$(MAKE) $(AM_MAKEFLAGS) $(check_LTLIBRARIES) $(check_PROGRAMS)
	$(MAKE) $(AM_MAKEFLAGS) check-TESTS
check: $(BUILT_SOURCES)
	$(MAKE) $(AM_MAKEFLAGS) check-am
all-am: Makefile $(LTLIBRARIES) $(PROGRAMS) $(SCRIPTS) $(MANS) $(DATA) \
		$(HEADERS) config.h
install-binPROGRAMS: install-libLTLIBRARIES

installdirs:
	for dir in "$(DESTDIR)$(libdir)" "$(DESTDIR)$(perlextdir)" "$(DESTDIR)$(pythonextdir)" "$(DESTDIR)$(rubyextdir)" "$(DESTDIR)$(bindir)" "$(DESTDIR)$(bindir)" "$(DESTDIR)$(perlextdir)" "$(DESTDIR)$(pythonextdir)" "$(DESTDIR)$(man1dir)" "$(DESTDIR)$(datadir)" "$(DESTDIR)$(pkgconfigdir)" "$(DESTDIR)$(library_includedir)"; do \
	  test -z "$$dir" || $(MKDIR_P) "$$dir"; \
	done
install: $(BUILT_SOURCES)
	$(MAKE) $(AM_MAKEFLAGS) install-am
install-exec: install-exec-am
install-data: install-data-am
uninstall: uninstall-am

install-am: all-am
	@$(MAKE) $(AM_MAKEFLAGS) install-exec-am install-data-am

installcheck: installcheck-am
install-strip:
	if test -z '$(STRIP)'; then \
	  $(MAKE) $(AM_MAKEFLAGS) INSTALL_PROGRAM="$(INSTALL_STRIP_PROGRAM)" \
	    install_sh_PROGRAM="$(INSTALL_STRIP_PROGRAM)" INSTALL_STRIP_FLAG=-s \
	      install; \
	else \
	  $(MAKE) $(AM_MAKEFLAGS) INSTALL_PROGRAM="$(INSTALL_STRIP_PROGRAM)" \
	    install_sh_PROGRAM="$(INSTALL_STRIP_PROGRAM)" INSTALL_STRIP_FLAG=-s \
	    "INSTALL_PROGRAM_ENV=STRIPPROG='$(STRIP)'" install; \
	fi
mostlyclean-generic:
	-test -z "$(TEST_LOGS)" || rm -f $(TEST_LOGS)
	-test -z "$(TEST_LOGS:.log=.trs)" || rm -f $(TEST_LOGS:.log=.trs)
	-test -z "$(TEST_SUITE_LOG)" || rm -f $(TEST_SUITE_LOG)

clean-generic:
	-test -z "$(CLEANFILES)" || rm -f $(CLEANFILES)

distclean-generic:
	-test -z "$(CONFIG_CLEAN_FILES)" || rm -f $(CONFIG_CLEAN_FILES)
	-test . = "$(srcdir)" || test -z "$(CONFIG_CLEAN_VPATH_FILES)" || rm -f $(CONFIG_CLEAN_VPATH_FILES)
	-rm -f bin/$(am__dirstamp)
	-rm -f jellyfish/$(DEPDIR)/$(am__dirstamp)
	-rm -f jellyfish/$(am__dirstamp)
	-rm -f lib/$(DEPDIR)/$(am__dirstamp)
	-rm -f lib/$(am__dirstamp)
	-rm -f sub_commands/$(DEPDIR)/$(am__dirstamp)
	-rm -f sub_commands/$(am__dirstamp)
	-rm -f swig/perl5/$(DEPDIR)/$(am__dirstamp)
	-rm -f swig/perl5/$(am__dirstamp)
	-rm -f swig/python/$(DEPDIR)/$(am__dirstamp)
	-rm -f swig/python/$(am__dirstamp)
	-rm -f swig/ruby/$(DEPDIR)/$(am__dirstamp)
	-rm -f swig/ruby/$(am__dirstamp)
	-rm -f unit_tests/$(DEPDIR)/$(am__dirstamp)
	-rm -f unit_tests/$(am__dirstamp)
	-rm -f unit_tests/gtest/src/$(DEPDIR)/$(am__dirstamp)
	-rm -f unit_tests/gtest/src/$(am__dirstamp)
	-test -z "$(DISTCLEANFILES)" || rm -f $(DISTCLEANFILES)

maintainer-clean-generic:
	@echo "This command is intended for maintainers to use"
	@echo "it deletes files that may require special tools to rebuild."
	-test -z "$(BUILT_SOURCES)" || rm -f $(BUILT_SOURCES)
clean: clean-am

clean-am: clean-binPROGRAMS clean-checkLTLIBRARIES clean-checkPROGRAMS \
	clean-generic clean-libLTLIBRARIES clean-libtool clean-local \
	clean-perlextLTLIBRARIES clean-pythonextLTLIBRARIES \
	clean-rubyextLTLIBRARIES mostlyclean-am

distclean: distclean-am
	-rm -f $(am__CONFIG_DISTCLEAN_FILES)
	-rm -rf jellyfish/$(DEPDIR) lib/$(DEPDIR) sub_commands/$(DEPDIR) swig/perl5/$(DEPDIR) swig/python/$(DEPDIR) swig/ruby/$(DEPDIR) unit_tests/$(DEPDIR) unit_tests/gtest/src/$(DEPDIR)
	-rm -f Makefile
distclean-am: clean-am distclean-compile distclean-generic \
	distclean-hdr distclean-libtool distclean-tags

dvi: dvi-am

dvi-am:

html: html-am

html-am:

info: info-am

info-am:

install-data-am: install-dataDATA install-library_includeHEADERS \
	install-man install-perlextLTLIBRARIES install-perlextSCRIPTS \
	install-pkgconfigDATA install-pythonextLTLIBRARIES \
	install-pythonextSCRIPTS install-rubyextLTLIBRARIES

install-dvi: install-dvi-am

install-dvi-am:

install-exec-am: install-binPROGRAMS install-dist_binSCRIPTS \
	install-libLTLIBRARIES

install-html: install-html-am

install-html-am:

install-info: install-info-am

install-info-am:

install-man: install-man1

install-pdf: install-pdf-am

install-pdf-am:

install-ps: install-ps-am

install-ps-am:

installcheck-am:

maintainer-clean: maintainer-clean-am
	-rm -f $(am__CONFIG_DISTCLEAN_FILES)
	-rm -rf $(top_srcdir)/autom4te.cache
	-rm -rf jellyfish/$(DEPDIR) lib/$(DEPDIR) sub_commands/$(DEPDIR) swig/perl5/$(DEPDIR) swig/python/$(DEPDIR) swig/ruby/$(DEPDIR) unit_tests/$(DEPDIR) unit_tests/gtest/src/$(DEPDIR)
	-rm -f Makefile
maintainer-clean-am: distclean-am maintainer-clean-generic

mostlyclean: mostlyclean-am

mostlyclean-am: mostlyclean-compile mostlyclean-generic \
	mostlyclean-libtool

pdf: pdf-am

pdf-am:

ps: ps-am

ps-am:

uninstall-am: uninstall-binPROGRAMS uninstall-dataDATA \
	uninstall-dist_binSCRIPTS uninstall-libLTLIBRARIES \
	uninstall-library_includeHEADERS uninstall-man \
	uninstall-perlextLTLIBRARIES uninstall-perlextSCRIPTS \
	uninstall-pkgconfigDATA uninstall-pythonextLTLIBRARIES \
	uninstall-pythonextSCRIPTS uninstall-rubyextLTLIBRARIES

uninstall-man: uninstall-man1

.MAKE: all check check-am install install-am install-strip

.PHONY: CTAGS GTAGS TAGS all all-am am--refresh check check-TESTS \
	check-am clean clean-binPROGRAMS clean-checkLTLIBRARIES \
	clean-checkPROGRAMS clean-cscope clean-generic \
	clean-libLTLIBRARIES clean-libtool clean-local \
	clean-perlextLTLIBRARIES clean-pythonextLTLIBRARIES \
	clean-rubyextLTLIBRARIES cscope cscopelist-am ctags ctags-am \
	dist dist-all dist-bzip2 dist-gzip dist-lzip dist-shar \
	dist-tarZ dist-xz dist-zip distcheck distclean \
	distclean-compile distclean-generic distclean-hdr \
	distclean-libtool distclean-tags distcleancheck distdir \
	distuninstallcheck dvi dvi-am html html-am info info-am \
	install install-am install-binPROGRAMS install-data \
	install-data-am install-dataDATA install-dist_binSCRIPTS \
	install-dvi install-dvi-am install-exec install-exec-am \
	install-html install-html-am install-info install-info-am \
	install-libLTLIBRARIES install-library_includeHEADERS \
	install-man install-man1 install-pdf install-pdf-am \
	install-perlextLTLIBRARIES install-perlextSCRIPTS \
	install-pkgconfigDATA install-ps install-ps-am \
	install-pythonextLTLIBRARIES install-pythonextSCRIPTS \
	install-rubyextLTLIBRARIES install-strip installcheck \
	installcheck-am installdirs maintainer-clean \
	maintainer-clean-generic mostlyclean mostlyclean-compile \
	mostlyclean-generic mostlyclean-libtool pdf pdf-am ps ps-am \
	recheck tags tags-am uninstall uninstall-am \
	uninstall-binPROGRAMS uninstall-dataDATA \
	uninstall-dist_binSCRIPTS uninstall-libLTLIBRARIES \
	uninstall-library_includeHEADERS uninstall-man uninstall-man1 \
	uninstall-perlextLTLIBRARIES uninstall-perlextSCRIPTS \
	uninstall-pkgconfigDATA uninstall-pythonextLTLIBRARIES \
	uninstall-pythonextSCRIPTS uninstall-rubyextLTLIBRARIES

.PRECIOUS: Makefile

.yaggo.hpp:
	$(V_YAGGO)$(YAGGO) --license $(srcdir)/header-license -o $@ $<
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
tests/swig_python.log: tests/generate_sequence.log
tests/swig_ruby.log: tests/generate_sequence.log
tests/swig_perl.log: tests/generate_sequence.log
#%/swig_wrap.cpp: $(SWIG_SRC)
#	$(SWIG_V_GEN)$(SWIG) -$(notdir $*) -I$(srcdir)/../include -o $@ $<
%/swig_wrap.cc:
	@echo >&2 SWIG >= 3.x.x not found. Make sure it is install and rerun configure
	@false
#%/__init__.pyc: %/jellyfish.py
#	$(PYTHONC_V_GEN)$(PYTHON) -c 'import py_compile, sys; py_compile.compile(sys.argv[1], sys.argv[2])' $< $@
#swig/python/jellyfish.py: swig/python/swig_wrap.cpp
#swig/perl5/jellyfish.pm: swig/perl5/swig_wrap.cpp

#################
# SWIG bindings #
#################

-include $(srcdir)/development.mk

# Print the value of a variable
print-%:
	@echo -n $($*)

# Tell versions [3.59,3.63) of GNU make to not export all variables.
# Otherwise a system limit (for SysV at least) may be exceeded.
.NOEXPORT: