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cufflinks 1.3.0-2
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# Makefile.in generated by automake 1.9.6 from Makefile.am.
# @configure_input@

# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
# 2003, 2004, 2005  Free Software Foundation, Inc.
# This Makefile.in is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
# with or without modifications, as long as this notice is preserved.

# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY, to the extent permitted by law; without
# even the implied warranty of MERCHANTABILITY or FITNESS FOR A
# PARTICULAR PURPOSE.

@SET_MAKE@

#include $(top_srcdir)/build-aux/cufflinks.mk




srcdir = @srcdir@
top_srcdir = @top_srcdir@
VPATH = @srcdir@
pkgdatadir = $(datadir)/@PACKAGE@
pkglibdir = $(libdir)/@PACKAGE@
pkgincludedir = $(includedir)/@PACKAGE@
top_builddir = ..
am__cd = CDPATH="$${ZSH_VERSION+.}$(PATH_SEPARATOR)" && cd
INSTALL = @INSTALL@
install_sh_DATA = $(install_sh) -c -m 644
install_sh_PROGRAM = $(install_sh) -c
install_sh_SCRIPT = $(install_sh) -c
INSTALL_HEADER = $(INSTALL_DATA)
transform = $(program_transform_name)
NORMAL_INSTALL = :
PRE_INSTALL = :
POST_INSTALL = :
NORMAL_UNINSTALL = :
PRE_UNINSTALL = :
POST_UNINSTALL = :
build_triplet = @build@
host_triplet = @host@
bin_PROGRAMS = cufflinks$(EXEEXT) cuffcompare$(EXEEXT) \
	cuffdiff$(EXEEXT) gtf_to_sam$(EXEEXT) compress_gtf$(EXEEXT) \
	gffread$(EXEEXT)
subdir = src
DIST_COMMON = $(dist_bin_SCRIPTS) $(noinst_HEADERS) \
	$(srcdir)/Makefile.am $(srcdir)/Makefile.in
ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
am__aclocal_m4_deps = $(top_srcdir)/ax_boost_base.m4 \
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am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
	$(ACLOCAL_M4)
mkinstalldirs = $(install_sh) -d
CONFIG_HEADER = $(top_builddir)/config.h
CONFIG_CLEAN_FILES =
LIBRARIES = $(noinst_LIBRARIES)
AR = ar
ARFLAGS = cru
libcufflinks_a_AR = $(AR) $(ARFLAGS)
libcufflinks_a_LIBADD =
am_libcufflinks_a_OBJECTS = clustering.$(OBJEXT) \
	differential.$(OBJEXT) common.$(OBJEXT) assemble.$(OBJEXT) \
	tokenize.$(OBJEXT) abundances.$(OBJEXT) scaffolds.$(OBJEXT) \
	hits.$(OBJEXT) genes.$(OBJEXT) bundles.$(OBJEXT) \
	filters.$(OBJEXT) scaffold_graph.$(OBJEXT) \
	matching_merge.$(OBJEXT) graph_optimize.$(OBJEXT) \
	biascorrection.$(OBJEXT) sampling.$(OBJEXT) adap.$(OBJEXT) \
	ar_funs.$(OBJEXT) arith.$(OBJEXT) band.$(OBJEXT) \
	c_args.$(OBJEXT) c_plot.$(OBJEXT) cmd.$(OBJEXT) \
	dens_haz.$(OBJEXT) dens_int.$(OBJEXT) dens_odi.$(OBJEXT) \
	density.$(OBJEXT) dist.$(OBJEXT) ev_atree.$(OBJEXT) \
	ev_interp.$(OBJEXT) ev_kdtre.$(OBJEXT) ev_main.$(OBJEXT) \
	ev_trian.$(OBJEXT) family.$(OBJEXT) fitted.$(OBJEXT) \
	frend.$(OBJEXT) help.$(OBJEXT) lf_dercor.$(OBJEXT) \
	lf_fitfun.$(OBJEXT) lf_robust.$(OBJEXT) lf_vari.$(OBJEXT) \
	lfd.$(OBJEXT) lfstr.$(OBJEXT) linalg.$(OBJEXT) \
	locfit.$(OBJEXT) m_chol.$(OBJEXT) m_eigen.$(OBJEXT) \
	m_jacob.$(OBJEXT) m_max.$(OBJEXT) makecmd.$(OBJEXT) \
	math.$(OBJEXT) minmax.$(OBJEXT) nbhd.$(OBJEXT) pcomp.$(OBJEXT) \
	pout.$(OBJEXT) preplot.$(OBJEXT) random.$(OBJEXT) \
	readfile.$(OBJEXT) scb.$(OBJEXT) scb_cons.$(OBJEXT) \
	simul.$(OBJEXT) solve.$(OBJEXT) startlf.$(OBJEXT) \
	strings.$(OBJEXT) vari.$(OBJEXT) wdiag.$(OBJEXT) \
	weight.$(OBJEXT) replicates.$(OBJEXT) multireads.$(OBJEXT) \
	jensen_shannon.$(OBJEXT)
libcufflinks_a_OBJECTS = $(am_libcufflinks_a_OBJECTS)
libgc_a_AR = $(AR) $(ARFLAGS)
libgc_a_LIBADD =
am_libgc_a_OBJECTS = codons.$(OBJEXT) GArgs.$(OBJEXT) GBase.$(OBJEXT) \
	gdna.$(OBJEXT) GStr.$(OBJEXT) GFaSeqGet.$(OBJEXT) \
	GFastaIndex.$(OBJEXT) gff.$(OBJEXT) gff_utils.$(OBJEXT) \
	gtf_tracking.$(OBJEXT)
libgc_a_OBJECTS = $(am_libgc_a_OBJECTS)
am__installdirs = "$(DESTDIR)$(bindir)" "$(DESTDIR)$(bindir)"
binPROGRAMS_INSTALL = $(INSTALL_PROGRAM)
PROGRAMS = $(bin_PROGRAMS)
am_compress_gtf_OBJECTS = compress_gtf.$(OBJEXT)
compress_gtf_OBJECTS = $(am_compress_gtf_OBJECTS)
am__DEPENDENCIES_1 =
compress_gtf_DEPENDENCIES = libcufflinks.a libgc.a \
	$(am__DEPENDENCIES_1) $(am__DEPENDENCIES_1)
am_cuffcompare_OBJECTS = cuffcompare.$(OBJEXT)
cuffcompare_OBJECTS = $(am_cuffcompare_OBJECTS)
cuffcompare_DEPENDENCIES = libgc.a
am_cuffdiff_OBJECTS = cuffdiff.$(OBJEXT)
cuffdiff_OBJECTS = $(am_cuffdiff_OBJECTS)
cuffdiff_DEPENDENCIES = libcufflinks.a libgc.a $(am__DEPENDENCIES_1) \
	$(am__DEPENDENCIES_1)
am_cufflinks_OBJECTS = cufflinks.$(OBJEXT)
cufflinks_OBJECTS = $(am_cufflinks_OBJECTS)
cufflinks_DEPENDENCIES = libcufflinks.a libgc.a $(am__DEPENDENCIES_1) \
	$(am__DEPENDENCIES_1)
am_gffread_OBJECTS = gffread.$(OBJEXT)
gffread_OBJECTS = $(am_gffread_OBJECTS)
gffread_DEPENDENCIES = libgc.a
am_gtf_to_sam_OBJECTS = gtf_to_sam.$(OBJEXT)
gtf_to_sam_OBJECTS = $(am_gtf_to_sam_OBJECTS)
gtf_to_sam_DEPENDENCIES = libcufflinks.a libgc.a $(am__DEPENDENCIES_1) \
	$(am__DEPENDENCIES_1)
dist_binSCRIPT_INSTALL = $(INSTALL_SCRIPT)
SCRIPTS = $(dist_bin_SCRIPTS)
DEFAULT_INCLUDES = -I. -I$(srcdir) -I$(top_builddir)
depcomp = $(SHELL) $(top_srcdir)/build-aux/depcomp
am__depfiles_maybe = depfiles
COMPILE = $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) \
	$(CPPFLAGS) $(AM_CFLAGS) $(CFLAGS)
CCLD = $(CC)
LINK = $(CCLD) $(AM_CFLAGS) $(CFLAGS) $(AM_LDFLAGS) $(LDFLAGS) -o $@
CXXCOMPILE = $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) \
	$(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS)
CXXLD = $(CXX)
CXXLINK = $(CXXLD) $(AM_CXXFLAGS) $(CXXFLAGS) $(AM_LDFLAGS) $(LDFLAGS) \
	-o $@
SOURCES = $(libcufflinks_a_SOURCES) $(libgc_a_SOURCES) \
	$(compress_gtf_SOURCES) $(cuffcompare_SOURCES) \
	$(cuffdiff_SOURCES) $(cufflinks_SOURCES) $(gffread_SOURCES) \
	$(gtf_to_sam_SOURCES)
DIST_SOURCES = $(libcufflinks_a_SOURCES) $(libgc_a_SOURCES) \
	$(compress_gtf_SOURCES) $(cuffcompare_SOURCES) \
	$(cuffdiff_SOURCES) $(cufflinks_SOURCES) $(gffread_SOURCES) \
	$(gtf_to_sam_SOURCES)
HEADERS = $(noinst_HEADERS)
ETAGS = etags
CTAGS = ctags
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BAM_LDFLAGS = @BAM_LDFLAGS@
BAM_LIB = @BAM_LIB@
BOOST_CPPFLAGS = @BOOST_CPPFLAGS@
BOOST_LDFLAGS = @BOOST_LDFLAGS@
BOOST_THREAD_LIB = @BOOST_THREAD_LIB@
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CFLAGS = @CFLAGS@
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CPPFLAGS = @CPPFLAGS@
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CXXFLAGS = @CXXFLAGS@
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ECHO_T = @ECHO_T@
EGREP = @EGREP@
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INSTALL_DATA = @INSTALL_DATA@
INSTALL_PROGRAM = @INSTALL_PROGRAM@
INSTALL_SCRIPT = @INSTALL_SCRIPT@
INSTALL_STRIP_PROGRAM = @INSTALL_STRIP_PROGRAM@
LDFLAGS = @LDFLAGS@
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PYTHON_PREFIX = @PYTHON_PREFIX@
PYTHON_VERSION = @PYTHON_VERSION@
RANLIB = @RANLIB@
SET_MAKE = @SET_MAKE@
SHELL = @SHELL@
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VERSION = @VERSION@
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exec_prefix = @exec_prefix@
host = @host@
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host_os = @host_os@
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includedir = @includedir@
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AM_CPPFLAGS = -I$(top_srcdir)/src 
EXTRA_DIST = \
    $(top_srcdir)/AUTHORS $(top_srcdir)/make_bin.sh

AM_CXXFLAGS = 
#    cuffcluster 
#	gtf_reads
noinst_HEADERS = \
	update_check.h \
	biascorrection.h \
	codons.h \
	clustering.h \
	differential.h \
	GArgs.h \
	GBase.h \
	gdna.h \
	GFaSeqGet.h \
	GFastaIndex.h \
	gff.h \
	GHash.hh \
	GList.hh \
	GStr.h \
	assemble.h \
	bundles.h \
	filters.h \
	hits.h \
	tokenize.h \
	scaffolds.h \
	abundances.h \
	genes.h \
	transitive_closure.h \
	transitive_reduction.h \
	gff_utils.h \
	gtf_tracking.h \
	progressbar.h \
	bundles.h \
    scaffold_graph.h \
    matching_merge.h \
    graph_optimize.h \
    jensen_shannon.h \
    sampling.h \
	lemon/maps.h \
	lemon/bin_heap.h \
	lemon/fib_heap.h \
	lemon/bipartite_matching.h \
	lemon/topology.h \
	lemon/bucket_heap.h \
	lemon/smart_graph.h \
	lemon/list_graph.h \
	lemon/error.h \
	lemon/graph_utils.h \
	lemon/bfs.h \
	lemon/dfs.h \
	lemon/math.h \
	lemon/tolerance.h \
	lemon/graph_adaptor.h \
	lemon/concept_check.h \
	lemon/bits/default_map.h \
	lemon/bits/array_map.h \
	lemon/bits/vector_map.h \
	lemon/bits/debug_map.h \
	lemon/bits/map_extender.h \
	lemon/bits/base_extender.h \
	lemon/bits/graph_adaptor_extender.h \
	lemon/bits/graph_extender.h \
	lemon/bits/invalid.h \
	lemon/bits/path_dump.h \
	lemon/bits/traits.h \
	lemon/bits/utility.h \
	lemon/bits/alteration_notifier.h \
	lemon/bits/variant.h \
	lemon/concepts/graph.h \
	lemon/concepts/bpugraph.h \
	lemon/concepts/graph_components.h \
	lemon/concepts/ugraph.h \
	lemon/concepts/heap.h \
	lemon/concepts/maps.h \
	lemon/concepts/path.h \
	lemon/concepts/matrix_maps.h \
    locfit/design.h	\
    locfit/lfcons.h	\
    locfit/lfstruc.h \
    locfit/local.h \
    locfit/imatlb.h	\
    locfit/lffuns.h	\
    locfit/lfwin.h \
    locfit/mutil.h \
    locfit/vari.hpp \
    replicates.h \
    multireads.h \
	common.h 

noinst_LIBRARIES = libcufflinks.a libgc.a
libcufflinks_a_SOURCES = \
	clustering.cpp \
	differential.cpp \
	common.cpp \
	assemble.cpp \
	tokenize.cpp \
	abundances.cpp \
	scaffolds.cpp \
	hits.cpp \
	genes.cpp \
	bundles.cpp \
	filters.cpp \
    scaffold_graph.cpp \
    matching_merge.cpp \
    graph_optimize.cpp \
    biascorrection.cpp \
    sampling.cpp \
    locfit/adap.c \
    locfit/ar_funs.c \
    locfit/arith.c \
    locfit/band.c \
    locfit/c_args.c \
    locfit/c_plot.c \
    locfit/cmd.c \
    locfit/dens_haz.c \
    locfit/dens_int.c \
    locfit/dens_odi.c \
    locfit/density.c \
    locfit/dist.c \
    locfit/ev_atree.c \
    locfit/ev_interp.c \
    locfit/ev_kdtre.c \
    locfit/ev_main.c \
    locfit/ev_trian.c \
    locfit/family.c \
    locfit/fitted.c \
    locfit/frend.c \
    locfit/help.c \
    locfit/lf_dercor.c \
    locfit/lf_fitfun.c \
    locfit/lf_robust.c \
    locfit/lf_vari.c \
    locfit/lfd.c \
    locfit/lfstr.c \
    locfit/linalg.c \
    locfit/locfit.c \
    locfit/m_chol.c \
    locfit/m_eigen.c \
    locfit/m_jacob.c \
    locfit/m_max.c \
    locfit/makecmd.c \
    locfit/math.c \
    locfit/minmax.c \
    locfit/nbhd.c \
    locfit/pcomp.c \
    locfit/pout.c \
    locfit/preplot.c \
    locfit/random.c \
    locfit/readfile.c \
    locfit/scb.c \
    locfit/scb_cons.c \
    locfit/simul.c \
    locfit/solve.c \
    locfit/startlf.c \
    locfit/strings.c \
    locfit/vari.cpp \
    locfit/wdiag.c \
    locfit/weight.c \
    replicates.cpp \
    multireads.cpp \
    jensen_shannon.cpp 

libgc_a_SOURCES = \
	codons.cpp \
	GArgs.cpp \
	GBase.cpp \
	gdna.cpp \
	GStr.cpp \
	GFaSeqGet.cpp \
	GFastaIndex.cpp \
	gff.cpp \
	gff_utils.cpp \
	gtf_tracking.cpp 


#-- scripts to be installed in $prefix/bin
dist_bin_SCRIPTS = \
	cuffmerge

CLEANFILES = $(bin_SCRIPTS)

#SUFFIXES = .py
#.py:
#	(echo '#!$(PYTHON)'; sed '/^#!/d' $<) > $@
cufflinks_SOURCES = cufflinks.cpp  
cufflinks_LDADD = libcufflinks.a libgc.a $(BOOST_THREAD_LIB) $(BAM_LIB) 
cufflinks_LDFLAGS = $(BOOST_LDFLAGS) $(BAM_LDFLAGS) #$(ZLIB_LDFLAGS) 
cuffcompare_SOURCES = cuffcompare.cpp
cuffcompare_LDADD = libgc.a
gffread_SOURCES = gffread.cpp
gffread_LDADD = libgc.a
cuffdiff_SOURCES = cuffdiff.cpp
cuffdiff_LDADD = libcufflinks.a libgc.a $(BOOST_THREAD_LIB) $(BAM_LIB)
cuffdiff_LDFLAGS = $(BOOST_LDFLAGS) $(BAM_LDFLAGS) 
gtf_to_sam_SOURCES = gtf_to_sam.cpp
gtf_to_sam_LDADD = libcufflinks.a libgc.a $(BOOST_THREAD_LIB) $(BAM_LIB)
gtf_to_sam_LDFLAGS = $(BOOST_LDFLAGS) $(BAM_LDFLAGS) 

#cuffcluster_SOURCES = cuffcluster.cpp
#cuffcluster_LDADD = libcufflinks.a libgc.a $(BOOST_THREAD_LIB) $(BAM_LIB)
#cuffcluster_LDFLAGS =  $(BOOST_LDFLAGS) $(BAM_LDFLAGS) 
compress_gtf_SOURCES = compress_gtf.cpp
compress_gtf_LDADD = libcufflinks.a libgc.a $(BOOST_THREAD_LIB) $(BAM_LIB)
compress_gtf_LDFLAGS = $(BOOST_LDFLAGS) $(BAM_LDFLAGS) 
all: all-am

.SUFFIXES:
.SUFFIXES: .c .cpp .o .obj
$(srcdir)/Makefile.in:  $(srcdir)/Makefile.am  $(am__configure_deps)
	@for dep in $?; do \
	  case '$(am__configure_deps)' in \
	    *$$dep*) \
	      cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh \
		&& exit 0; \
	      exit 1;; \
	  esac; \
	done; \
	echo ' cd $(top_srcdir) && $(AUTOMAKE) --foreign  src/Makefile'; \
	cd $(top_srcdir) && \
	  $(AUTOMAKE) --foreign  src/Makefile
.PRECIOUS: Makefile
Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status
	@case '$?' in \
	  *config.status*) \
	    cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh;; \
	  *) \
	    echo ' cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe)'; \
	    cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe);; \
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$(top_builddir)/config.status: $(top_srcdir)/configure $(CONFIG_STATUS_DEPENDENCIES)
	cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh

$(top_srcdir)/configure:  $(am__configure_deps)
	cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
$(ACLOCAL_M4):  $(am__aclocal_m4_deps)
	cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh

clean-noinstLIBRARIES:
	-test -z "$(noinst_LIBRARIES)" || rm -f $(noinst_LIBRARIES)
libcufflinks.a: $(libcufflinks_a_OBJECTS) $(libcufflinks_a_DEPENDENCIES) 
	-rm -f libcufflinks.a
	$(libcufflinks_a_AR) libcufflinks.a $(libcufflinks_a_OBJECTS) $(libcufflinks_a_LIBADD)
	$(RANLIB) libcufflinks.a
libgc.a: $(libgc_a_OBJECTS) $(libgc_a_DEPENDENCIES) 
	-rm -f libgc.a
	$(libgc_a_AR) libgc.a $(libgc_a_OBJECTS) $(libgc_a_LIBADD)
	$(RANLIB) libgc.a
install-binPROGRAMS: $(bin_PROGRAMS)
	@$(NORMAL_INSTALL)
	test -z "$(bindir)" || $(mkdir_p) "$(DESTDIR)$(bindir)"
	@list='$(bin_PROGRAMS)'; for p in $$list; do \
	  p1=`echo $$p|sed 's/$(EXEEXT)$$//'`; \
	  if test -f $$p \
	  ; then \
	    f=`echo "$$p1" | sed 's,^.*/,,;$(transform);s/$$/$(EXEEXT)/'`; \
	   echo " $(INSTALL_PROGRAM_ENV) $(binPROGRAMS_INSTALL) '$$p' '$(DESTDIR)$(bindir)/$$f'"; \
	   $(INSTALL_PROGRAM_ENV) $(binPROGRAMS_INSTALL) "$$p" "$(DESTDIR)$(bindir)/$$f" || exit 1; \
	  else :; fi; \
	done

uninstall-binPROGRAMS:
	@$(NORMAL_UNINSTALL)
	@list='$(bin_PROGRAMS)'; for p in $$list; do \
	  f=`echo "$$p" | sed 's,^.*/,,;s/$(EXEEXT)$$//;$(transform);s/$$/$(EXEEXT)/'`; \
	  echo " rm -f '$(DESTDIR)$(bindir)/$$f'"; \
	  rm -f "$(DESTDIR)$(bindir)/$$f"; \
	done

clean-binPROGRAMS:
	-test -z "$(bin_PROGRAMS)" || rm -f $(bin_PROGRAMS)
compress_gtf$(EXEEXT): $(compress_gtf_OBJECTS) $(compress_gtf_DEPENDENCIES) 
	@rm -f compress_gtf$(EXEEXT)
	$(CXXLINK) $(compress_gtf_LDFLAGS) $(compress_gtf_OBJECTS) $(compress_gtf_LDADD) $(LIBS)
cuffcompare$(EXEEXT): $(cuffcompare_OBJECTS) $(cuffcompare_DEPENDENCIES) 
	@rm -f cuffcompare$(EXEEXT)
	$(CXXLINK) $(cuffcompare_LDFLAGS) $(cuffcompare_OBJECTS) $(cuffcompare_LDADD) $(LIBS)
cuffdiff$(EXEEXT): $(cuffdiff_OBJECTS) $(cuffdiff_DEPENDENCIES) 
	@rm -f cuffdiff$(EXEEXT)
	$(CXXLINK) $(cuffdiff_LDFLAGS) $(cuffdiff_OBJECTS) $(cuffdiff_LDADD) $(LIBS)
cufflinks$(EXEEXT): $(cufflinks_OBJECTS) $(cufflinks_DEPENDENCIES) 
	@rm -f cufflinks$(EXEEXT)
	$(CXXLINK) $(cufflinks_LDFLAGS) $(cufflinks_OBJECTS) $(cufflinks_LDADD) $(LIBS)
gffread$(EXEEXT): $(gffread_OBJECTS) $(gffread_DEPENDENCIES) 
	@rm -f gffread$(EXEEXT)
	$(CXXLINK) $(gffread_LDFLAGS) $(gffread_OBJECTS) $(gffread_LDADD) $(LIBS)
gtf_to_sam$(EXEEXT): $(gtf_to_sam_OBJECTS) $(gtf_to_sam_DEPENDENCIES) 
	@rm -f gtf_to_sam$(EXEEXT)
	$(CXXLINK) $(gtf_to_sam_LDFLAGS) $(gtf_to_sam_OBJECTS) $(gtf_to_sam_LDADD) $(LIBS)
install-dist_binSCRIPTS: $(dist_bin_SCRIPTS)
	@$(NORMAL_INSTALL)
	test -z "$(bindir)" || $(mkdir_p) "$(DESTDIR)$(bindir)"
	@list='$(dist_bin_SCRIPTS)'; for p in $$list; do \
	  if test -f "$$p"; then d=; else d="$(srcdir)/"; fi; \
	  if test -f $$d$$p; then \
	    f=`echo "$$p" | sed 's|^.*/||;$(transform)'`; \
	    echo " $(dist_binSCRIPT_INSTALL) '$$d$$p' '$(DESTDIR)$(bindir)/$$f'"; \
	    $(dist_binSCRIPT_INSTALL) "$$d$$p" "$(DESTDIR)$(bindir)/$$f"; \
	  else :; fi; \
	done

uninstall-dist_binSCRIPTS:
	@$(NORMAL_UNINSTALL)
	@list='$(dist_bin_SCRIPTS)'; for p in $$list; do \
	  f=`echo "$$p" | sed 's|^.*/||;$(transform)'`; \
	  echo " rm -f '$(DESTDIR)$(bindir)/$$f'"; \
	  rm -f "$(DESTDIR)$(bindir)/$$f"; \
	done

mostlyclean-compile:
	-rm -f *.$(OBJEXT)

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

@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/GArgs.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/GBase.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/GFaSeqGet.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/GFastaIndex.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/GStr.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/abundances.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/adap.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/ar_funs.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/arith.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/assemble.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/band.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/biascorrection.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/bundles.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/c_args.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/c_plot.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/clustering.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/cmd.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/codons.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/common.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/compress_gtf.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/cuffcompare.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/cuffdiff.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/cufflinks.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/dens_haz.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/dens_int.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/dens_odi.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/density.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/differential.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/dist.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/ev_atree.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/ev_interp.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/ev_kdtre.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/ev_main.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/ev_trian.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/family.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/filters.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/fitted.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/frend.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/gdna.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/genes.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/gff.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/gff_utils.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/gffread.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/graph_optimize.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/gtf_to_sam.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/gtf_tracking.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/help.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/hits.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/jensen_shannon.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/lf_dercor.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/lf_fitfun.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/lf_robust.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/lf_vari.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/lfd.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/lfstr.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/linalg.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/locfit.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/m_chol.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/m_eigen.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/m_jacob.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/m_max.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/makecmd.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/matching_merge.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/math.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/minmax.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/multireads.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/nbhd.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/pcomp.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/pout.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/preplot.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/random.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/readfile.Po@am__quote@
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@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/sampling.Po@am__quote@
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#gtf_reads_SOURCES = gtf_reads.cpp
#gtf_reads_LDADD = libcufflinks.a libgc.a $(BOOST_THREAD_LIB) $(BAM_LIB) 
#gtf_reads_LDFLAGS =  $(BOOST_LDFLAGS) $(BAM_LDFLAGS) #$(ZLIB_LDFLAGS)
# 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: