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PERL_EXT_LIB = @PERL_EXT_LIB@
PERL_EXT_PREFIX = @PERL_EXT_PREFIX@
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PYTHON = @PYTHON@
PYTHON_CPPFLAGS = @PYTHON_CPPFLAGS@
PYTHON_EXTRA_LDFLAGS = @PYTHON_EXTRA_LDFLAGS@
PYTHON_EXTRA_LIBS = @PYTHON_EXTRA_LIBS@
PYTHON_LDFLAGS = @PYTHON_LDFLAGS@
PYTHON_SITE_PKG = @PYTHON_SITE_PKG@
PYTHON_VERSION = @PYTHON_VERSION@
RANLIB = @RANLIB@
RUBY = @RUBY@
RUBY_EXT_CFLAGS = @RUBY_EXT_CFLAGS@
RUBY_EXT_LDFLAGS = @RUBY_EXT_LDFLAGS@
RUBY_EXT_LIB = @RUBY_EXT_LIB@
RUBY_EXT_LIBS = @RUBY_EXT_LIBS@
RUBY_VERSION = @RUBY_VERSION@
SED = @SED@
SET_MAKE = @SET_MAKE@
SHELL = @SHELL@
STATIC_FLAGS = @STATIC_FLAGS@
STRIP = @STRIP@
SWIG = @SWIG@
SWIG_LIB = @SWIG_LIB@
VALGRIND_CFLAGS = @VALGRIND_CFLAGS@
VALGRIND_LIBS = @VALGRIND_LIBS@
VERSION = @VERSION@
YAGGO = @YAGGO@
abs_builddir = @abs_builddir@
abs_srcdir = @abs_srcdir@
abs_top_builddir = @abs_top_builddir@
abs_top_srcdir = @abs_top_srcdir@
ac_ct_AR = @ac_ct_AR@
ac_ct_CC = @ac_ct_CC@
ac_ct_CXX = @ac_ct_CXX@
ac_ct_DUMPBIN = @ac_ct_DUMPBIN@
am__include = @am__include@
am__leading_dot = @am__leading_dot@
am__quote = @am__quote@
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builddir = @builddir@
datadir = @datadir@
datarootdir = @datarootdir@
docdir = @docdir@
dvidir = @dvidir@
exec_prefix = @exec_prefix@
host = @host@
host_alias = @host_alias@
host_cpu = @host_cpu@
host_os = @host_os@
host_vendor = @host_vendor@
htmldir = @htmldir@
includedir = @includedir@
infodir = @infodir@
install_sh = @install_sh@
libdir = @libdir@
libexecdir = @libexecdir@
localedir = @localedir@
localstatedir = @localstatedir@
mandir = @mandir@
mkdir_p = @mkdir_p@
oldincludedir = @oldincludedir@
pdfdir = @pdfdir@
prefix = @prefix@
program_transform_name = @program_transform_name@
psdir = @psdir@
sbindir = @sbindir@
sharedstatedir = @sharedstatedir@
srcdir = @srcdir@
sysconfdir = @sysconfdir@
target_alias = @target_alias@
top_build_prefix = @top_build_prefix@
top_builddir = @top_builddir@
top_srcdir = @top_srcdir@
ACLOCAL_AMFLAGS = -I m4
EXTRA_DIST = doc/jellyfish.pdf doc/jellyfish.man README LICENSE \
	$(TESTS) swig/python/test_mer_file.py \
	swig/python/test_hash_counter.py \
	swig/python/test_string_mers.py swig/ruby/test_mer_file.rb \
	swig/ruby/test_hash_counter.rb swig/ruby/test_string_mers.rb \
	swig/perl5/t/test_mer_file.t swig/perl5/t/test_hash_counter.t \
	swig/perl5/t/test_string_mers.t $(am__append_3) \
	$(am__append_8) $(GTEST_SRC)
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) jellyfish/fstream_default.hpp \
	jellyfish/dbg.hpp jellyfish/randomc.h \
	jellyfish/merge_files.hpp unit_tests/test_main.hpp
dist_bin_SCRIPTS = 
data_DATA = 
BUILT_SOURCES = $(YAGGO_SOURCES) $(am__append_1) $(am__append_4) \
	$(am__append_6)
CLEANFILES = $(am__append_2) $(am__append_5) $(am__append_7)
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-@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


###############
# 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

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

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

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

# Perl5 support
@PERL_BINDING_TRUE@PERL_BUILT = swig/perl5/swig_wrap.cpp swig/perl5/jellyfish.pm
@PERL_BINDING_TRUE@perlextdir = $(PERL_EXT_LIB)
@PERL_BINDING_TRUE@perlext_SCRIPTS = swig/perl5/jellyfish.pm
@PERL_BINDING_TRUE@perlext_LTLIBRARIES = swig/perl5/jellyfish.la
@PERL_BINDING_TRUE@swig_perl5_jellyfish_la_SOURCES = swig/perl5/swig_wrap.cpp $(SWIG_SRC)
@PERL_BINDING_TRUE@swig_perl5_jellyfish_la_CPPFLAGS = $(PERL_EXT_CPPFLAGS) -I$(PERL_EXT_INC) -I$(srcdir)/include
@PERL_BINDING_TRUE@swig_perl5_jellyfish_la_LDFLAGS = -module
@PERL_BINDING_TRUE@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
	$(MAKE) $(AM_MAKEFLAGS) all-am

.SUFFIXES:
.SUFFIXES: .cc .cpp .hpp .lo .log .o .obj .sh .sh$(EXEEXT) .trs .yaggo
am--refresh: Makefile
	@:
$(srcdir)/Makefile.in:  $(srcdir)/Makefile.am $(srcdir)/swig/Makefile.am $(srcdir)/gtest.mk $(am__configure_deps)
	@for dep in $?; do \
	  case '$(am__configure_deps)' in \
	    *$$dep*) \
	      echo ' cd $(srcdir) && $(AUTOMAKE) --foreign'; \
	      $(am__cd) $(srcdir) && $(AUTOMAKE) --foreign \
		&& exit 0; \
	      exit 1;; \
	  esac; \
	done; \
	echo ' cd $(top_srcdir) && $(AUTOMAKE) --foreign Makefile'; \
	$(am__cd) $(top_srcdir) && \
	  $(AUTOMAKE) --foreign Makefile
.PRECIOUS: Makefile
Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status
	@case '$?' in \
	  *config.status*) \
	    echo ' $(SHELL) ./config.status'; \
	    $(SHELL) ./config.status;; \
	  *) \
	    echo ' cd $(top_builddir) && $(SHELL) ./config.status $@ $(am__depfiles_maybe)'; \
	    cd $(top_builddir) && $(SHELL) ./config.status $@ $(am__depfiles_maybe);; \
	esac;
$(srcdir)/swig/Makefile.am $(srcdir)/gtest.mk:

$(top_builddir)/config.status: $(top_srcdir)/configure $(CONFIG_STATUS_DEPENDENCIES)
	$(SHELL) ./config.status --recheck

$(top_srcdir)/configure:  $(am__configure_deps)
	$(am__cd) $(srcdir) && $(AUTOCONF)
$(ACLOCAL_M4):  $(am__aclocal_m4_deps)
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$(am__aclocal_m4_deps):

config.h: stamp-h1
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	@test -f $@ || $(MAKE) $(AM_MAKEFLAGS) stamp-h1

stamp-h1: $(srcdir)/config.h.in $(top_builddir)/config.status
	@rm -f stamp-h1
	cd $(top_builddir) && $(SHELL) ./config.status config.h
$(srcdir)/config.h.in:  $(am__configure_deps) 
	($(am__cd) $(top_srcdir) && $(AUTOHEADER))
	rm -f stamp-h1
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distclean-hdr:
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tests/compat.sh: $(top_builddir)/config.status $(top_srcdir)/tests/compat.sh.in
	cd $(top_builddir) && $(SHELL) ./config.status $@
jellyfish-2.0.pc: $(top_builddir)/config.status $(srcdir)/jellyfish-2.0.pc.in
	cd $(top_builddir) && $(SHELL) ./config.status $@

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	locs=`for p in $$list; do echo $$p; done | \
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	      sort -u`; \
	test -z "$$locs" || { \
	  echo rm -f $${locs}; \
	  rm -f $${locs}; \
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install-libLTLIBRARIES: $(lib_LTLIBRARIES)
	@$(NORMAL_INSTALL)
	@list='$(lib_LTLIBRARIES)'; test -n "$(libdir)" || list=; \
	list2=; for p in $$list; do \
	  if test -f $$p; then \
	    list2="$$list2 $$p"; \
	  else :; fi; \
	done; \
	test -z "$$list2" || { \
	  echo " $(MKDIR_P) '$(DESTDIR)$(libdir)'"; \
	  $(MKDIR_P) "$(DESTDIR)$(libdir)" || exit 1; \
	  echo " $(LIBTOOL) $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) --mode=install $(INSTALL) $(INSTALL_STRIP_FLAG) $$list2 '$(DESTDIR)$(libdir)'"; \
	  $(LIBTOOL) $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) --mode=install $(INSTALL) $(INSTALL_STRIP_FLAG) $$list2 "$(DESTDIR)$(libdir)"; \
	}

uninstall-libLTLIBRARIES:
	@$(NORMAL_UNINSTALL)
	@list='$(lib_LTLIBRARIES)'; test -n "$(libdir)" || list=; \
	for p in $$list; do \
	  $(am__strip_dir) \
	  echo " $(LIBTOOL) $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) --mode=uninstall rm -f '$(DESTDIR)$(libdir)/$$f'"; \
	  $(LIBTOOL) $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) --mode=uninstall rm -f "$(DESTDIR)$(libdir)/$$f"; \
	done

clean-libLTLIBRARIES:
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	@list='$(lib_LTLIBRARIES)'; \
	locs=`for p in $$list; do echo $$p; done | \
	      sed 's|^[^/]*$$|.|; s|/[^/]*$$||; s|$$|/so_locations|' | \
	      sort -u`; \
	test -z "$$locs" || { \
	  echo rm -f $${locs}; \
	  rm -f $${locs}; \
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install-perlextLTLIBRARIES: $(perlext_LTLIBRARIES)
	@$(NORMAL_INSTALL)
	@list='$(perlext_LTLIBRARIES)'; test -n "$(perlextdir)" || list=; \
	list2=; for p in $$list; do \
	  if test -f $$p; then \
	    list2="$$list2 $$p"; \
	  else :; fi; \
	done; \
	test -z "$$list2" || { \
	  echo " $(MKDIR_P) '$(DESTDIR)$(perlextdir)'"; \
	  $(MKDIR_P) "$(DESTDIR)$(perlextdir)" || exit 1; \
	  echo " $(LIBTOOL) $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) --mode=install $(INSTALL) $(INSTALL_STRIP_FLAG) $$list2 '$(DESTDIR)$(perlextdir)'"; \
	  $(LIBTOOL) $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) --mode=install $(INSTALL) $(INSTALL_STRIP_FLAG) $$list2 "$(DESTDIR)$(perlextdir)"; \
	}

uninstall-perlextLTLIBRARIES:
	@$(NORMAL_UNINSTALL)
	@list='$(perlext_LTLIBRARIES)'; test -n "$(perlextdir)" || list=; \
	for p in $$list; do \
	  $(am__strip_dir) \
	  echo " $(LIBTOOL) $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) --mode=uninstall rm -f '$(DESTDIR)$(perlextdir)/$$f'"; \
	  $(LIBTOOL) $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) --mode=uninstall rm -f "$(DESTDIR)$(perlextdir)/$$f"; \
	done

clean-perlextLTLIBRARIES:
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	@list='$(perlext_LTLIBRARIES)'; \
	locs=`for p in $$list; do echo $$p; done | \
	      sed 's|^[^/]*$$|.|; s|/[^/]*$$||; s|$$|/so_locations|' | \
	      sort -u`; \
	test -z "$$locs" || { \
	  echo rm -f $${locs}; \
	  rm -f $${locs}; \
	}

install-pythonextLTLIBRARIES: $(pythonext_LTLIBRARIES)
	@$(NORMAL_INSTALL)
	@list='$(pythonext_LTLIBRARIES)'; test -n "$(pythonextdir)" || list=; \
	list2=; for p in $$list; do \
	  if test -f $$p; then \
	    list2="$$list2 $$p"; \
	  else :; fi; \
	done; \
	test -z "$$list2" || { \
	  echo " $(MKDIR_P) '$(DESTDIR)$(pythonextdir)'"; \
	  $(MKDIR_P) "$(DESTDIR)$(pythonextdir)" || exit 1; \
	  echo " $(LIBTOOL) $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) --mode=install $(INSTALL) $(INSTALL_STRIP_FLAG) $$list2 '$(DESTDIR)$(pythonextdir)'"; \
	  $(LIBTOOL) $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) --mode=install $(INSTALL) $(INSTALL_STRIP_FLAG) $$list2 "$(DESTDIR)$(pythonextdir)"; \
	}

uninstall-pythonextLTLIBRARIES:
	@$(NORMAL_UNINSTALL)
	@list='$(pythonext_LTLIBRARIES)'; test -n "$(pythonextdir)" || list=; \
	for p in $$list; do \
	  $(am__strip_dir) \
	  echo " $(LIBTOOL) $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) --mode=uninstall rm -f '$(DESTDIR)$(pythonextdir)/$$f'"; \
	  $(LIBTOOL) $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) --mode=uninstall rm -f "$(DESTDIR)$(pythonextdir)/$$f"; \
	done

clean-pythonextLTLIBRARIES:
	-test -z "$(pythonext_LTLIBRARIES)" || rm -f $(pythonext_LTLIBRARIES)
	@list='$(pythonext_LTLIBRARIES)'; \
	locs=`for p in $$list; do echo $$p; done | \
	      sed 's|^[^/]*$$|.|; s|/[^/]*$$||; s|$$|/so_locations|' | \
	      sort -u`; \
	test -z "$$locs" || { \
	  echo rm -f $${locs}; \
	  rm -f $${locs}; \
	}

install-rubyextLTLIBRARIES: $(rubyext_LTLIBRARIES)
	@$(NORMAL_INSTALL)
	@list='$(rubyext_LTLIBRARIES)'; test -n "$(rubyextdir)" || list=; \
	list2=; for p in $$list; do \
	  if test -f $$p; then \
	    list2="$$list2 $$p"; \
	  else :; fi; \
	done; \
	test -z "$$list2" || { \
	  echo " $(MKDIR_P) '$(DESTDIR)$(rubyextdir)'"; \
	  $(MKDIR_P) "$(DESTDIR)$(rubyextdir)" || exit 1; \
	  echo " $(LIBTOOL) $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) --mode=install $(INSTALL) $(INSTALL_STRIP_FLAG) $$list2 '$(DESTDIR)$(rubyextdir)'"; \
	  $(LIBTOOL) $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) --mode=install $(INSTALL) $(INSTALL_STRIP_FLAG) $$list2 "$(DESTDIR)$(rubyextdir)"; \
	}

uninstall-rubyextLTLIBRARIES:
	@$(NORMAL_UNINSTALL)
	@list='$(rubyext_LTLIBRARIES)'; test -n "$(rubyextdir)" || list=; \
	for p in $$list; do \
	  $(am__strip_dir) \
	  echo " $(LIBTOOL) $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) --mode=uninstall rm -f '$(DESTDIR)$(rubyextdir)/$$f'"; \
	  $(LIBTOOL) $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) --mode=uninstall rm -f "$(DESTDIR)$(rubyextdir)/$$f"; \
	done

clean-rubyextLTLIBRARIES:
	-test -z "$(rubyext_LTLIBRARIES)" || rm -f $(rubyext_LTLIBRARIES)
	@list='$(rubyext_LTLIBRARIES)'; \
	locs=`for p in $$list; do echo $$p; done | \
	      sed 's|^[^/]*$$|.|; s|/[^/]*$$||; s|$$|/so_locations|' | \
	      sort -u`; \
	test -z "$$locs" || { \
	  echo rm -f $${locs}; \
	  rm -f $${locs}; \
	}
unit_tests/gtest/src/$(am__dirstamp):
	@$(MKDIR_P) unit_tests/gtest/src
	@: > unit_tests/gtest/src/$(am__dirstamp)
unit_tests/gtest/src/$(DEPDIR)/$(am__dirstamp):
	@$(MKDIR_P) unit_tests/gtest/src/$(DEPDIR)
	@: > unit_tests/gtest/src/$(DEPDIR)/$(am__dirstamp)
unit_tests/gtest/src/libgtest_la-gtest-all.lo:  \
	unit_tests/gtest/src/$(am__dirstamp) \
	unit_tests/gtest/src/$(DEPDIR)/$(am__dirstamp)

libgtest.la: $(libgtest_la_OBJECTS) $(libgtest_la_DEPENDENCIES) $(EXTRA_libgtest_la_DEPENDENCIES) 
	$(AM_V_CXXLD)$(libgtest_la_LINK)  $(libgtest_la_OBJECTS) $(libgtest_la_LIBADD) $(LIBS)
unit_tests/gtest/src/libgtest_main_la-gtest_main.lo:  \
	unit_tests/gtest/src/$(am__dirstamp) \
	unit_tests/gtest/src/$(DEPDIR)/$(am__dirstamp)

libgtest_main.la: $(libgtest_main_la_OBJECTS) $(libgtest_main_la_DEPENDENCIES) $(EXTRA_libgtest_main_la_DEPENDENCIES) 
	$(AM_V_CXXLD)$(libgtest_main_la_LINK)  $(libgtest_main_la_OBJECTS) $(libgtest_main_la_LIBADD) $(LIBS)
lib/$(am__dirstamp):
	@$(MKDIR_P) lib
	@: > lib/$(am__dirstamp)
lib/$(DEPDIR)/$(am__dirstamp):
	@$(MKDIR_P) lib/$(DEPDIR)
	@: > lib/$(DEPDIR)/$(am__dirstamp)
lib/rectangular_binary_matrix.lo: lib/$(am__dirstamp) \
	lib/$(DEPDIR)/$(am__dirstamp)
lib/mer_dna.lo: lib/$(am__dirstamp) lib/$(DEPDIR)/$(am__dirstamp)
lib/storage.lo: lib/$(am__dirstamp) lib/$(DEPDIR)/$(am__dirstamp)
lib/allocators_mmap.lo: lib/$(am__dirstamp) \
	lib/$(DEPDIR)/$(am__dirstamp)
lib/misc.lo: lib/$(am__dirstamp) lib/$(DEPDIR)/$(am__dirstamp)
lib/int128.lo: lib/$(am__dirstamp) lib/$(DEPDIR)/$(am__dirstamp)
lib/thread_exec.lo: lib/$(am__dirstamp) lib/$(DEPDIR)/$(am__dirstamp)
lib/jsoncpp.lo: lib/$(am__dirstamp) lib/$(DEPDIR)/$(am__dirstamp)
lib/time.lo: lib/$(am__dirstamp) lib/$(DEPDIR)/$(am__dirstamp)
lib/generator_manager.lo: lib/$(am__dirstamp) \
	lib/$(DEPDIR)/$(am__dirstamp)

libjellyfish-2.0.la: $(libjellyfish_2_0_la_OBJECTS) $(libjellyfish_2_0_la_DEPENDENCIES) $(EXTRA_libjellyfish_2_0_la_DEPENDENCIES) 
	$(AM_V_CXXLD)$(libjellyfish_2_0_la_LINK) -rpath $(libdir) $(libjellyfish_2_0_la_OBJECTS) $(libjellyfish_2_0_la_LIBADD) $(LIBS)
swig/perl5/$(am__dirstamp):
	@$(MKDIR_P) swig/perl5
	@: > swig/perl5/$(am__dirstamp)
swig/perl5/$(DEPDIR)/$(am__dirstamp):
	@$(MKDIR_P) swig/perl5/$(DEPDIR)
	@: > swig/perl5/$(DEPDIR)/$(am__dirstamp)
swig/perl5/swig_perl5_jellyfish_la-swig_wrap.lo:  \
	swig/perl5/$(am__dirstamp) \
	swig/perl5/$(DEPDIR)/$(am__dirstamp)

swig/perl5/jellyfish.la: $(swig_perl5_jellyfish_la_OBJECTS) $(swig_perl5_jellyfish_la_DEPENDENCIES) $(EXTRA_swig_perl5_jellyfish_la_DEPENDENCIES) swig/perl5/$(am__dirstamp)
	$(AM_V_CXXLD)$(swig_perl5_jellyfish_la_LINK) $(am_swig_perl5_jellyfish_la_rpath) $(swig_perl5_jellyfish_la_OBJECTS) $(swig_perl5_jellyfish_la_LIBADD) $(LIBS)
swig/python/$(am__dirstamp):
	@$(MKDIR_P) swig/python
	@: > swig/python/$(am__dirstamp)
swig/python/$(DEPDIR)/$(am__dirstamp):
	@$(MKDIR_P) swig/python/$(DEPDIR)
	@: > swig/python/$(DEPDIR)/$(am__dirstamp)
swig/python/swig_python__jellyfish_la-swig_wrap.lo:  \
	swig/python/$(am__dirstamp) \
	swig/python/$(DEPDIR)/$(am__dirstamp)

swig/python/_jellyfish.la: $(swig_python__jellyfish_la_OBJECTS) $(swig_python__jellyfish_la_DEPENDENCIES) $(EXTRA_swig_python__jellyfish_la_DEPENDENCIES) swig/python/$(am__dirstamp)
	$(AM_V_CXXLD)$(swig_python__jellyfish_la_LINK) $(am_swig_python__jellyfish_la_rpath) $(swig_python__jellyfish_la_OBJECTS) $(swig_python__jellyfish_la_LIBADD) $(LIBS)
swig/ruby/$(am__dirstamp):
	@$(MKDIR_P) swig/ruby
	@: > swig/ruby/$(am__dirstamp)
swig/ruby/$(DEPDIR)/$(am__dirstamp):
	@$(MKDIR_P) swig/ruby/$(DEPDIR)
	@: > swig/ruby/$(DEPDIR)/$(am__dirstamp)
swig/ruby/swig_ruby_jellyfish_la-swig_wrap.lo:  \
	swig/ruby/$(am__dirstamp) swig/ruby/$(DEPDIR)/$(am__dirstamp)

swig/ruby/jellyfish.la: $(swig_ruby_jellyfish_la_OBJECTS) $(swig_ruby_jellyfish_la_DEPENDENCIES) $(EXTRA_swig_ruby_jellyfish_la_DEPENDENCIES) swig/ruby/$(am__dirstamp)
	$(AM_V_CXXLD)$(swig_ruby_jellyfish_la_LINK) $(am_swig_ruby_jellyfish_la_rpath) $(swig_ruby_jellyfish_la_OBJECTS) $(swig_ruby_jellyfish_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/$(am__dirstamp):
	@$(MKDIR_P) jellyfish
	@: > jellyfish/$(am__dirstamp)
jellyfish/$(DEPDIR)/$(am__dirstamp):
	@$(MKDIR_P) jellyfish/$(DEPDIR)
	@: > jellyfish/$(DEPDIR)/$(am__dirstamp)
jellyfish/generate_sequence.$(OBJEXT): jellyfish/$(am__dirstamp) \
	jellyfish/$(DEPDIR)/$(am__dirstamp)
jellyfish/mersenne.$(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)/$(am__dirstamp)
bin/$(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) $(LIBS)
sub_commands/$(am__dirstamp):
	@$(MKDIR_P) sub_commands
	@: > sub_commands/$(am__dirstamp)
sub_commands/$(DEPDIR)/$(am__dirstamp):
	@$(MKDIR_P) sub_commands/$(DEPDIR)
	@: > sub_commands/$(DEPDIR)/$(am__dirstamp)
sub_commands/jellyfish.$(OBJEXT): sub_commands/$(am__dirstamp) \
	sub_commands/$(DEPDIR)/$(am__dirstamp)
sub_commands/count_main.$(OBJEXT): sub_commands/$(am__dirstamp) \
	sub_commands/$(DEPDIR)/$(am__dirstamp)
sub_commands/info_main.$(OBJEXT): sub_commands/$(am__dirstamp) \
	sub_commands/$(DEPDIR)/$(am__dirstamp)
sub_commands/dump_main.$(OBJEXT): sub_commands/$(am__dirstamp) \
	sub_commands/$(DEPDIR)/$(am__dirstamp)
sub_commands/histo_main.$(OBJEXT): sub_commands/$(am__dirstamp) \
	sub_commands/$(DEPDIR)/$(am__dirstamp)
sub_commands/stats_main.$(OBJEXT): sub_commands/$(am__dirstamp) \
	sub_commands/$(DEPDIR)/$(am__dirstamp)
sub_commands/merge_main.$(OBJEXT): sub_commands/$(am__dirstamp) \
	sub_commands/$(DEPDIR)/$(am__dirstamp)
sub_commands/bc_main.$(OBJEXT): sub_commands/$(am__dirstamp) \
	sub_commands/$(DEPDIR)/$(am__dirstamp)
sub_commands/query_main.$(OBJEXT): sub_commands/$(am__dirstamp) \
	sub_commands/$(DEPDIR)/$(am__dirstamp)
sub_commands/cite_main.$(OBJEXT): sub_commands/$(am__dirstamp) \
	sub_commands/$(DEPDIR)/$(am__dirstamp)
sub_commands/mem_main.$(OBJEXT): sub_commands/$(am__dirstamp) \
	sub_commands/$(DEPDIR)/$(am__dirstamp)
jellyfish/merge_files.$(OBJEXT): jellyfish/$(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)
	$(AM_V_CXXLD)$(bin_jellyfish_LINK) $(bin_jellyfish_OBJECTS) $(bin_jellyfish_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_all-test_main.$(OBJEXT):  \
	unit_tests/$(am__dirstamp) \
	unit_tests/$(DEPDIR)/$(am__dirstamp)
unit_tests/bin_test_all-test_misc.$(OBJEXT):  \
	unit_tests/$(am__dirstamp) \
	unit_tests/$(DEPDIR)/$(am__dirstamp)
unit_tests/bin_test_all-test_offsets_key_value.$(OBJEXT):  \
	unit_tests/$(am__dirstamp) \
	unit_tests/$(DEPDIR)/$(am__dirstamp)
unit_tests/bin_test_all-test_simple_circular_buffer.$(OBJEXT):  \
	unit_tests/$(am__dirstamp) \
	unit_tests/$(DEPDIR)/$(am__dirstamp)
unit_tests/bin_test_all-test_rectangular_binary_matrix.$(OBJEXT):  \
	unit_tests/$(am__dirstamp) \
	unit_tests/$(DEPDIR)/$(am__dirstamp)
unit_tests/bin_test_all-test_mer_dna.$(OBJEXT):  \
	unit_tests/$(am__dirstamp) \
	unit_tests/$(DEPDIR)/$(am__dirstamp)
unit_tests/bin_test_all-test_large_hash_array.$(OBJEXT):  \
	unit_tests/$(am__dirstamp) \
	unit_tests/$(DEPDIR)/$(am__dirstamp)
unit_tests/bin_test_all-test_mer_overlap_sequence_parser.$(OBJEXT):  \
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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

.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
@HAVE_SWIG_TRUE@%/swig_wrap.cpp: $(SWIG_SRC)
@HAVE_SWIG_TRUE@	$(SWIG_V_GEN)$(SWIG) -$(notdir $*) -I$(srcdir)/../include -o $@ $<
@HAVE_SWIG_FALSE@%/swig_wrap.cpp:
@HAVE_SWIG_FALSE@	@echo >&2 SWIG >= 3.x.x not found. Make sure it is install and rerun configure
@HAVE_SWIG_FALSE@	@false
@PYTHON_BINDING_TRUE@%/__init__.pyc: %/jellyfish.py
@PYTHON_BINDING_TRUE@	$(PYTHONC_V_GEN)$(PYTHON) -c 'import py_compile, sys; py_compile.compile(sys.argv[1], sys.argv[2])' $< $@
@PYTHON_BINDING_TRUE@swig/python/jellyfish.py: swig/python/swig_wrap.cpp
@PERL_BINDING_TRUE@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:
