From f06a9bbbdea4a11e31b073e29b93c51df0872f24 Mon Sep 17 00:00:00 2001
From: Veronique Legrand <vlegrand@pasteur.fr>
Date: Thu, 6 Jan 2022 17:42:41 +0100
Subject: [PATCH] put back these files taht are usefu and that I had removed by
 mistake

---
 Makefile.in      |  760 ++++++++++++++++++++++++++++++++
 aclocal.m4       | 1088 ++++++++++++++++++++++++++++++++++++++++++++++
 doc/Makefile.in  |  499 +++++++++++++++++++++
 src/Makefile.in  |  685 +++++++++++++++++++++++++++++
 test/Makefile.in |  801 ++++++++++++++++++++++++++++++++++
 5 files changed, 3833 insertions(+)
 create mode 100644 Makefile.in
 create mode 100644 aclocal.m4
 create mode 100644 doc/Makefile.in
 create mode 100644 src/Makefile.in
 create mode 100644 test/Makefile.in

diff --git a/Makefile.in b/Makefile.in
new file mode 100644
index 0000000..05d2fbf
--- /dev/null
+++ b/Makefile.in
@@ -0,0 +1,760 @@
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+	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) ;;\
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+	  lzip -dc $(distdir).tar.lz | $(am__untar) ;;\
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+	  xz -dc $(distdir).tar.xz | $(am__untar) ;;\
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+	  GZIP=$(GZIP_ENV) gzip -dc $(distdir).shar.gz | unshar ;;\
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+	  unzip $(distdir).zip ;;\
+	esac
+	chmod -R a-w $(distdir)
+	chmod u+w $(distdir)
+	mkdir $(distdir)/_build $(distdir)/_build/sub $(distdir)/_inst
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+	dc_install_base=`$(am__cd) $(distdir)/_inst && pwd | sed -e 's,^[^:\\/]:[\\/],/,'` \
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+	  && $(MAKE) $(AM_MAKEFLAGS) distuninstallcheck_dir="$$dc_install_base" \
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+	       (cd ../.. && umask 077 && mkdir "$$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) | \
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+	@test -n '$(distuninstallcheck_dir)' || { \
+	  echo 'ERROR: trying to run $@ with an empty' \
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+	$(am__cd) '$(distuninstallcheck_dir)' || { \
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+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:" ; \
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+	  $(MAKE) $(AM_MAKEFLAGS) INSTALL_PROGRAM="$(INSTALL_STRIP_PROGRAM)" \
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+	fi
+mostlyclean-generic:
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+distclean-generic:
+	-test -z "$(CONFIG_CLEAN_FILES)" || rm -f $(CONFIG_CLEAN_FILES)
+	-test . = "$(srcdir)" || test -z "$(CONFIG_CLEAN_VPATH_FILES)" || rm -f $(CONFIG_CLEAN_VPATH_FILES)
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+	distcheck distclean distclean-generic distclean-tags \
+	distcleancheck distdir distuninstallcheck dvi dvi-am html \
+	html-am info info-am install install-am install-data \
+	install-data-am install-dvi install-dvi-am install-exec \
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diff --git a/aclocal.m4 b/aclocal.m4
new file mode 100644
index 0000000..bf79d07
--- /dev/null
+++ b/aclocal.m4
@@ -0,0 +1,1088 @@
+# generated automatically by aclocal 1.15 -*- Autoconf -*-
+
+# Copyright (C) 1996-2014 Free Software Foundation, Inc.
+
+# This file is free software; the Free Software Foundation
+# gives unlimited permission to copy and/or distribute it,
+# with or without modifications, as long as this notice is preserved.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY, to the extent permitted by law; without
+# even the implied warranty of MERCHANTABILITY or FITNESS FOR A
+# PARTICULAR PURPOSE.
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+# Copyright (C) 2002-2014 Free Software Foundation, Inc.
+#
+# This file is free software; the Free Software Foundation
+# gives unlimited permission to copy and/or distribute it,
+# with or without modifications, as long as this notice is preserved.
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+# AM_AUX_DIR_EXPAND                                         -*- Autoconf -*-
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+# Copyright (C) 1999-2014 Free Software Foundation, Inc.
+#
+# This file is free software; the Free Software Foundation
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+[AC_REQUIRE([AM_SET_LEADING_DOT])dnl
+AC_SUBST([DEPDIR], ["${am__leading_dot}deps"])dnl
+])
+
+
+# AM_DEP_TRACK
+# ------------
+AC_DEFUN([AM_DEP_TRACK],
+[AC_ARG_ENABLE([dependency-tracking], [dnl
+AS_HELP_STRING(
+  [--enable-dependency-tracking],
+  [do not reject slow dependency extractors])
+AS_HELP_STRING(
+  [--disable-dependency-tracking],
+  [speeds up one-time build])])
+if test "x$enable_dependency_tracking" != xno; then
+  am_depcomp="$ac_aux_dir/depcomp"
+  AMDEPBACKSLASH='\'
+  am__nodep='_no'
+fi
+AM_CONDITIONAL([AMDEP], [test "x$enable_dependency_tracking" != xno])
+AC_SUBST([AMDEPBACKSLASH])dnl
+_AM_SUBST_NOTMAKE([AMDEPBACKSLASH])dnl
+AC_SUBST([am__nodep])dnl
+_AM_SUBST_NOTMAKE([am__nodep])dnl
+])
+
+# Generate code to set up dependency tracking.              -*- Autoconf -*-
+
+# Copyright (C) 1999-2014 Free Software Foundation, Inc.
+#
+# This file 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.
+
+
+# _AM_OUTPUT_DEPENDENCY_COMMANDS
+# ------------------------------
+AC_DEFUN([_AM_OUTPUT_DEPENDENCY_COMMANDS],
+[{
+  # Older Autoconf quotes --file arguments for eval, but not when files
+  # are listed without --file.  Let's play safe and only enable the eval
+  # if we detect the quoting.
+  case $CONFIG_FILES in
+  *\'*) eval set x "$CONFIG_FILES" ;;
+  *)   set x $CONFIG_FILES ;;
+  esac
+  shift
+  for mf
+  do
+    # Strip MF so we end up with the name of the file.
+    mf=`echo "$mf" | sed -e 's/:.*$//'`
+    # Check whether this is an Automake generated Makefile or not.
+    # We used to match only the files named 'Makefile.in', but
+    # some people rename them; so instead we look at the file content.
+    # Grep'ing the first line is not enough: some people post-process
+    # each Makefile.in and add a new line on top of each file to say so.
+    # Grep'ing the whole file is not good either: AIX grep has a line
+    # limit of 2048, but all sed's we know have understand at least 4000.
+    if sed -n 's,^#.*generated by automake.*,X,p' "$mf" | grep X >/dev/null 2>&1; then
+      dirpart=`AS_DIRNAME("$mf")`
+    else
+      continue
+    fi
+    # Extract the definition of DEPDIR, am__include, and am__quote
+    # from the Makefile without running 'make'.
+    DEPDIR=`sed -n 's/^DEPDIR = //p' < "$mf"`
+    test -z "$DEPDIR" && continue
+    am__include=`sed -n 's/^am__include = //p' < "$mf"`
+    test -z "$am__include" && continue
+    am__quote=`sed -n 's/^am__quote = //p' < "$mf"`
+    # Find all dependency output files, they are included files with
+    # $(DEPDIR) in their names.  We invoke sed twice because it is the
+    # simplest approach to changing $(DEPDIR) to its actual value in the
+    # expansion.
+    for file in `sed -n "
+      s/^$am__include $am__quote\(.*(DEPDIR).*\)$am__quote"'$/\1/p' <"$mf" | \
+	 sed -e 's/\$(DEPDIR)/'"$DEPDIR"'/g'`; do
+      # Make sure the directory exists.
+      test -f "$dirpart/$file" && continue
+      fdir=`AS_DIRNAME(["$file"])`
+      AS_MKDIR_P([$dirpart/$fdir])
+      # echo "creating $dirpart/$file"
+      echo '# dummy' > "$dirpart/$file"
+    done
+  done
+}
+])# _AM_OUTPUT_DEPENDENCY_COMMANDS
+
+
+# AM_OUTPUT_DEPENDENCY_COMMANDS
+# -----------------------------
+# This macro should only be invoked once -- use via AC_REQUIRE.
+#
+# This code is only required when automatic dependency tracking
+# is enabled.  FIXME.  This creates each '.P' file that we will
+# need in order to bootstrap the dependency handling code.
+AC_DEFUN([AM_OUTPUT_DEPENDENCY_COMMANDS],
+[AC_CONFIG_COMMANDS([depfiles],
+     [test x"$AMDEP_TRUE" != x"" || _AM_OUTPUT_DEPENDENCY_COMMANDS],
+     [AMDEP_TRUE="$AMDEP_TRUE" ac_aux_dir="$ac_aux_dir"])
+])
+
+# Do all the work for Automake.                             -*- Autoconf -*-
+
+# Copyright (C) 1996-2014 Free Software Foundation, Inc.
+#
+# This file is free software; the Free Software Foundation
+# gives unlimited permission to copy and/or distribute it,
+# with or without modifications, as long as this notice is preserved.
+
+# This macro actually does too much.  Some checks are only needed if
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+dnl Redefine AC_PROG_CC to automatically invoke _AM_PROG_CC_C_O.
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+m4_defn([AC_PROG_CC])
+[_AM_PROG_CC_C_O
+])
+
+# AM_INIT_AUTOMAKE(PACKAGE, VERSION, [NO-DEFINE])
+# AM_INIT_AUTOMAKE([OPTIONS])
+# -----------------------------------------------
+# The call with PACKAGE and VERSION arguments is the old style
+# call (pre autoconf-2.50), which is being phased out.  PACKAGE
+# and VERSION should now be passed to AC_INIT and removed from
+# the call to AM_INIT_AUTOMAKE.
+# We support both call styles for the transition.  After
+# the next Automake release, Autoconf can make the AC_INIT
+# arguments mandatory, and then we can depend on a new Autoconf
+# release and drop the old call support.
+AC_DEFUN([AM_INIT_AUTOMAKE],
+[AC_PREREQ([2.65])dnl
+dnl Autoconf wants to disallow AM_ names.  We explicitly allow
+dnl the ones we care about.
+m4_pattern_allow([^AM_[A-Z]+FLAGS$])dnl
+AC_REQUIRE([AM_SET_CURRENT_AUTOMAKE_VERSION])dnl
+AC_REQUIRE([AC_PROG_INSTALL])dnl
+if test "`cd $srcdir && pwd`" != "`pwd`"; then
+  # Use -I$(srcdir) only when $(srcdir) != ., so that make's output
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+  AC_SUBST([am__isrc], [' -I$(srcdir)'])_AM_SUBST_NOTMAKE([am__isrc])dnl
+  # test to see if srcdir already configured
+  if test -f $srcdir/config.status; then
+    AC_MSG_ERROR([source directory already configured; run "make distclean" there first])
+  fi
+fi
+
+# test whether we have cygpath
+if test -z "$CYGPATH_W"; then
+  if (cygpath --version) >/dev/null 2>/dev/null; then
+    CYGPATH_W='cygpath -w'
+  else
+    CYGPATH_W=echo
+  fi
+fi
+AC_SUBST([CYGPATH_W])
+
+# Define the identity of the package.
+dnl Distinguish between old-style and new-style calls.
+m4_ifval([$2],
+[AC_DIAGNOSE([obsolete],
+             [$0: two- and three-arguments forms are deprecated.])
+m4_ifval([$3], [_AM_SET_OPTION([no-define])])dnl
+ AC_SUBST([PACKAGE], [$1])dnl
+ AC_SUBST([VERSION], [$2])],
+[_AM_SET_OPTIONS([$1])dnl
+dnl Diagnose old-style AC_INIT with new-style AM_AUTOMAKE_INIT.
+m4_if(
+  m4_ifdef([AC_PACKAGE_NAME], [ok]):m4_ifdef([AC_PACKAGE_VERSION], [ok]),
+  [ok:ok],,
+  [m4_fatal([AC_INIT should be called with package and version arguments])])dnl
+ AC_SUBST([PACKAGE], ['AC_PACKAGE_TARNAME'])dnl
+ AC_SUBST([VERSION], ['AC_PACKAGE_VERSION'])])dnl
+
+_AM_IF_OPTION([no-define],,
+[AC_DEFINE_UNQUOTED([PACKAGE], ["$PACKAGE"], [Name of package])
+ AC_DEFINE_UNQUOTED([VERSION], ["$VERSION"], [Version number of package])])dnl
+
+# Some tools Automake needs.
+AC_REQUIRE([AM_SANITY_CHECK])dnl
+AC_REQUIRE([AC_ARG_PROGRAM])dnl
+AM_MISSING_PROG([ACLOCAL], [aclocal-${am__api_version}])
+AM_MISSING_PROG([AUTOCONF], [autoconf])
+AM_MISSING_PROG([AUTOMAKE], [automake-${am__api_version}])
+AM_MISSING_PROG([AUTOHEADER], [autoheader])
+AM_MISSING_PROG([MAKEINFO], [makeinfo])
+AC_REQUIRE([AM_PROG_INSTALL_SH])dnl
+AC_REQUIRE([AM_PROG_INSTALL_STRIP])dnl
+AC_REQUIRE([AC_PROG_MKDIR_P])dnl
+# For better backward compatibility.  To be removed once Automake 1.9.x
+# dies out for good.  For more background, see:
+# <http://lists.gnu.org/archive/html/automake/2012-07/msg00001.html>
+# <http://lists.gnu.org/archive/html/automake/2012-07/msg00014.html>
+AC_SUBST([mkdir_p], ['$(MKDIR_P)'])
+# We need awk for the "check" target (and possibly the TAP driver).  The
+# system "awk" is bad on some platforms.
+AC_REQUIRE([AC_PROG_AWK])dnl
+AC_REQUIRE([AC_PROG_MAKE_SET])dnl
+AC_REQUIRE([AM_SET_LEADING_DOT])dnl
+_AM_IF_OPTION([tar-ustar], [_AM_PROG_TAR([ustar])],
+	      [_AM_IF_OPTION([tar-pax], [_AM_PROG_TAR([pax])],
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+_AM_IF_OPTION([no-dependencies],,
+[AC_PROVIDE_IFELSE([AC_PROG_CC],
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+		  [m4_define([AC_PROG_CC],
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+AC_PROVIDE_IFELSE([AC_PROG_CXX],
+		  [_AM_DEPENDENCIES([CXX])],
+		  [m4_define([AC_PROG_CXX],
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+AC_PROVIDE_IFELSE([AC_PROG_OBJC],
+		  [_AM_DEPENDENCIES([OBJC])],
+		  [m4_define([AC_PROG_OBJC],
+			     m4_defn([AC_PROG_OBJC])[_AM_DEPENDENCIES([OBJC])])])dnl
+AC_PROVIDE_IFELSE([AC_PROG_OBJCXX],
+		  [_AM_DEPENDENCIES([OBJCXX])],
+		  [m4_define([AC_PROG_OBJCXX],
+			     m4_defn([AC_PROG_OBJCXX])[_AM_DEPENDENCIES([OBJCXX])])])dnl
+])
+AC_REQUIRE([AM_SILENT_RULES])dnl
+dnl The testsuite driver may need to know about EXEEXT, so add the
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+AC_CONFIG_COMMANDS_PRE(dnl
+[m4_provide_if([_AM_COMPILER_EXEEXT],
+  [AM_CONDITIONAL([am__EXEEXT], [test -n "$EXEEXT"])])])dnl
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+# POSIX will say in a future version that running "rm -f" with no argument
+# is OK; and we want to be able to make that assumption in our Makefile
+# recipes.  So use an aggressive probe to check that the usage we want is
+# actually supported "in the wild" to an acceptable degree.
+# See automake bug#10828.
+# To make any issue more visible, cause the running configure to be aborted
+# by default if the 'rm' program in use doesn't match our expectations; the
+# user can still override this though.
+if rm -f && rm -fr && rm -rf; then : OK; else
+  cat >&2 <<'END'
+Oops!
+
+Your 'rm' program seems unable to run without file operands specified
+on the command line, even when the '-f' option is present.  This is contrary
+to the behaviour of most rm programs out there, and not conforming with
+the upcoming POSIX standard: <http://austingroupbugs.net/view.php?id=542>
+
+Please tell bug-automake@gnu.org about your system, including the value
+of your $PATH and any error possibly output before this message.  This
+can help us improve future automake versions.
+
+END
+  if test x"$ACCEPT_INFERIOR_RM_PROGRAM" = x"yes"; then
+    echo 'Configuration will proceed anyway, since you have set the' >&2
+    echo 'ACCEPT_INFERIOR_RM_PROGRAM variable to "yes"' >&2
+    echo >&2
+  else
+    cat >&2 <<'END'
+Aborting the configuration process, to ensure you take notice of the issue.
+
+You can download and install GNU coreutils to get an 'rm' implementation
+that behaves properly: <http://www.gnu.org/software/coreutils/>.
+
+If you want to complete the configuration process using your problematic
+'rm' anyway, export the environment variable ACCEPT_INFERIOR_RM_PROGRAM
+to "yes", and re-run configure.
+
+END
+    AC_MSG_ERROR([Your 'rm' program is bad, sorry.])
+  fi
+fi
+dnl The trailing newline in this macro's definition is deliberate, for
+dnl backward compatibility and to allow trailing 'dnl'-style comments
+dnl after the AM_INIT_AUTOMAKE invocation. See automake bug#16841.
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+
+dnl Hook into '_AC_COMPILER_EXEEXT' early to learn its expansion.  Do not
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+# When config.status generates a header, we must update the stamp-h file.
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+# Autoconf calls _AC_AM_CONFIG_HEADER_HOOK (when defined) in the
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+AC_DEFUN([_AC_AM_CONFIG_HEADER_HOOK],
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+echo "timestamp for $_am_arg" >`AS_DIRNAME(["$_am_arg"])`/stamp-h[]$_am_stamp_count])
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+# Copyright (C) 2001-2014 Free Software Foundation, Inc.
+#
+# This file is free software; the Free Software Foundation
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+# with or without modifications, as long as this notice is preserved.
+
+# AM_PROG_INSTALL_SH
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+AC_DEFUN([AM_PROG_INSTALL_SH],
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+if test x"${install_sh+set}" != xset; then
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+  *\ * | *\	*)
+    install_sh="\${SHELL} '$am_aux_dir/install-sh'" ;;
+  *)
+    install_sh="\${SHELL} $am_aux_dir/install-sh"
+  esac
+fi
+AC_SUBST([install_sh])])
+
+# Copyright (C) 2003-2014 Free Software Foundation, Inc.
+#
+# This file is free software; the Free Software Foundation
+# gives unlimited permission to copy and/or distribute it,
+# with or without modifications, as long as this notice is preserved.
+
+# Check whether the underlying file-system supports filenames
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+AC_DEFUN([AM_SET_LEADING_DOT],
+[rm -rf .tst 2>/dev/null
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+  am__leading_dot=.
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+  am__leading_dot=_
+fi
+rmdir .tst 2>/dev/null
+AC_SUBST([am__leading_dot])])
+
+# Check to see how 'make' treats includes.	            -*- Autoconf -*-
+
+# Copyright (C) 2001-2014 Free Software Foundation, Inc.
+#
+# This file is free software; the Free Software Foundation
+# gives unlimited permission to copy and/or distribute it,
+# with or without modifications, as long as this notice is preserved.
+
+# AM_MAKE_INCLUDE()
+# -----------------
+# Check to see how make treats includes.
+AC_DEFUN([AM_MAKE_INCLUDE],
+[am_make=${MAKE-make}
+cat > confinc << 'END'
+am__doit:
+	@echo this is the am__doit target
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+  am__include=include
+  am__quote=
+  _am_result=GNU
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+# Now try BSD make style include.
+if test "$am__include" = "#"; then
+   echo '.include "confinc"' > confmf
+   case `$am_make -s -f confmf 2> /dev/null` in #(
+   *the\ am__doit\ target*)
+     am__include=.include
+     am__quote="\""
+     _am_result=BSD
+     ;;
+   esac
+fi
+AC_SUBST([am__include])
+AC_SUBST([am__quote])
+AC_MSG_RESULT([$_am_result])
+rm -f confinc confmf
+])
+
+# Fake the existence of programs that GNU maintainers use.  -*- Autoconf -*-
+
+# Copyright (C) 1997-2014 Free Software Foundation, Inc.
+#
+# This file 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.
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+# AM_MISSING_PROG(NAME, PROGRAM)
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+AC_DEFUN([AM_MISSING_PROG],
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+# AM_MISSING_HAS_RUN
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+AC_DEFUN([AM_MISSING_HAS_RUN],
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+
+# Helper functions for option handling.                     -*- Autoconf -*-
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+# Copyright (C) 2001-2014 Free Software Foundation, Inc.
+#
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+# Check to make sure that the build environment is sane.    -*- Autoconf -*-
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+# Copyright (C) 1996-2014 Free Software Foundation, Inc.
+#
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+# Copyright (C) 2009-2014 Free Software Foundation, Inc.
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+  recheck = 1; \
+  while ((rc = (getline line < ($$0 ".trs"))) != 0) \
+    { \
+      if (rc < 0) \
+        { \
+          if ((getline line2 < ($$0 ".log")) < 0) \
+	    recheck = 0; \
+          break; \
+        } \
+      else if (line ~ /$(am__recheck_rx)[nN][Oo]/) \
+        { \
+          recheck = 0; \
+          break; \
+        } \
+      else if (line ~ /$(am__recheck_rx)[yY][eE][sS]/) \
+        { \
+          break; \
+        } \
+    }; \
+  if (recheck) \
+    print $$0; \
+  close ($$0 ".trs"); \
+  close ($$0 ".log"); \
+}'
+# A command that, given a newline-separated list of test names on the
+# standard input, create the global log from their .trs and .log files.
+am__create_global_log = $(AWK) ' \
+function fatal(msg) \
+{ \
+  print "fatal: making $@: " msg | "cat >&2"; \
+  exit 1; \
+} \
+function rst_section(header) \
+{ \
+  print header; \
+  len = length(header); \
+  for (i = 1; i <= len; i = i + 1) \
+    printf "="; \
+  printf "\n\n"; \
+} \
+{ \
+  copy_in_global_log = 1; \
+  global_test_result = "RUN"; \
+  while ((rc = (getline line < ($$0 ".trs"))) != 0) \
+    { \
+      if (rc < 0) \
+         fatal("failed to read from " $$0 ".trs"); \
+      if (line ~ /$(am__global_test_result_rx)/) \
+        { \
+          sub("$(am__global_test_result_rx)", "", line); \
+          sub("[ 	]*$$", "", line); \
+          global_test_result = line; \
+        } \
+      else if (line ~ /$(am__copy_in_global_log_rx)[nN][oO]/) \
+        copy_in_global_log = 0; \
+    }; \
+  if (copy_in_global_log) \
+    { \
+      rst_section(global_test_result ": " $$0); \
+      while ((rc = (getline line < ($$0 ".log"))) != 0) \
+      { \
+        if (rc < 0) \
+          fatal("failed to read from " $$0 ".log"); \
+        print line; \
+      }; \
+      printf "\n"; \
+    }; \
+  close ($$0 ".trs"); \
+  close ($$0 ".log"); \
+}'
+# Restructured Text title.
+am__rst_title = { sed 's/.*/   &   /;h;s/./=/g;p;x;s/ *$$//;p;g' && echo; }
+# Solaris 10 'make', and several other traditional 'make' implementations,
+# pass "-e" to $(SHELL), and POSIX 2008 even requires this.  Work around it
+# by disabling -e (using the XSI extension "set +e") if it's set.
+am__sh_e_setup = case $$- in *e*) set +e;; esac
+# Default flags passed to test drivers.
+am__common_driver_flags = \
+  --color-tests "$$am__color_tests" \
+  --enable-hard-errors "$$am__enable_hard_errors" \
+  --expect-failure "$$am__expect_failure"
+# To be inserted before the command running the test.  Creates the
+# directory for the log if needed.  Stores in $dir the directory
+# containing $f, in $tst the test, in $log the log.  Executes the
+# developer- defined test setup AM_TESTS_ENVIRONMENT (if any), and
+# passes TESTS_ENVIRONMENT.  Set up options for the wrapper that
+# will run the test scripts (or their associated LOG_COMPILER, if
+# thy have one).
+am__check_pre = \
+$(am__sh_e_setup);					\
+$(am__vpath_adj_setup) $(am__vpath_adj)			\
+$(am__tty_colors);					\
+srcdir=$(srcdir); export srcdir;			\
+case "$@" in						\
+  */*) am__odir=`echo "./$@" | sed 's|/[^/]*$$||'`;;	\
+    *) am__odir=.;; 					\
+esac;							\
+test "x$$am__odir" = x"." || test -d "$$am__odir" 	\
+  || $(MKDIR_P) "$$am__odir" || exit $$?;		\
+if test -f "./$$f"; then dir=./;			\
+elif test -f "$$f"; then dir=;				\
+else dir="$(srcdir)/"; fi;				\
+tst=$$dir$$f; log='$@'; 				\
+if test -n '$(DISABLE_HARD_ERRORS)'; then		\
+  am__enable_hard_errors=no; 				\
+else							\
+  am__enable_hard_errors=yes; 				\
+fi; 							\
+case " $(XFAIL_TESTS) " in				\
+  *[\ \	]$$f[\ \	]* | *[\ \	]$$dir$$f[\ \	]*) \
+    am__expect_failure=yes;;				\
+  *)							\
+    am__expect_failure=no;;				\
+esac; 							\
+$(AM_TESTS_ENVIRONMENT) $(TESTS_ENVIRONMENT)
+# A shell command to get the names of the tests scripts with any registered
+# extension removed (i.e., equivalently, the names of the test logs, with
+# the '.log' extension removed).  The result is saved in the shell variable
+# '$bases'.  This honors runtime overriding of TESTS and TEST_LOGS.  Sadly,
+# we cannot use something simpler, involving e.g., "$(TEST_LOGS:.log=)",
+# since that might cause problem with VPATH rewrites for suffix-less tests.
+# See also 'test-harness-vpath-rewrite.sh' and 'test-trs-basic.sh'.
+am__set_TESTS_bases = \
+  bases='$(TEST_LOGS)'; \
+  bases=`for i in $$bases; do echo $$i; done | sed 's/\.log$$//'`; \
+  bases=`echo $$bases`
+RECHECK_LOGS = $(TEST_LOGS)
+AM_RECURSIVE_TARGETS = check recheck
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+LOG_COMPILE = $(LOG_COMPILER) $(AM_LOG_FLAGS) $(LOG_FLAGS)
+am__set_b = \
+  case '$@' in \
+    */*) \
+      case '$*' in \
+        */*) b='$*';; \
+          *) b=`echo '$@' | sed 's/\.log$$//'`; \
+       esac;; \
+    *) \
+      b='$*';; \
+  esac
+am__test_logs1 = $(TESTS:=.log)
+am__test_logs2 = $(am__test_logs1:@EXEEXT@.log=.log)
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+TEST_LOG_DRIVER = $(SHELL) $(top_srcdir)/test-driver
+TEST_LOG_COMPILE = $(TEST_LOG_COMPILER) $(AM_TEST_LOG_FLAGS) \
+	$(TEST_LOG_FLAGS)
+am__DIST_COMMON = $(srcdir)/Makefile.in $(top_srcdir)/test-driver
+DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
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+AMTAR = @AMTAR@
+AM_DEFAULT_VERBOSITY = @AM_DEFAULT_VERBOSITY@
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+top_build_prefix = @top_build_prefix@
+top_builddir = @top_builddir@
+top_srcdir = @top_srcdir@
+AM_COLOR_TESTS = no
+LOG_COMPILER = $(SHELL)
+TESTS = rock.sh
+EXTRA_DIST = $(TESTS) rock_mem.sh data/iofiles.args/extract_klebsiella_long_reads_100.txt \
+data/iofiles.args/extract_klebsiella_long_reads_100_filtered.txt data/fastq.raw/klebsiella_100_1.fq \
+data/fastq.raw/klebsiella_100_2.fq data/unit/klebsiella_PE1.fq data/unit/klebsiella_PE2.fq data/unit/test_PE1.fq \
+data/unit/test_PE2.fq data/unit/test_PE1_2.fq data/unit/test_PE2_2.fq data/unit/test_single2.fq \
+data/unit/test_single.fq data/unit/list_input1.txt data/unit/list_output1.txt data/unit/list_input2.txt \
+data/unit/list_output2.txt data/unit/list_input3.txt data/unit/list_output3.txt \
+data/iofiles.args/output_files_noNQ_Thres.txt data/iofiles.args/output_files_NQ_Thres_very_low.txt \
+data/iofiles.args/output_files_NQ_Thres_12.txt data/iofiles.args/output_files_NQ_Thres_13.txt \
+data/unit/09-4607_S43_R1.fastq data/unit/09-4607_S43_R2.fastq data/unit/09-4607_S43_R1_big.fastq \
+data/unit/09-4607_S43_R2_big.fastq data/unit/thres_100_09-4607_S43_R1.undef.fastq \
+data/unit/thres_100_09-4607_S43_R2.undef.fastq data/unit/thres_180_09-4607_S43_R1.undef.fastq \
+data/unit/thres_180_09-4607_S43_R2.undef.fastq data/fastq.raw/klebsiella_5_1_bad_scores.fq \
+data/fastq.raw/klebsiella_5_2_bad_scores.fq data/iofiles.args/output_files_2_PE_separated.txt \
+data/unit/test_PE1_PE_not_as_single.fq data/unit/test_PE2_PE_not_as_single.fq \
+data/unit/expected_PE1_PE_not_as_single.undef.fastq data/unit/expected_PE2_PE_not_as_single.undef.fastq \
+data/unit/test_PE1_PE_not_as_single_pathological.fq data/unit/test_PE2_PE_not_as_single_pathological.fq \
+data/unit/fake_PE1.fq data/unit/fake_PE2.fq \
+data/iofiles.args/output_files_2_PE_separated_lenient.txt data/fastq.raw/klebsiella_6_1_bad_scores.fq data/fastq.raw/klebsiella_6_2_bad_scores.fq
+
+all: all-am
+
+.SUFFIXES:
+.SUFFIXES: .log .test .test$(EXEEXT) .trs
+$(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 ) \
+	        && { if test -f $@; then exit 0; else break; fi; }; \
+	      exit 1;; \
+	  esac; \
+	done; \
+	echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnu test/Makefile'; \
+	$(am__cd) $(top_srcdir) && \
+	  $(AUTOMAKE) --gnu test/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 $(subdir)/$@ $(am__depfiles_maybe);; \
+	esac;
+
+$(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) $(AM_MAKEFLAGS) am--refresh
+$(am__aclocal_m4_deps):
+tags TAGS:
+
+ctags CTAGS:
+
+cscope cscopelist:
+
+
+# Recover from deleted '.trs' file; this should ensure that
+# "rm -f foo.log; make foo.trs" re-run 'foo.test', and re-create
+# both 'foo.log' and 'foo.trs'.  Break the recipe in two subshells
+# to avoid problems with "make -n".
+.log.trs:
+	rm -f $< $@
+	$(MAKE) $(AM_MAKEFLAGS) $<
+
+# Leading 'am--fnord' is there to ensure the list of targets does not
+# expand to empty, as could happen e.g. with make check TESTS=''.
+am--fnord $(TEST_LOGS) $(TEST_LOGS:.log=.trs): $(am__force_recheck)
+am--force-recheck:
+	@:
+
+$(TEST_SUITE_LOG): $(TEST_LOGS)
+	@$(am__set_TESTS_bases); \
+	am__f_ok () { test -f "$$1" && test -r "$$1"; }; \
+	redo_bases=`for i in $$bases; do \
+	              am__f_ok $$i.trs && am__f_ok $$i.log || echo $$i; \
+	            done`; \
+	if test -n "$$redo_bases"; then \
+	  redo_logs=`for i in $$redo_bases; do echo $$i.log; done`; \
+	  redo_results=`for i in $$redo_bases; do echo $$i.trs; done`; \
+	  if $(am__make_dryrun); then :; else \
+	    rm -f $$redo_logs && rm -f $$redo_results || exit 1; \
+	  fi; \
+	fi; \
+	if test -n "$$am__remaking_logs"; then \
+	  echo "fatal: making $(TEST_SUITE_LOG): possible infinite" \
+	       "recursion detected" >&2; \
+	elif test -n "$$redo_logs"; then \
+	  am__remaking_logs=yes $(MAKE) $(AM_MAKEFLAGS) $$redo_logs; \
+	fi; \
+	if $(am__make_dryrun); then :; else \
+	  st=0;  \
+	  errmsg="fatal: making $(TEST_SUITE_LOG): failed to create"; \
+	  for i in $$redo_bases; do \
+	    test -f $$i.trs && test -r $$i.trs \
+	      || { echo "$$errmsg $$i.trs" >&2; st=1; }; \
+	    test -f $$i.log && test -r $$i.log \
+	      || { echo "$$errmsg $$i.log" >&2; st=1; }; \
+	  done; \
+	  test $$st -eq 0 || exit 1; \
+	fi
+	@$(am__sh_e_setup); $(am__tty_colors); $(am__set_TESTS_bases); \
+	ws='[ 	]'; \
+	results=`for b in $$bases; do echo $$b.trs; done`; \
+	test -n "$$results" || results=/dev/null; \
+	all=`  grep "^$$ws*:test-result:"           $$results | wc -l`; \
+	pass=` grep "^$$ws*:test-result:$$ws*PASS"  $$results | wc -l`; \
+	fail=` grep "^$$ws*:test-result:$$ws*FAIL"  $$results | wc -l`; \
+	skip=` grep "^$$ws*:test-result:$$ws*SKIP"  $$results | wc -l`; \
+	xfail=`grep "^$$ws*:test-result:$$ws*XFAIL" $$results | wc -l`; \
+	xpass=`grep "^$$ws*:test-result:$$ws*XPASS" $$results | wc -l`; \
+	error=`grep "^$$ws*:test-result:$$ws*ERROR" $$results | wc -l`; \
+	if test `expr $$fail + $$xpass + $$error` -eq 0; then \
+	  success=true; \
+	else \
+	  success=false; \
+	fi; \
+	br='==================='; br=$$br$$br$$br$$br; \
+	result_count () \
+	{ \
+	    if test x"$$1" = x"--maybe-color"; then \
+	      maybe_colorize=yes; \
+	    elif test x"$$1" = x"--no-color"; then \
+	      maybe_colorize=no; \
+	    else \
+	      echo "$@: invalid 'result_count' usage" >&2; exit 4; \
+	    fi; \
+	    shift; \
+	    desc=$$1 count=$$2; \
+	    if test $$maybe_colorize = yes && test $$count -gt 0; then \
+	      color_start=$$3 color_end=$$std; \
+	    else \
+	      color_start= color_end=; \
+	    fi; \
+	    echo "$${color_start}# $$desc $$count$${color_end}"; \
+	}; \
+	create_testsuite_report () \
+	{ \
+	  result_count $$1 "TOTAL:" $$all   "$$brg"; \
+	  result_count $$1 "PASS: " $$pass  "$$grn"; \
+	  result_count $$1 "SKIP: " $$skip  "$$blu"; \
+	  result_count $$1 "XFAIL:" $$xfail "$$lgn"; \
+	  result_count $$1 "FAIL: " $$fail  "$$red"; \
+	  result_count $$1 "XPASS:" $$xpass "$$red"; \
+	  result_count $$1 "ERROR:" $$error "$$mgn"; \
+	}; \
+	{								\
+	  echo "$(PACKAGE_STRING): $(subdir)/$(TEST_SUITE_LOG)" |	\
+	    $(am__rst_title);						\
+	  create_testsuite_report --no-color;				\
+	  echo;								\
+	  echo ".. contents:: :depth: 2";				\
+	  echo;								\
+	  for b in $$bases; do echo $$b; done				\
+	    | $(am__create_global_log);					\
+	} >$(TEST_SUITE_LOG).tmp || exit 1;				\
+	mv $(TEST_SUITE_LOG).tmp $(TEST_SUITE_LOG);			\
+	if $$success; then						\
+	  col="$$grn";							\
+	 else								\
+	  col="$$red";							\
+	  test x"$$VERBOSE" = x || cat $(TEST_SUITE_LOG);		\
+	fi;								\
+	echo "$${col}$$br$${std}"; 					\
+	echo "$${col}Testsuite summary for $(PACKAGE_STRING)$${std}";	\
+	echo "$${col}$$br$${std}"; 					\
+	create_testsuite_report --maybe-color;				\
+	echo "$$col$$br$$std";						\
+	if $$success; then :; else					\
+	  echo "$${col}See $(subdir)/$(TEST_SUITE_LOG)$${std}";		\
+	  if test -n "$(PACKAGE_BUGREPORT)"; then			\
+	    echo "$${col}Please report to $(PACKAGE_BUGREPORT)$${std}";	\
+	  fi;								\
+	  echo "$$col$$br$$std";					\
+	fi;								\
+	$$success || exit 1
+
+check-TESTS:
+	@list='$(RECHECK_LOGS)';           test -z "$$list" || rm -f $$list
+	@list='$(RECHECK_LOGS:.log=.trs)'; test -z "$$list" || rm -f $$list
+	@test -z "$(TEST_SUITE_LOG)" || rm -f $(TEST_SUITE_LOG)
+	@set +e; $(am__set_TESTS_bases); \
+	log_list=`for i in $$bases; do echo $$i.log; done`; \
+	trs_list=`for i in $$bases; do echo $$i.trs; done`; \
+	log_list=`echo $$log_list`; trs_list=`echo $$trs_list`; \
+	$(MAKE) $(AM_MAKEFLAGS) $(TEST_SUITE_LOG) TEST_LOGS="$$log_list"; \
+	exit $$?;
+recheck: all 
+	@test -z "$(TEST_SUITE_LOG)" || rm -f $(TEST_SUITE_LOG)
+	@set +e; $(am__set_TESTS_bases); \
+	bases=`for i in $$bases; do echo $$i; done \
+	         | $(am__list_recheck_tests)` || exit 1; \
+	log_list=`for i in $$bases; do echo $$i.log; done`; \
+	log_list=`echo $$log_list`; \
+	$(MAKE) $(AM_MAKEFLAGS) $(TEST_SUITE_LOG) \
+	        am__force_recheck=am--force-recheck \
+	        TEST_LOGS="$$log_list"; \
+	exit $$?
+rock.sh.log: rock.sh
+	@p='rock.sh'; \
+	b='rock.sh'; \
+	$(am__check_pre) $(LOG_DRIVER) --test-name "$$f" \
+	--log-file $$b.log --trs-file $$b.trs \
+	$(am__common_driver_flags) $(AM_LOG_DRIVER_FLAGS) $(LOG_DRIVER_FLAGS) -- $(LOG_COMPILE) \
+	"$$tst" $(AM_TESTS_FD_REDIRECT)
+.test.log:
+	@p='$<'; \
+	$(am__set_b); \
+	$(am__check_pre) $(TEST_LOG_DRIVER) --test-name "$$f" \
+	--log-file $$b.log --trs-file $$b.trs \
+	$(am__common_driver_flags) $(AM_TEST_LOG_DRIVER_FLAGS) $(TEST_LOG_DRIVER_FLAGS) -- $(TEST_LOG_COMPILE) \
+	"$$tst" $(AM_TESTS_FD_REDIRECT)
+@am__EXEEXT_TRUE@.test$(EXEEXT).log:
+@am__EXEEXT_TRUE@	@p='$<'; \
+@am__EXEEXT_TRUE@	$(am__set_b); \
+@am__EXEEXT_TRUE@	$(am__check_pre) $(TEST_LOG_DRIVER) --test-name "$$f" \
+@am__EXEEXT_TRUE@	--log-file $$b.log --trs-file $$b.trs \
+@am__EXEEXT_TRUE@	$(am__common_driver_flags) $(AM_TEST_LOG_DRIVER_FLAGS) $(TEST_LOG_DRIVER_FLAGS) -- $(TEST_LOG_COMPILE) \
+@am__EXEEXT_TRUE@	"$$tst" $(AM_TESTS_FD_REDIRECT)
+
+distdir: $(DISTFILES)
+	@srcdirstrip=`echo "$(srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
+	topsrcdirstrip=`echo "$(top_srcdir)" | sed 's/[].[^$$\\*]/\\\\&/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
+check-am: all-am
+	$(MAKE) $(AM_MAKEFLAGS) check-TESTS
+check: check-am
+all-am: Makefile
+installdirs:
+install: install-am
+install-exec: install-exec-am
+install-data: install-data-am
+uninstall: uninstall-am
+
+install-am: all-am
+	@$(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-generic mostlyclean-am
+
+distclean: distclean-am
+	-rm -f Makefile
+distclean-am: clean-am distclean-generic
+
+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-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 Makefile
+maintainer-clean-am: distclean-am maintainer-clean-generic
+
+mostlyclean: mostlyclean-am
+
+mostlyclean-am: mostlyclean-generic
+
+pdf: pdf-am
+
+pdf-am:
+
+ps: ps-am
+
+ps-am:
+
+uninstall-am:
+
+.MAKE: check-am install-am install-strip
+
+.PHONY: all all-am check check-TESTS check-am clean clean-generic \
+	cscopelist-am ctags-am distclean distclean-generic distdir dvi \
+	dvi-am html html-am info info-am install install-am \
+	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-generic pdf \
+	pdf-am ps ps-am recheck tags-am uninstall uninstall-am
+
+.PRECIOUS: Makefile
+
+
+# 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:
-- 
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