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#OPTIMIZATION = -O1 -g -Wall
OPTIMIZATION = -O3 -Wall -mfpmath=sse -msse -msse2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -funsafe-math-optimizations -lgsl -lgslcblas
finestructure_CXXFLAGS = $(GSL_CFLAGS) $(OPTIMIZATION) -Wall 
finestructure_LDFLAGS = $(OPTIMIZATION) 
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finestructure_SOURCES = safegetline.h data.h fsxml.h state.h node.h inf1.h infadmixture.h infextract.h infextract2.h infextract3.h infextract4.h infextract5.h infmcmc.h fines.h finesfunctions.h rng.h safegetline.cpp data.cpp fsxml.cpp state.cpp node.cpp inf1.cpp infadmixture.cpp infextract.cpp infextract2.cpp infextract3.cpp infextract4.cpp infextract5.cpp infmcmc.cpp finesfunctions.cpp fines.cpp rng.cpp
RADpainter_CXXFLAGS = $(GSL_CFLAGS) -std=c++0x
RADpainter_LDADD = $(GSL_LIBS)
RADpainter_SOURCES = tagPainter.h paintSql.h utils.h tagPainter.cpp paintSql.cpp utils.cpp hapsFromVCF.h hapsFromVCF.cpp gzstream.h gzstream.cpp
check_SCRIPTS = profilerun.sh
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RADpainter-tagPainter.o: tagPainter.cpp
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RADpainter-tagPainter.obj: tagPainter.cpp
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RADpainter-paintSql.o: paintSql.cpp
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RADpainter-paintSql.obj: paintSql.cpp
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RADpainter-utils.o: utils.cpp
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RADpainter-utils.obj: utils.cpp
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RADpainter-hapsFromVCF.o: hapsFromVCF.cpp
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RADpainter-hapsFromVCF.obj: hapsFromVCF.cpp
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RADpainter-gzstream.o: gzstream.cpp
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RADpainter-gzstream.obj: gzstream.cpp
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finestructure-safegetline.o: safegetline.cpp
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finestructure-safegetline.obj: safegetline.cpp
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finestructure-data.o: data.cpp
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finestructure-data.obj: data.cpp
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finestructure-infadmixture.o: infadmixture.cpp
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finestructure-infextract.o: infextract.cpp
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	topsrcdirstrip=`echo "$(top_srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
	list='$(DISTFILES)'; \
	  dist_files=`for file in $$list; do echo $$file; done | \
	  sed -e "s|^$$srcdirstrip/||;t" \
	      -e "s|^$$topsrcdirstrip/|$(top_builddir)/|;t"`; \
	case $$dist_files in \
	  */*) $(MKDIR_P) `echo "$$dist_files" | \
			   sed '/\//!d;s|^|$(distdir)/|;s,/[^/]*$$,,' | \
			   sort -u` ;; \
	esac; \
	for file in $$dist_files; do \
	  if test -f $$file || test -d $$file; then d=.; else d=$(srcdir); fi; \
	  if test -d $$d/$$file; then \
	    dir=`echo "/$$file" | sed -e 's,/[^/]*$$,,'`; \
	    if test -d "$(distdir)/$$file"; then \
	      find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \
	    fi; \
	    if test -d $(srcdir)/$$file && test $$d != $(srcdir); then \
	      cp -fpR $(srcdir)/$$file "$(distdir)$$dir" || exit 1; \
	      find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \
	    fi; \
	    cp -fpR $$d/$$file "$(distdir)$$dir" || exit 1; \
	  else \
	    test -f "$(distdir)/$$file" \
	    || cp -p $$d/$$file "$(distdir)/$$file" \
	    || exit 1; \
	  fi; \
	done
	-test -n "$(am__skip_mode_fix)" \
	|| find "$(distdir)" -type d ! -perm -755 \
		-exec chmod u+rwx,go+rx {} \; -o \
	  ! -type d ! -perm -444 -links 1 -exec chmod a+r {} \; -o \
	  ! -type d ! -perm -400 -exec chmod a+r {} \; -o \
	  ! -type d ! -perm -444 -exec $(install_sh) -c -m a+r {} {} \; \
	|| chmod -R a+r "$(distdir)"
dist-gzip: distdir
	tardir=$(distdir) && $(am__tar) | GZIP=$(GZIP_ENV) gzip -c >$(distdir).tar.gz
	$(am__post_remove_distdir)

dist-bzip2: distdir
	tardir=$(distdir) && $(am__tar) | BZIP2=$${BZIP2--9} bzip2 -c >$(distdir).tar.bz2
	$(am__post_remove_distdir)

dist-lzip: distdir
	tardir=$(distdir) && $(am__tar) | lzip -c $${LZIP_OPT--9} >$(distdir).tar.lz
	$(am__post_remove_distdir)

dist-xz: distdir
	tardir=$(distdir) && $(am__tar) | XZ_OPT=$${XZ_OPT--e} xz -c >$(distdir).tar.xz
	$(am__post_remove_distdir)

dist-tarZ: distdir
	@echo WARNING: "Support for shar distribution archives 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 distribution archives compressed with" \
		       "legacy program 'compress' 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)/_inst
	chmod a-w $(distdir)
	test -d $(distdir)/_build || exit 0; \
	dc_install_base=`$(am__cd) $(distdir)/_inst && pwd | sed -e 's,^[^:\\/]:[\\/],/,'` \
	  && dc_destdir="$${TMPDIR-/tmp}/am-dc-$$$$/" \
	  && am__cwd=`pwd` \
	  && $(am__cd) $(distdir)/_build \
	  && ../configure --srcdir=.. --prefix="$$dc_install_base" \
	    $(AM_DISTCHECK_CONFIGURE_FLAGS) \
	    $(DISTCHECK_CONFIGURE_FLAGS) \
	  && $(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' \
	       '$$(distuninstallcheck_dir)' >&2; \
	  exit 1; \
	}; \
	$(am__cd) '$(distuninstallcheck_dir)' || { \
	  echo 'ERROR: cannot chdir into $(distuninstallcheck_dir)' >&2; \
	  exit 1; \
	}; \
	test `$(am__distuninstallcheck_listfiles) | wc -l` -eq 0 \
	   || { echo "ERROR: files left after uninstall:" ; \
	        if test -n "$(DESTDIR)"; then \
	          echo "  (check DESTDIR support)"; \
	        fi ; \
	        $(distuninstallcheck_listfiles) ; \
	        exit 1; } >&2
distcleancheck: distclean
	@if test '$(srcdir)' = . ; then \
	  echo "ERROR: distcleancheck can only run from a VPATH build" ; \
	  exit 1 ; \
	fi
	@test `$(distcleancheck_listfiles) | wc -l` -eq 0 \
	  || { echo "ERROR: files left in build directory after distclean:" ; \
	       $(distcleancheck_listfiles) ; \
	       exit 1; } >&2
check-am: all-am
	$(MAKE) $(AM_MAKEFLAGS) $(check_SCRIPTS)
	$(MAKE) $(AM_MAKEFLAGS) check-TESTS
check: check-am
all-am: Makefile $(PROGRAMS)
installdirs:
	for dir in "$(DESTDIR)$(bindir)"; do \
	  test -z "$$dir" || $(MKDIR_P) "$$dir"; \
	done
install: 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:

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)

maintainer-clean-generic:
	@echo "This command is intended for maintainers to use"
	@echo "it deletes files that may require special tools to rebuild."
clean: clean-am

clean-am: clean-binPROGRAMS clean-generic mostlyclean-am

distclean: distclean-am
	-rm -f $(am__CONFIG_DISTCLEAN_FILES)
	-rm -rf ./$(DEPDIR)
	-rm -f Makefile
distclean-am: clean-am distclean-compile distclean-generic \
	distclean-tags

dvi: dvi-am

dvi-am:

html: html-am

html-am:

info: info-am

info-am:

install-data-am:

install-dvi: install-dvi-am

install-dvi-am:

install-exec-am: install-binPROGRAMS

install-html: install-html-am

install-html-am:

install-info: install-info-am

install-info-am:

install-man:

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 $(top_srcdir)/autom4te.cache
	-rm -rf ./$(DEPDIR)
	-rm -f Makefile
maintainer-clean-am: distclean-am maintainer-clean-generic

mostlyclean: mostlyclean-am

mostlyclean-am: mostlyclean-compile mostlyclean-generic

pdf: pdf-am

pdf-am:

ps: ps-am

ps-am:

uninstall-am: uninstall-binPROGRAMS

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

.PHONY: CTAGS GTAGS TAGS all all-am am--refresh check check-TESTS \
	check-am clean clean-binPROGRAMS clean-cscope clean-generic \
	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-tags distcleancheck distdir distuninstallcheck dvi \
	dvi-am html html-am info info-am install install-am \
	install-binPROGRAMS install-data install-data-am install-dvi \
	install-dvi-am install-exec install-exec-am install-html \
	install-html-am install-info install-info-am install-man \
	install-pdf install-pdf-am install-ps install-ps-am \
	install-strip installcheck installcheck-am installdirs \
	maintainer-clean maintainer-clean-generic mostlyclean \
	mostlyclean-compile mostlyclean-generic pdf pdf-am ps ps-am \
	recheck tags tags-am uninstall uninstall-am \
	uninstall-binPROGRAMS


profilerun.sh:
	echo './finestructure -s 532772982 -x 100 -y 50 testout' > profilerun.sh
	chmod +x profilerun.sh

# 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: