#! /bin/sh
# Guess values for system-dependent variables and create Makefiles.
# Generated by GNU Autoconf 2.72d for BCFtools 1.19.
#
# Report bugs to <samtools-help@lists.sourceforge.net>.
#
#
# Copyright (C) 1992-1996, 1998-2017, 2020-2023 Free Software Foundation,
# Inc.
#
#
# This configure script is free software; the Free Software Foundation
# gives unlimited permission to copy, distribute and modify it.
#
# Portions copyright (C) 2015,2017-2020 Genome Research Ltd.
#
# This configure script is free software: you are free to change and
# redistribute it.  There is NO WARRANTY, to the extent permitted by law.
## -------------------- ##
## M4sh Initialization. ##
## -------------------- ##

# Be more Bourne compatible
DUALCASE=1; export DUALCASE # for MKS sh
if test ${ZSH_VERSION+y} && (emulate sh) >/dev/null 2>&1
then :
  emulate sh
  NULLCMD=:
  # Pre-4.2 versions of Zsh do word splitting on ${1+"$@"}, which
  # is contrary to our usage.  Disable this feature.
  alias -g '${1+"$@"}'='"$@"'
  setopt NO_GLOB_SUBST
else case e in #(
  e) case `(set -o) 2>/dev/null` in #(
  *posix*) :
    set -o posix ;; #(
  *) :
     ;;
esac ;;
esac
fi



# Reset variables that may have inherited troublesome values from
# the environment.

# IFS needs to be set, to space, tab, and newline, in precisely that order.
# (If _AS_PATH_WALK were called with IFS unset, it would have the
# side effect of setting IFS to empty, thus disabling word splitting.)
# Quoting is to prevent editors from complaining about space-tab.
as_nl='
'
export as_nl
IFS=" ""	$as_nl"

PS1='$ '
PS2='> '
PS4='+ '

# Ensure predictable behavior from utilities with locale-dependent output.
LC_ALL=C
export LC_ALL
LANGUAGE=C
export LANGUAGE

# We cannot yet rely on "unset" to work, but we need these variables
# to be unset--not just set to an empty or harmless value--now, to
# avoid bugs in old shells (e.g. pre-3.0 UWIN ksh).  This construct
# also avoids known problems related to "unset" and subshell syntax
# in other old shells (e.g. bash 2.01 and pdksh 5.2.14).
for as_var in BASH_ENV ENV MAIL MAILPATH CDPATH
do eval test \${$as_var+y} \
  && ( (unset $as_var) || exit 1) >/dev/null 2>&1 && unset $as_var || :
done

# Ensure that fds 0, 1, and 2 are open.
if (exec 3>&0) 2>/dev/null; then :; else exec 0</dev/null; fi
if (exec 3>&1) 2>/dev/null; then :; else exec 1>/dev/null; fi
if (exec 3>&2)            ; then :; else exec 2>/dev/null; fi

# The user is always right.
if ${PATH_SEPARATOR+false} :; then
  PATH_SEPARATOR=:
  (PATH='/bin;/bin'; FPATH=$PATH; sh -c :) >/dev/null 2>&1 && {
    (PATH='/bin:/bin'; FPATH=$PATH; sh -c :) >/dev/null 2>&1 ||
      PATH_SEPARATOR=';'
  }
fi


# Find who we are.  Look in the path if we contain no directory separator.
as_myself=
case $0 in #((
  *[\\/]* ) as_myself=$0 ;;
  *) as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
for as_dir in $PATH
do
  IFS=$as_save_IFS
  case $as_dir in #(((
    '') as_dir=./ ;;
    */) ;;
    *) as_dir=$as_dir/ ;;
  esac
    test -r "$as_dir$0" && as_myself=$as_dir$0 && break
  done
IFS=$as_save_IFS

     ;;
esac
# We did not find ourselves, most probably we were run as 'sh COMMAND'
# in which case we are not to be found in the path.
if test "x$as_myself" = x; then
  as_myself=$0
fi
if test ! -f "$as_myself"; then
  printf "%s\n" "$as_myself: error: cannot find myself; rerun with an absolute file name" >&2
  exit 1
fi


# Use a proper internal environment variable to ensure we don't fall
  # into an infinite loop, continuously re-executing ourselves.
  if test x"${_as_can_reexec}" != xno && test "x$CONFIG_SHELL" != x; then
    _as_can_reexec=no; export _as_can_reexec;
    # We cannot yet assume a decent shell, so we have to provide a
# neutralization value for shells without unset; and this also
# works around shells that cannot unset nonexistent variables.
# Preserve -v and -x to the replacement shell.
BASH_ENV=/dev/null
ENV=/dev/null
(unset BASH_ENV) >/dev/null 2>&1 && unset BASH_ENV ENV
case $- in # ((((
  *v*x* | *x*v* ) as_opts=-vx ;;
  *v* ) as_opts=-v ;;
  *x* ) as_opts=-x ;;
  * ) as_opts= ;;
esac
exec $CONFIG_SHELL $as_opts "$as_myself" ${1+"$@"}
# Admittedly, this is quite paranoid, since all the known shells bail
# out after a failed 'exec'.
printf "%s\n" "$0: could not re-execute with $CONFIG_SHELL" >&2
exit 255
  fi
  # We don't want this to propagate to other subprocesses.
          { _as_can_reexec=; unset _as_can_reexec;}
if test "x$CONFIG_SHELL" = x; then
  as_bourne_compatible="if test \${ZSH_VERSION+y} && (emulate sh) >/dev/null 2>&1
then :
  emulate sh
  NULLCMD=:
  # Pre-4.2 versions of Zsh do word splitting on \${1+\"\$@\"}, which
  # is contrary to our usage.  Disable this feature.
  alias -g '\${1+\"\$@\"}'='\"\$@\"'
  setopt NO_GLOB_SUBST
else case e in #(
  e) case \`(set -o) 2>/dev/null\` in #(
  *posix*) :
    set -o posix ;; #(
  *) :
     ;;
esac ;;
esac
fi
"
  as_required="as_fn_return () { (exit \$1); }
as_fn_success () { as_fn_return 0; }
as_fn_failure () { as_fn_return 1; }
as_fn_ret_success () { return 0; }
as_fn_ret_failure () { return 1; }

exitcode=0
as_fn_success || { exitcode=1; echo as_fn_success failed.; }
as_fn_failure && { exitcode=1; echo as_fn_failure succeeded.; }
as_fn_ret_success || { exitcode=1; echo as_fn_ret_success failed.; }
as_fn_ret_failure && { exitcode=1; echo as_fn_ret_failure succeeded.; }
if ( set x; as_fn_ret_success y && test x = \"\$1\" )
then :

else case e in #(
  e) exitcode=1; echo positional parameters were not saved. ;;
esac
fi
test x\$exitcode = x0 || exit 1
blah=\$(echo \$(echo blah))
test x\"\$blah\" = xblah || exit 1
test -x / || exit 1"
  as_suggested="  as_lineno_1=";as_suggested=$as_suggested$LINENO;as_suggested=$as_suggested" as_lineno_1a=\$LINENO
  as_lineno_2=";as_suggested=$as_suggested$LINENO;as_suggested=$as_suggested" as_lineno_2a=\$LINENO
  eval 'test \"x\$as_lineno_1'\$as_run'\" != \"x\$as_lineno_2'\$as_run'\" &&
  test \"x\`expr \$as_lineno_1'\$as_run' + 1\`\" = \"x\$as_lineno_2'\$as_run'\"' || exit 1
test \$(( 1 + 1 )) = 2 || exit 1"
  if (eval "$as_required") 2>/dev/null
then :
  as_have_required=yes
else case e in #(
  e) as_have_required=no ;;
esac
fi
  if test x$as_have_required = xyes && (eval "$as_suggested") 2>/dev/null
then :

else case e in #(
  e) as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
as_found=false
for as_dir in /bin$PATH_SEPARATOR/usr/bin$PATH_SEPARATOR$PATH
do
  IFS=$as_save_IFS
  case $as_dir in #(((
    '') as_dir=./ ;;
    */) ;;
    *) as_dir=$as_dir/ ;;
  esac
  as_found=:
  case $as_dir in #(
	 /*)
	   for as_base in sh bash ksh sh5; do
	     # Try only shells that exist, to save several forks.
	     as_shell=$as_dir$as_base
	     if { test -f "$as_shell" || test -f "$as_shell.exe"; } &&
		    as_run=a "$as_shell" -c "$as_bourne_compatible""$as_required" 2>/dev/null
then :
  CONFIG_SHELL=$as_shell as_have_required=yes
		   if as_run=a "$as_shell" -c "$as_bourne_compatible""$as_suggested" 2>/dev/null
then :
  break 2
fi
fi
	   done;;
       esac
  as_found=false
done
IFS=$as_save_IFS
if $as_found
then :

else case e in #(
  e) if { test -f "$SHELL" || test -f "$SHELL.exe"; } &&
	      as_run=a "$SHELL" -c "$as_bourne_compatible""$as_required" 2>/dev/null
then :
  CONFIG_SHELL=$SHELL as_have_required=yes
fi ;;
esac
fi


      if test "x$CONFIG_SHELL" != x
then :
  export CONFIG_SHELL
             # We cannot yet assume a decent shell, so we have to provide a
# neutralization value for shells without unset; and this also
# works around shells that cannot unset nonexistent variables.
# Preserve -v and -x to the replacement shell.
BASH_ENV=/dev/null
ENV=/dev/null
(unset BASH_ENV) >/dev/null 2>&1 && unset BASH_ENV ENV
case $- in # ((((
  *v*x* | *x*v* ) as_opts=-vx ;;
  *v* ) as_opts=-v ;;
  *x* ) as_opts=-x ;;
  * ) as_opts= ;;
esac
exec $CONFIG_SHELL $as_opts "$as_myself" ${1+"$@"}
# Admittedly, this is quite paranoid, since all the known shells bail
# out after a failed 'exec'.
printf "%s\n" "$0: could not re-execute with $CONFIG_SHELL" >&2
exit 255
fi

    if test x$as_have_required = xno
then :
  printf "%s\n" "$0: This script requires a shell more modern than all"
  printf "%s\n" "$0: the shells that I found on your system."
  if test ${ZSH_VERSION+y} ; then
    printf "%s\n" "$0: In particular, zsh $ZSH_VERSION has bugs and should"
    printf "%s\n" "$0: be upgraded to zsh 4.3.4 or later."
  else
    printf "%s\n" "$0: Please tell bug-autoconf@gnu.org and
$0: samtools-help@lists.sourceforge.net about your system,
$0: including any error possibly output before this
$0: message. Then install a modern shell, or manually run
$0: the script under such a shell if you do have one."
  fi
  exit 1
fi ;;
esac
fi
fi
SHELL=${CONFIG_SHELL-/bin/sh}
export SHELL
# Unset more variables known to interfere with behavior of common tools.
CLICOLOR_FORCE= GREP_OPTIONS=
unset CLICOLOR_FORCE GREP_OPTIONS

## --------------------- ##
## M4sh Shell Functions. ##
## --------------------- ##
# as_fn_unset VAR
# ---------------
# Portably unset VAR.
as_fn_unset ()
{
  { eval $1=; unset $1;}
}
as_unset=as_fn_unset


# as_fn_set_status STATUS
# -----------------------
# Set $? to STATUS, without forking.
as_fn_set_status ()
{
  return $1
} # as_fn_set_status

# as_fn_exit STATUS
# -----------------
# Exit the shell with STATUS, even in a "trap 0" or "set -e" context.
as_fn_exit ()
{
  set +e
  as_fn_set_status $1
  exit $1
} # as_fn_exit

# as_fn_mkdir_p
# -------------
# Create "$as_dir" as a directory, including parents if necessary.
as_fn_mkdir_p ()
{

  case $as_dir in #(
  -*) as_dir=./$as_dir;;
  esac
  test -d "$as_dir" || eval $as_mkdir_p || {
    as_dirs=
    while :; do
      case $as_dir in #(
      *\'*) as_qdir=`printf "%s\n" "$as_dir" | sed "s/'/'\\\\\\\\''/g"`;; #'(
      *) as_qdir=$as_dir;;
      esac
      as_dirs="'$as_qdir' $as_dirs"
      as_dir=`$as_dirname -- "$as_dir" ||
$as_expr X"$as_dir" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \
	 X"$as_dir" : 'X\(//\)[^/]' \| \
	 X"$as_dir" : 'X\(//\)$' \| \
	 X"$as_dir" : 'X\(/\)' \| . 2>/dev/null ||
printf "%s\n" X"$as_dir" |
    sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{
	    s//\1/
	    q
	  }
	  /^X\(\/\/\)[^/].*/{
	    s//\1/
	    q
	  }
	  /^X\(\/\/\)$/{
	    s//\1/
	    q
	  }
	  /^X\(\/\).*/{
	    s//\1/
	    q
	  }
	  s/.*/./; q'`
      test -d "$as_dir" && break
    done
    test -z "$as_dirs" || eval "mkdir $as_dirs"
  } || test -d "$as_dir" || as_fn_error $? "cannot create directory $as_dir"


} # as_fn_mkdir_p

# as_fn_executable_p FILE
# -----------------------
# Test if FILE is an executable regular file.
as_fn_executable_p ()
{
  test -f "$1" && test -x "$1"
} # as_fn_executable_p
# as_fn_append VAR VALUE
# ----------------------
# Append the text in VALUE to the end of the definition contained in VAR. Take
# advantage of any shell optimizations that allow amortized linear growth over
# repeated appends, instead of the typical quadratic growth present in naive
# implementations.
if (eval "as_var=1; as_var+=2; test x\$as_var = x12") 2>/dev/null
then :
  eval 'as_fn_append ()
  {
    eval $1+=\$2
  }'
else case e in #(
  e) as_fn_append ()
  {
    eval $1=\$$1\$2
  } ;;
esac
fi # as_fn_append

# as_fn_arith ARG...
# ------------------
# Perform arithmetic evaluation on the ARGs, and store the result in the
# global $as_val. Take advantage of shells that can avoid forks. The arguments
# must be portable across $(()) and expr.
if (eval "test \$(( 1 + 1 )) = 2") 2>/dev/null
then :
  eval 'as_fn_arith ()
  {
    as_val=$(( $* ))
  }'
else case e in #(
  e) as_fn_arith ()
  {
    as_val=`expr "$@" || test $? -eq 1`
  } ;;
esac
fi # as_fn_arith


# as_fn_error STATUS ERROR [LINENO LOG_FD]
# ----------------------------------------
# Output "`basename $0`: error: ERROR" to stderr. If LINENO and LOG_FD are
# provided, also output the error to LOG_FD, referencing LINENO. Then exit the
# script with STATUS, using 1 if that was 0.
as_fn_error ()
{
  as_status=$1; test $as_status -eq 0 && as_status=1
  if test "$4"; then
    as_lineno=${as_lineno-"$3"} as_lineno_stack=as_lineno_stack=$as_lineno_stack
    printf "%s\n" "$as_me:${as_lineno-$LINENO}: error: $2" >&$4
  fi
  printf "%s\n" "$as_me: error: $2" >&2
  as_fn_exit $as_status
} # as_fn_error

if expr a : '\(a\)' >/dev/null 2>&1 &&
   test "X`expr 00001 : '.*\(...\)'`" = X001; then
  as_expr=expr
else
  as_expr=false
fi

if (basename -- /) >/dev/null 2>&1 && test "X`basename -- / 2>&1`" = "X/"; then
  as_basename=basename
else
  as_basename=false
fi

if (as_dir=`dirname -- /` && test "X$as_dir" = X/) >/dev/null 2>&1; then
  as_dirname=dirname
else
  as_dirname=false
fi

as_me=`$as_basename -- "$0" ||
$as_expr X/"$0" : '.*/\([^/][^/]*\)/*$' \| \
	 X"$0" : 'X\(//\)$' \| \
	 X"$0" : 'X\(/\)' \| . 2>/dev/null ||
printf "%s\n" X/"$0" |
    sed '/^.*\/\([^/][^/]*\)\/*$/{
	    s//\1/
	    q
	  }
	  /^X\/\(\/\/\)$/{
	    s//\1/
	    q
	  }
	  /^X\/\(\/\).*/{
	    s//\1/
	    q
	  }
	  s/.*/./; q'`

# Avoid depending upon Character Ranges.
as_cr_letters='abcdefghijklmnopqrstuvwxyz'
as_cr_LETTERS='ABCDEFGHIJKLMNOPQRSTUVWXYZ'
as_cr_Letters=$as_cr_letters$as_cr_LETTERS
as_cr_digits='0123456789'
as_cr_alnum=$as_cr_Letters$as_cr_digits


  as_lineno_1=$LINENO as_lineno_1a=$LINENO
  as_lineno_2=$LINENO as_lineno_2a=$LINENO
  eval 'test "x$as_lineno_1'$as_run'" != "x$as_lineno_2'$as_run'" &&
  test "x`expr $as_lineno_1'$as_run' + 1`" = "x$as_lineno_2'$as_run'"' || {
  # Blame Lee E. McMahon (1931-1989) for sed's syntax.  :-)
  sed -n '
    p
    /[$]LINENO/=
  ' <$as_myself |
    sed '
      t clear
      :clear
      s/[$]LINENO.*/&-/
      t lineno
      b
      :lineno
      N
      :loop
      s/[$]LINENO\([^'$as_cr_alnum'_].*\n\)\(.*\)/\2\1\2/
      t loop
      s/-\n.*//
    ' >$as_me.lineno &&
  chmod +x "$as_me.lineno" ||
    { printf "%s\n" "$as_me: error: cannot create $as_me.lineno; rerun with a POSIX shell" >&2; as_fn_exit 1; }

  # If we had to re-execute with $CONFIG_SHELL, we're ensured to have
  # already done that, so ensure we don't try to do so again and fall
  # in an infinite loop.  This has already happened in practice.
  _as_can_reexec=no; export _as_can_reexec
  # Don't try to exec as it changes $[0], causing all sort of problems
  # (the dirname of $[0] is not the place where we might find the
  # original and so on.  Autoconf is especially sensitive to this).
  . "./$as_me.lineno"
  # Exit status is that of the last command.
  exit
}


# Determine whether it's possible to make 'echo' print without a newline.
# These variables are no longer used directly by Autoconf, but are AC_SUBSTed
# for compatibility with existing Makefiles.
ECHO_C= ECHO_N= ECHO_T=
case `echo -n x` in #(((((
-n*)
  case `echo 'xy\c'` in
  *c*) ECHO_T='	';;	# ECHO_T is single tab character.
  xy)  ECHO_C='\c';;
  *)   echo `echo ksh88 bug on AIX 6.1` > /dev/null
       ECHO_T='	';;
  esac;;
*)
  ECHO_N='-n';;
esac

# For backward compatibility with old third-party macros, we provide
# the shell variables $as_echo and $as_echo_n.  New code should use
# AS_ECHO(["message"]) and AS_ECHO_N(["message"]), respectively.
as_echo='printf %s\n'
as_echo_n='printf %s'

rm -f conf$$ conf$$.exe conf$$.file
if test -d conf$$.dir; then
  rm -f conf$$.dir/conf$$.file
else
  rm -f conf$$.dir
  mkdir conf$$.dir 2>/dev/null
fi
if (echo >conf$$.file) 2>/dev/null; then
  if ln -s conf$$.file conf$$ 2>/dev/null; then
    as_ln_s='ln -s'
    # ... but there are two gotchas:
    # 1) On MSYS, both 'ln -s file dir' and 'ln file dir' fail.
    # 2) DJGPP < 2.04 has no symlinks; 'ln -s' creates a wrapper executable.
    # In both cases, we have to default to 'cp -pR'.
    ln -s conf$$.file conf$$.dir 2>/dev/null && test ! -f conf$$.exe ||
      as_ln_s='cp -pR'
  elif ln conf$$.file conf$$ 2>/dev/null; then
    as_ln_s=ln
  else
    as_ln_s='cp -pR'
  fi
else
  as_ln_s='cp -pR'
fi
rm -f conf$$ conf$$.exe conf$$.dir/conf$$.file conf$$.file
rmdir conf$$.dir 2>/dev/null

if mkdir -p . 2>/dev/null; then
  as_mkdir_p='mkdir -p "$as_dir"'
else
  test -d ./-p && rmdir ./-p
  as_mkdir_p=false
fi

as_test_x='test -x'
as_executable_p=as_fn_executable_p

# Sed expression to map a string onto a valid CPP name.
as_sed_cpp="y%*$as_cr_letters%P$as_cr_LETTERS%;s%[^_$as_cr_alnum]%_%g"
as_tr_cpp="eval sed '$as_sed_cpp'" # deprecated

# Sed expression to map a string onto a valid variable name.
as_sed_sh="y%*+%pp%;s%[^_$as_cr_alnum]%_%g"
as_tr_sh="eval sed '$as_sed_sh'" # deprecated


test -n "$DJDIR" || exec 7<&0 </dev/null
exec 6>&1

# Name of the host.
# hostname on some systems (SVR3.2, old GNU/Linux) returns a bogus exit status,
# so uname gets run too.
ac_hostname=`(hostname || uname -n) 2>/dev/null | sed 1q`

#
# Initializations.
#
ac_default_prefix=/usr/local
ac_clean_files=
ac_config_libobj_dir=.
LIBOBJS=
cross_compiling=no
subdirs=
MFLAGS=
MAKEFLAGS=

# Identity of this package.
PACKAGE_NAME='BCFtools'
PACKAGE_TARNAME='bcftools'
PACKAGE_VERSION='1.19'
PACKAGE_STRING='BCFtools 1.19'
PACKAGE_BUGREPORT='samtools-help@lists.sourceforge.net'
PACKAGE_URL='http://www.htslib.org/'

ac_unique_file="main.c"
enable_option_checking=no
enable_year2038=no
ac_subst_vars='LTLIBOBJS
LIBOBJS
PERL_LIBS
PERL_CCOPTS
GSL_LIBS
USE_GPL
CC_RDYNAMIC_OPT
HTSLIB_DLL
PLUGIN_EXT
PLATFORM
Hinstall
Hsource
HTSLIB_LDFLAGS
HTSLIB_CPPFLAGS
HTSDIR
subdirs
enable_perl_filters
bcf_pluginpath
bcf_plugindir
enable_bcftools_plugins
GREP
OBJEXT
EXEEXT
ac_ct_CC
CPPFLAGS
LDFLAGS
CFLAGS
CC
target_alias
host_alias
build_alias
LIBS
ECHO_T
ECHO_N
ECHO_C
DEFS
mandir
localedir
libdir
psdir
pdfdir
dvidir
htmldir
infodir
docdir
oldincludedir
includedir
runstatedir
localstatedir
sharedstatedir
sysconfdir
datadir
datarootdir
libexecdir
sbindir
bindir
program_transform_name
prefix
exec_prefix
PACKAGE_URL
PACKAGE_BUGREPORT
PACKAGE_STRING
PACKAGE_VERSION
PACKAGE_TARNAME
PACKAGE_NAME
PATH_SEPARATOR
SHELL'
ac_subst_files=''
ac_user_opts='
enable_option_checking
enable_warnings
enable_werror
enable_largefile
enable_bcftools_plugins
with_bcf_plugin_dir
with_bcf_plugin_path
enable_perl_filters
enable_libgsl
with_cblas
with_htslib
enable_configure_htslib
enable_year2038
'
      ac_precious_vars='build_alias
host_alias
target_alias
CC
CFLAGS
LDFLAGS
LIBS
CPPFLAGS'
ac_subdirs_all='$HTSDIR'

# Initialize some variables set by options.
ac_init_help=
ac_init_version=false
ac_unrecognized_opts=
ac_unrecognized_sep=
# The variables have the same names as the options, with
# dashes changed to underlines.
cache_file=/dev/null
exec_prefix=NONE
no_create=
no_recursion=
prefix=NONE
program_prefix=NONE
program_suffix=NONE
program_transform_name=s,x,x,
silent=
site=
srcdir=
verbose=
x_includes=NONE
x_libraries=NONE

# Installation directory options.
# These are left unexpanded so users can "make install exec_prefix=/foo"
# and all the variables that are supposed to be based on exec_prefix
# by default will actually change.
# Use braces instead of parens because sh, perl, etc. also accept them.
# (The list follows the same order as the GNU Coding Standards.)
bindir='${exec_prefix}/bin'
sbindir='${exec_prefix}/sbin'
libexecdir='${exec_prefix}/libexec'
datarootdir='${prefix}/share'
datadir='${datarootdir}'
sysconfdir='${prefix}/etc'
sharedstatedir='${prefix}/com'
localstatedir='${prefix}/var'
runstatedir='${localstatedir}/run'
includedir='${prefix}/include'
oldincludedir='/usr/include'
docdir='${datarootdir}/doc/${PACKAGE_TARNAME}'
infodir='${datarootdir}/info'
htmldir='${docdir}'
dvidir='${docdir}'
pdfdir='${docdir}'
psdir='${docdir}'
libdir='${exec_prefix}/lib'
localedir='${datarootdir}/locale'
mandir='${datarootdir}/man'

ac_prev=
ac_dashdash=
for ac_option
do
  # If the previous option needs an argument, assign it.
  if test -n "$ac_prev"; then
    eval $ac_prev=\$ac_option
    ac_prev=
    continue
  fi

  case $ac_option in
  *=?*) ac_optarg=`expr "X$ac_option" : '[^=]*=\(.*\)'` ;;
  *=)   ac_optarg= ;;
  *)    ac_optarg=yes ;;
  esac

  case $ac_dashdash$ac_option in
  --)
    ac_dashdash=yes ;;

  -bindir | --bindir | --bindi | --bind | --bin | --bi)
    ac_prev=bindir ;;
  -bindir=* | --bindir=* | --bindi=* | --bind=* | --bin=* | --bi=*)
    bindir=$ac_optarg ;;

  -build | --build | --buil | --bui | --bu)
    ac_prev=build_alias ;;
  -build=* | --build=* | --buil=* | --bui=* | --bu=*)
    build_alias=$ac_optarg ;;

  -cache-file | --cache-file | --cache-fil | --cache-fi \
  | --cache-f | --cache- | --cache | --cach | --cac | --ca | --c)
    ac_prev=cache_file ;;
  -cache-file=* | --cache-file=* | --cache-fil=* | --cache-fi=* \
  | --cache-f=* | --cache-=* | --cache=* | --cach=* | --cac=* | --ca=* | --c=*)
    cache_file=$ac_optarg ;;

  --config-cache | -C)
    cache_file=config.cache ;;

  -datadir | --datadir | --datadi | --datad)
    ac_prev=datadir ;;
  -datadir=* | --datadir=* | --datadi=* | --datad=*)
    datadir=$ac_optarg ;;

  -datarootdir | --datarootdir | --datarootdi | --datarootd | --dataroot \
  | --dataroo | --dataro | --datar)
    ac_prev=datarootdir ;;
  -datarootdir=* | --datarootdir=* | --datarootdi=* | --datarootd=* \
  | --dataroot=* | --dataroo=* | --dataro=* | --datar=*)
    datarootdir=$ac_optarg ;;

  -disable-* | --disable-*)
    ac_useropt=`expr "x$ac_option" : 'x-*disable-\(.*\)'`
    # Reject names that are not valid shell variable names.
    expr "x$ac_useropt" : ".*[^-+._$as_cr_alnum]" >/dev/null &&
      as_fn_error $? "invalid feature name: '$ac_useropt'"
    ac_useropt_orig=$ac_useropt
    ac_useropt=`printf "%s\n" "$ac_useropt" | sed 's/[-+.]/_/g'`
    case $ac_user_opts in
      *"
"enable_$ac_useropt"
"*) ;;
      *) ac_unrecognized_opts="$ac_unrecognized_opts$ac_unrecognized_sep--disable-$ac_useropt_orig"
	 ac_unrecognized_sep=', ';;
    esac
    eval enable_$ac_useropt=no ;;

  -docdir | --docdir | --docdi | --doc | --do)
    ac_prev=docdir ;;
  -docdir=* | --docdir=* | --docdi=* | --doc=* | --do=*)
    docdir=$ac_optarg ;;

  -dvidir | --dvidir | --dvidi | --dvid | --dvi | --dv)
    ac_prev=dvidir ;;
  -dvidir=* | --dvidir=* | --dvidi=* | --dvid=* | --dvi=* | --dv=*)
    dvidir=$ac_optarg ;;

  -enable-* | --enable-*)
    ac_useropt=`expr "x$ac_option" : 'x-*enable-\([^=]*\)'`
    # Reject names that are not valid shell variable names.
    expr "x$ac_useropt" : ".*[^-+._$as_cr_alnum]" >/dev/null &&
      as_fn_error $? "invalid feature name: '$ac_useropt'"
    ac_useropt_orig=$ac_useropt
    ac_useropt=`printf "%s\n" "$ac_useropt" | sed 's/[-+.]/_/g'`
    case $ac_user_opts in
      *"
"enable_$ac_useropt"
"*) ;;
      *) ac_unrecognized_opts="$ac_unrecognized_opts$ac_unrecognized_sep--enable-$ac_useropt_orig"
	 ac_unrecognized_sep=', ';;
    esac
    eval enable_$ac_useropt=\$ac_optarg ;;

  -exec-prefix | --exec_prefix | --exec-prefix | --exec-prefi \
  | --exec-pref | --exec-pre | --exec-pr | --exec-p | --exec- \
  | --exec | --exe | --ex)
    ac_prev=exec_prefix ;;
  -exec-prefix=* | --exec_prefix=* | --exec-prefix=* | --exec-prefi=* \
  | --exec-pref=* | --exec-pre=* | --exec-pr=* | --exec-p=* | --exec-=* \
  | --exec=* | --exe=* | --ex=*)
    exec_prefix=$ac_optarg ;;

  -gas | --gas | --ga | --g)
    # Obsolete; use --with-gas.
    with_gas=yes ;;

  -help | --help | --hel | --he | -h)
    ac_init_help=long ;;
  -help=r* | --help=r* | --hel=r* | --he=r* | -hr*)
    ac_init_help=recursive ;;
  -help=s* | --help=s* | --hel=s* | --he=s* | -hs*)
    ac_init_help=short ;;

  -host | --host | --hos | --ho)
    ac_prev=host_alias ;;
  -host=* | --host=* | --hos=* | --ho=*)
    host_alias=$ac_optarg ;;

  -htmldir | --htmldir | --htmldi | --htmld | --html | --htm | --ht)
    ac_prev=htmldir ;;
  -htmldir=* | --htmldir=* | --htmldi=* | --htmld=* | --html=* | --htm=* \
  | --ht=*)
    htmldir=$ac_optarg ;;

  -includedir | --includedir | --includedi | --included | --include \
  | --includ | --inclu | --incl | --inc)
    ac_prev=includedir ;;
  -includedir=* | --includedir=* | --includedi=* | --included=* | --include=* \
  | --includ=* | --inclu=* | --incl=* | --inc=*)
    includedir=$ac_optarg ;;

  -infodir | --infodir | --infodi | --infod | --info | --inf)
    ac_prev=infodir ;;
  -infodir=* | --infodir=* | --infodi=* | --infod=* | --info=* | --inf=*)
    infodir=$ac_optarg ;;

  -libdir | --libdir | --libdi | --libd)
    ac_prev=libdir ;;
  -libdir=* | --libdir=* | --libdi=* | --libd=*)
    libdir=$ac_optarg ;;

  -libexecdir | --libexecdir | --libexecdi | --libexecd | --libexec \
  | --libexe | --libex | --libe)
    ac_prev=libexecdir ;;
  -libexecdir=* | --libexecdir=* | --libexecdi=* | --libexecd=* | --libexec=* \
  | --libexe=* | --libex=* | --libe=*)
    libexecdir=$ac_optarg ;;

  -localedir | --localedir | --localedi | --localed | --locale)
    ac_prev=localedir ;;
  -localedir=* | --localedir=* | --localedi=* | --localed=* | --locale=*)
    localedir=$ac_optarg ;;

  -localstatedir | --localstatedir | --localstatedi | --localstated \
  | --localstate | --localstat | --localsta | --localst | --locals)
    ac_prev=localstatedir ;;
  -localstatedir=* | --localstatedir=* | --localstatedi=* | --localstated=* \
  | --localstate=* | --localstat=* | --localsta=* | --localst=* | --locals=*)
    localstatedir=$ac_optarg ;;

  -mandir | --mandir | --mandi | --mand | --man | --ma | --m)
    ac_prev=mandir ;;
  -mandir=* | --mandir=* | --mandi=* | --mand=* | --man=* | --ma=* | --m=*)
    mandir=$ac_optarg ;;

  -nfp | --nfp | --nf)
    # Obsolete; use --without-fp.
    with_fp=no ;;

  -no-create | --no-create | --no-creat | --no-crea | --no-cre \
  | --no-cr | --no-c | -n)
    no_create=yes ;;

  -no-recursion | --no-recursion | --no-recursio | --no-recursi \
  | --no-recurs | --no-recur | --no-recu | --no-rec | --no-re | --no-r)
    no_recursion=yes ;;

  -oldincludedir | --oldincludedir | --oldincludedi | --oldincluded \
  | --oldinclude | --oldinclud | --oldinclu | --oldincl | --oldinc \
  | --oldin | --oldi | --old | --ol | --o)
    ac_prev=oldincludedir ;;
  -oldincludedir=* | --oldincludedir=* | --oldincludedi=* | --oldincluded=* \
  | --oldinclude=* | --oldinclud=* | --oldinclu=* | --oldincl=* | --oldinc=* \
  | --oldin=* | --oldi=* | --old=* | --ol=* | --o=*)
    oldincludedir=$ac_optarg ;;

  -prefix | --prefix | --prefi | --pref | --pre | --pr | --p)
    ac_prev=prefix ;;
  -prefix=* | --prefix=* | --prefi=* | --pref=* | --pre=* | --pr=* | --p=*)
    prefix=$ac_optarg ;;

  -program-prefix | --program-prefix | --program-prefi | --program-pref \
  | --program-pre | --program-pr | --program-p)
    ac_prev=program_prefix ;;
  -program-prefix=* | --program-prefix=* | --program-prefi=* \
  | --program-pref=* | --program-pre=* | --program-pr=* | --program-p=*)
    program_prefix=$ac_optarg ;;

  -program-suffix | --program-suffix | --program-suffi | --program-suff \
  | --program-suf | --program-su | --program-s)
    ac_prev=program_suffix ;;
  -program-suffix=* | --program-suffix=* | --program-suffi=* \
  | --program-suff=* | --program-suf=* | --program-su=* | --program-s=*)
    program_suffix=$ac_optarg ;;

  -program-transform-name | --program-transform-name \
  | --program-transform-nam | --program-transform-na \
  | --program-transform-n | --program-transform- \
  | --program-transform | --program-transfor \
  | --program-transfo | --program-transf \
  | --program-trans | --program-tran \
  | --progr-tra | --program-tr | --program-t)
    ac_prev=program_transform_name ;;
  -program-transform-name=* | --program-transform-name=* \
  | --program-transform-nam=* | --program-transform-na=* \
  | --program-transform-n=* | --program-transform-=* \
  | --program-transform=* | --program-transfor=* \
  | --program-transfo=* | --program-transf=* \
  | --program-trans=* | --program-tran=* \
  | --progr-tra=* | --program-tr=* | --program-t=*)
    program_transform_name=$ac_optarg ;;

  -pdfdir | --pdfdir | --pdfdi | --pdfd | --pdf | --pd)
    ac_prev=pdfdir ;;
  -pdfdir=* | --pdfdir=* | --pdfdi=* | --pdfd=* | --pdf=* | --pd=*)
    pdfdir=$ac_optarg ;;

  -psdir | --psdir | --psdi | --psd | --ps)
    ac_prev=psdir ;;
  -psdir=* | --psdir=* | --psdi=* | --psd=* | --ps=*)
    psdir=$ac_optarg ;;

  -q | -quiet | --quiet | --quie | --qui | --qu | --q \
  | -silent | --silent | --silen | --sile | --sil)
    silent=yes ;;

  -runstatedir | --runstatedir | --runstatedi | --runstated \
  | --runstate | --runstat | --runsta | --runst | --runs \
  | --run | --ru | --r)
    ac_prev=runstatedir ;;
  -runstatedir=* | --runstatedir=* | --runstatedi=* | --runstated=* \
  | --runstate=* | --runstat=* | --runsta=* | --runst=* | --runs=* \
  | --run=* | --ru=* | --r=*)
    runstatedir=$ac_optarg ;;

  -sbindir | --sbindir | --sbindi | --sbind | --sbin | --sbi | --sb)
    ac_prev=sbindir ;;
  -sbindir=* | --sbindir=* | --sbindi=* | --sbind=* | --sbin=* \
  | --sbi=* | --sb=*)
    sbindir=$ac_optarg ;;

  -sharedstatedir | --sharedstatedir | --sharedstatedi \
  | --sharedstated | --sharedstate | --sharedstat | --sharedsta \
  | --sharedst | --shareds | --shared | --share | --shar \
  | --sha | --sh)
    ac_prev=sharedstatedir ;;
  -sharedstatedir=* | --sharedstatedir=* | --sharedstatedi=* \
  | --sharedstated=* | --sharedstate=* | --sharedstat=* | --sharedsta=* \
  | --sharedst=* | --shareds=* | --shared=* | --share=* | --shar=* \
  | --sha=* | --sh=*)
    sharedstatedir=$ac_optarg ;;

  -site | --site | --sit)
    ac_prev=site ;;
  -site=* | --site=* | --sit=*)
    site=$ac_optarg ;;

  -srcdir | --srcdir | --srcdi | --srcd | --src | --sr)
    ac_prev=srcdir ;;
  -srcdir=* | --srcdir=* | --srcdi=* | --srcd=* | --src=* | --sr=*)
    srcdir=$ac_optarg ;;

  -sysconfdir | --sysconfdir | --sysconfdi | --sysconfd | --sysconf \
  | --syscon | --sysco | --sysc | --sys | --sy)
    ac_prev=sysconfdir ;;
  -sysconfdir=* | --sysconfdir=* | --sysconfdi=* | --sysconfd=* | --sysconf=* \
  | --syscon=* | --sysco=* | --sysc=* | --sys=* | --sy=*)
    sysconfdir=$ac_optarg ;;

  -target | --target | --targe | --targ | --tar | --ta | --t)
    ac_prev=target_alias ;;
  -target=* | --target=* | --targe=* | --targ=* | --tar=* | --ta=* | --t=*)
    target_alias=$ac_optarg ;;

  -v | -verbose | --verbose | --verbos | --verbo | --verb)
    verbose=yes ;;

  -version | --version | --versio | --versi | --vers | -V)
    ac_init_version=: ;;

  -with-* | --with-*)
    ac_useropt=`expr "x$ac_option" : 'x-*with-\([^=]*\)'`
    # Reject names that are not valid shell variable names.
    expr "x$ac_useropt" : ".*[^-+._$as_cr_alnum]" >/dev/null &&
      as_fn_error $? "invalid package name: '$ac_useropt'"
    ac_useropt_orig=$ac_useropt
    ac_useropt=`printf "%s\n" "$ac_useropt" | sed 's/[-+.]/_/g'`
    case $ac_user_opts in
      *"
"with_$ac_useropt"
"*) ;;
      *) ac_unrecognized_opts="$ac_unrecognized_opts$ac_unrecognized_sep--with-$ac_useropt_orig"
	 ac_unrecognized_sep=', ';;
    esac
    eval with_$ac_useropt=\$ac_optarg ;;

  -without-* | --without-*)
    ac_useropt=`expr "x$ac_option" : 'x-*without-\(.*\)'`
    # Reject names that are not valid shell variable names.
    expr "x$ac_useropt" : ".*[^-+._$as_cr_alnum]" >/dev/null &&
      as_fn_error $? "invalid package name: '$ac_useropt'"
    ac_useropt_orig=$ac_useropt
    ac_useropt=`printf "%s\n" "$ac_useropt" | sed 's/[-+.]/_/g'`
    case $ac_user_opts in
      *"
"with_$ac_useropt"
"*) ;;
      *) ac_unrecognized_opts="$ac_unrecognized_opts$ac_unrecognized_sep--without-$ac_useropt_orig"
	 ac_unrecognized_sep=', ';;
    esac
    eval with_$ac_useropt=no ;;

  --x)
    # Obsolete; use --with-x.
    with_x=yes ;;

  -x-includes | --x-includes | --x-include | --x-includ | --x-inclu \
  | --x-incl | --x-inc | --x-in | --x-i)
    ac_prev=x_includes ;;
  -x-includes=* | --x-includes=* | --x-include=* | --x-includ=* | --x-inclu=* \
  | --x-incl=* | --x-inc=* | --x-in=* | --x-i=*)
    x_includes=$ac_optarg ;;

  -x-libraries | --x-libraries | --x-librarie | --x-librari \
  | --x-librar | --x-libra | --x-libr | --x-lib | --x-li | --x-l)
    ac_prev=x_libraries ;;
  -x-libraries=* | --x-libraries=* | --x-librarie=* | --x-librari=* \
  | --x-librar=* | --x-libra=* | --x-libr=* | --x-lib=* | --x-li=* | --x-l=*)
    x_libraries=$ac_optarg ;;

  -*) as_fn_error $? "unrecognized option: '$ac_option'
Try '$0 --help' for more information"
    ;;

  *=*)
    ac_envvar=`expr "x$ac_option" : 'x\([^=]*\)='`
    # Reject names that are not valid shell variable names.
    case $ac_envvar in #(
      '' | [0-9]* | *[!_$as_cr_alnum]* )
      as_fn_error $? "invalid variable name: '$ac_envvar'" ;;
    esac
    eval $ac_envvar=\$ac_optarg
    export $ac_envvar ;;

  *)
    # FIXME: should be removed in autoconf 3.0.
    printf "%s\n" "$as_me: WARNING: you should use --build, --host, --target" >&2
    expr "x$ac_option" : ".*[^-._$as_cr_alnum]" >/dev/null &&
      printf "%s\n" "$as_me: WARNING: invalid host type: $ac_option" >&2
    : "${build_alias=$ac_option} ${host_alias=$ac_option} ${target_alias=$ac_option}"
    ;;

  esac
done

if test -n "$ac_prev"; then
  ac_option=--`echo $ac_prev | sed 's/_/-/g'`
  as_fn_error $? "missing argument to $ac_option"
fi

if test -n "$ac_unrecognized_opts"; then
  case $enable_option_checking in
    no) ;;
    fatal) as_fn_error $? "unrecognized options: $ac_unrecognized_opts" ;;
    *)     printf "%s\n" "$as_me: WARNING: unrecognized options: $ac_unrecognized_opts" >&2 ;;
  esac
fi

# Check all directory arguments for consistency.
for ac_var in	exec_prefix prefix bindir sbindir libexecdir datarootdir \
		datadir sysconfdir sharedstatedir localstatedir includedir \
		oldincludedir docdir infodir htmldir dvidir pdfdir psdir \
		libdir localedir mandir runstatedir
do
  eval ac_val=\$$ac_var
  # Remove trailing slashes.
  case $ac_val in
    */ )
      ac_val=`expr "X$ac_val" : 'X\(.*[^/]\)' \| "X$ac_val" : 'X\(.*\)'`
      eval $ac_var=\$ac_val;;
  esac
  # Be sure to have absolute directory names.
  case $ac_val in
    [\\/$]* | ?:[\\/]* )  continue;;
    NONE | '' ) case $ac_var in *prefix ) continue;; esac;;
  esac
  as_fn_error $? "expected an absolute directory name for --$ac_var: $ac_val"
done

# There might be people who depend on the old broken behavior: '$host'
# used to hold the argument of --host etc.
# FIXME: To remove some day.
build=$build_alias
host=$host_alias
target=$target_alias

# FIXME: To remove some day.
if test "x$host_alias" != x; then
  if test "x$build_alias" = x; then
    cross_compiling=maybe
  elif test "x$build_alias" != "x$host_alias"; then
    cross_compiling=yes
  fi
fi

ac_tool_prefix=
test -n "$host_alias" && ac_tool_prefix=$host_alias-

test "$silent" = yes && exec 6>/dev/null


ac_pwd=`pwd` && test -n "$ac_pwd" &&
ac_ls_di=`ls -di .` &&
ac_pwd_ls_di=`cd "$ac_pwd" && ls -di .` ||
  as_fn_error $? "working directory cannot be determined"
test "X$ac_ls_di" = "X$ac_pwd_ls_di" ||
  as_fn_error $? "pwd does not report name of working directory"


# Find the source files, if location was not specified.
if test -z "$srcdir"; then
  ac_srcdir_defaulted=yes
  # Try the directory containing this script, then the parent directory.
  ac_confdir=`$as_dirname -- "$as_myself" ||
$as_expr X"$as_myself" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \
	 X"$as_myself" : 'X\(//\)[^/]' \| \
	 X"$as_myself" : 'X\(//\)$' \| \
	 X"$as_myself" : 'X\(/\)' \| . 2>/dev/null ||
printf "%s\n" X"$as_myself" |
    sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{
	    s//\1/
	    q
	  }
	  /^X\(\/\/\)[^/].*/{
	    s//\1/
	    q
	  }
	  /^X\(\/\/\)$/{
	    s//\1/
	    q
	  }
	  /^X\(\/\).*/{
	    s//\1/
	    q
	  }
	  s/.*/./; q'`
  srcdir=$ac_confdir
  if test ! -r "$srcdir/$ac_unique_file"; then
    srcdir=..
  fi
else
  ac_srcdir_defaulted=no
fi
if test ! -r "$srcdir/$ac_unique_file"; then
  test "$ac_srcdir_defaulted" = yes && srcdir="$ac_confdir or .."
  as_fn_error $? "cannot find sources ($ac_unique_file) in $srcdir"
fi
ac_msg="sources are in $srcdir, but 'cd $srcdir' does not work"
ac_abs_confdir=`(
	cd "$srcdir" && test -r "./$ac_unique_file" || as_fn_error $? "$ac_msg"
	pwd)`
# When building in place, set srcdir=.
if test "$ac_abs_confdir" = "$ac_pwd"; then
  srcdir=.
fi
# Remove unnecessary trailing slashes from srcdir.
# Double slashes in file names in object file debugging info
# mess up M-x gdb in Emacs.
case $srcdir in
*/) srcdir=`expr "X$srcdir" : 'X\(.*[^/]\)' \| "X$srcdir" : 'X\(.*\)'`;;
esac
for ac_var in $ac_precious_vars; do
  eval ac_env_${ac_var}_set=\${${ac_var}+set}
  eval ac_env_${ac_var}_value=\$${ac_var}
  eval ac_cv_env_${ac_var}_set=\${${ac_var}+set}
  eval ac_cv_env_${ac_var}_value=\$${ac_var}
done

#
# Report the --help message.
#
if test "$ac_init_help" = "long"; then
  # Omit some internal or obsolete options to make the list less imposing.
  # This message is too long to be a string in the A/UX 3.1 sh.
  cat <<_ACEOF
'configure' configures BCFtools 1.19 to adapt to many kinds of systems.

Usage: $0 [OPTION]... [VAR=VALUE]...

To assign environment variables (e.g., CC, CFLAGS...), specify them as
VAR=VALUE.  See below for descriptions of some of the useful variables.

Defaults for the options are specified in brackets.

Configuration:
  -h, --help              display this help and exit
      --help=short        display options specific to this package
      --help=recursive    display the short help of all the included packages
  -V, --version           display version information and exit
  -q, --quiet, --silent   do not print 'checking ...' messages
      --cache-file=FILE   cache test results in FILE [disabled]
  -C, --config-cache      alias for '--cache-file=config.cache'
  -n, --no-create         do not create output files
      --srcdir=DIR        find the sources in DIR [configure dir or '..']

Installation directories:
  --prefix=PREFIX         install architecture-independent files in PREFIX
                          [$ac_default_prefix]
  --exec-prefix=EPREFIX   install architecture-dependent files in EPREFIX
                          [PREFIX]

By default, 'make install' will install all the files in
'$ac_default_prefix/bin', '$ac_default_prefix/lib' etc.  You can specify
an installation prefix other than '$ac_default_prefix' using '--prefix',
for instance '--prefix=\$HOME'.

For better control, use the options below.

Fine tuning of the installation directories:
  --bindir=DIR            user executables [EPREFIX/bin]
  --sbindir=DIR           system admin executables [EPREFIX/sbin]
  --libexecdir=DIR        program executables [EPREFIX/libexec]
  --sysconfdir=DIR        read-only single-machine data [PREFIX/etc]
  --sharedstatedir=DIR    modifiable architecture-independent data [PREFIX/com]
  --localstatedir=DIR     modifiable single-machine data [PREFIX/var]
  --runstatedir=DIR       modifiable per-process data [LOCALSTATEDIR/run]
  --libdir=DIR            object code libraries [EPREFIX/lib]
  --includedir=DIR        C header files [PREFIX/include]
  --oldincludedir=DIR     C header files for non-gcc [/usr/include]
  --datarootdir=DIR       read-only arch.-independent data root [PREFIX/share]
  --datadir=DIR           read-only architecture-independent data [DATAROOTDIR]
  --infodir=DIR           info documentation [DATAROOTDIR/info]
  --localedir=DIR         locale-dependent data [DATAROOTDIR/locale]
  --mandir=DIR            man documentation [DATAROOTDIR/man]
  --docdir=DIR            documentation root [DATAROOTDIR/doc/bcftools]
  --htmldir=DIR           html documentation [DOCDIR]
  --dvidir=DIR            dvi documentation [DOCDIR]
  --pdfdir=DIR            pdf documentation [DOCDIR]
  --psdir=DIR             ps documentation [DOCDIR]
_ACEOF

  cat <<\_ACEOF
_ACEOF
fi

if test -n "$ac_init_help"; then
  case $ac_init_help in
     short | recursive ) echo "Configuration of BCFtools 1.19:";;
   esac
  cat <<\_ACEOF

Optional Features:
  --disable-option-checking  ignore unrecognized --enable/--with options
  --disable-FEATURE       do not include FEATURE (same as --enable-FEATURE=no)
  --enable-FEATURE[=ARG]  include FEATURE [ARG=yes]
  --disable-warnings      turn off compiler warnings
  --enable-werror         change warnings into errors, where supported
  --disable-largefile     omit support for large files
  --disable-bcftools-plugins
                          do not build optional plugins
  --enable-perl-filters   build in support for PERL scripts in -i/-e filtering
                          expressions
  --enable-libgsl         build options that require the GNU scientific
                          library (changes bcftools license to GPL, see
                          INSTALL for details)
  --enable-configure-htslib
                          run configure for htslib as well
                          [default=only_in_subdir]
  --enable-year2038       support timestamps after 2038

Optional Packages:
  --with-PACKAGE[=ARG]    use PACKAGE [ARG=yes]
  --without-PACKAGE       do not use PACKAGE (same as --with-PACKAGE=no)
  --with-bcf-plugin-dir=DIR
                          plugin installation location [LIBEXECDIR/bcftools]
  --with-bcf-plugin-path=PATH
                          default BCFTOOLS_PLUGINS plugin search path
                          [PLUGINDIR]
  --with-cblas            which cblas library to use (only needed with libgsl;
                          default: try cblas then gslcblas)
  --with-htslib=DIR       use the HTSlib source tree or installation in DIR
  --with-htslib=system    use only a system HTSlib installation

Some influential environment variables:
  CC          C compiler command
  CFLAGS      C compiler flags
  LDFLAGS     linker flags, e.g. -L<lib dir> if you have libraries in a
              nonstandard directory <lib dir>
  LIBS        libraries to pass to the linker, e.g. -l<library>
  CPPFLAGS    (Objective) C/C++ preprocessor flags, e.g. -I<include dir> if
              you have headers in a nonstandard directory <include dir>

Use these variables to override the choices made by 'configure' or to help
it to find libraries and programs with nonstandard names/locations.

Report bugs to <samtools-help@lists.sourceforge.net>.
BCFtools home page: <http://www.htslib.org/>.
_ACEOF
ac_status=$?
fi

if test "$ac_init_help" = "recursive"; then
  # If there are subdirs, report their specific --help.
  for ac_dir in : $ac_subdirs_all; do test "x$ac_dir" = x: && continue
    test -d "$ac_dir" ||
      { cd "$srcdir" && ac_pwd=`pwd` && srcdir=. && test -d "$ac_dir"; } ||
      continue
    ac_builddir=.

case "$ac_dir" in
.) ac_dir_suffix= ac_top_builddir_sub=. ac_top_build_prefix= ;;
*)
  ac_dir_suffix=/`printf "%s\n" "$ac_dir" | sed 's|^\.[\\/]||'`
  # A ".." for each directory in $ac_dir_suffix.
  ac_top_builddir_sub=`printf "%s\n" "$ac_dir_suffix" | sed 's|/[^\\/]*|/..|g;s|/||'`
  case $ac_top_builddir_sub in
  "") ac_top_builddir_sub=. ac_top_build_prefix= ;;
  *)  ac_top_build_prefix=$ac_top_builddir_sub/ ;;
  esac ;;
esac
ac_abs_top_builddir=$ac_pwd
ac_abs_builddir=$ac_pwd$ac_dir_suffix
# for backward compatibility:
ac_top_builddir=$ac_top_build_prefix

case $srcdir in
  .)  # We are building in place.
    ac_srcdir=.
    ac_top_srcdir=$ac_top_builddir_sub
    ac_abs_top_srcdir=$ac_pwd ;;
  [\\/]* | ?:[\\/]* )  # Absolute name.
    ac_srcdir=$srcdir$ac_dir_suffix;
    ac_top_srcdir=$srcdir
    ac_abs_top_srcdir=$srcdir ;;
  *) # Relative name.
    ac_srcdir=$ac_top_build_prefix$srcdir$ac_dir_suffix
    ac_top_srcdir=$ac_top_build_prefix$srcdir
    ac_abs_top_srcdir=$ac_pwd/$srcdir ;;
esac
ac_abs_srcdir=$ac_abs_top_srcdir$ac_dir_suffix

    cd "$ac_dir" || { ac_status=$?; continue; }
    # Check for configure.gnu first; this name is used for a wrapper for
    # Metaconfig's "Configure" on case-insensitive file systems.
    if test -f "$ac_srcdir/configure.gnu"; then
      echo &&
      $SHELL "$ac_srcdir/configure.gnu" --help=recursive
    elif test -f "$ac_srcdir/configure"; then
      echo &&
      $SHELL "$ac_srcdir/configure" --help=recursive
    else
      printf "%s\n" "$as_me: WARNING: no configuration information is in $ac_dir" >&2
    fi || ac_status=$?
    cd "$ac_pwd" || { ac_status=$?; break; }
  done
fi

test -n "$ac_init_help" && exit $ac_status
if $ac_init_version; then
  cat <<\_ACEOF
BCFtools configure 1.19
generated by GNU Autoconf 2.72d

Copyright (C) 2023 Free Software Foundation, Inc.
This configure script is free software; the Free Software Foundation
gives unlimited permission to copy, distribute and modify it.

Portions copyright (C) 2015,2017-2020 Genome Research Ltd.

This configure script is free software: you are free to change and
redistribute it.  There is NO WARRANTY, to the extent permitted by law.
_ACEOF
  exit
fi

## ------------------------ ##
## Autoconf initialization. ##
## ------------------------ ##

# ac_fn_c_try_compile LINENO
# --------------------------
# Try to compile conftest.$ac_ext, and return whether this succeeded.
ac_fn_c_try_compile ()
{
  as_lineno=${as_lineno-"$1"} as_lineno_stack=as_lineno_stack=$as_lineno_stack
  rm -f conftest.$ac_objext conftest.beam
  if { { ac_try="$ac_compile"
case "(($ac_try" in
  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
  *) ac_try_echo=$ac_try;;
esac
eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\""
printf "%s\n" "$ac_try_echo"; } >&5
  (eval "$ac_compile") 2>conftest.err
  ac_status=$?
  if test -s conftest.err; then
    grep -v '^ *+' conftest.err >conftest.er1
    cat conftest.er1 >&5
    mv -f conftest.er1 conftest.err
  fi
  printf "%s\n" "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
  test $ac_status = 0; } && {
	 test -z "$ac_c_werror_flag" ||
	 test ! -s conftest.err
       } && test -s conftest.$ac_objext
then :
  ac_retval=0
else case e in #(
  e) printf "%s\n" "$as_me: failed program was:" >&5
sed 's/^/| /' conftest.$ac_ext >&5

	ac_retval=1 ;;
esac
fi
  eval $as_lineno_stack; ${as_lineno_stack:+:} unset as_lineno
  as_fn_set_status $ac_retval

} # ac_fn_c_try_compile

# ac_fn_c_check_header_compile LINENO HEADER VAR INCLUDES
# -------------------------------------------------------
# Tests whether HEADER exists and can be compiled using the include files in
# INCLUDES, setting the cache variable VAR accordingly.
ac_fn_c_check_header_compile ()
{
  as_lineno=${as_lineno-"$1"} as_lineno_stack=as_lineno_stack=$as_lineno_stack
  { printf "%s\n" "$as_me:${as_lineno-$LINENO}: checking for $2" >&5
printf %s "checking for $2... " >&6; }
if eval test \${$3+y}
then :
  printf %s "(cached) " >&6
else case e in #(
  e) cat confdefs.h - <<_ACEOF >conftest.$ac_ext
/* end confdefs.h.  */
$4
#include <$2>
_ACEOF
if ac_fn_c_try_compile "$LINENO"
then :
  eval "$3=yes"
else case e in #(
  e) eval "$3=no" ;;
esac
fi
rm -f core conftest.err conftest.$ac_objext conftest.beam conftest.$ac_ext ;;
esac
fi
eval ac_res=\$$3
	       { printf "%s\n" "$as_me:${as_lineno-$LINENO}: result: $ac_res" >&5
printf "%s\n" "$ac_res" >&6; }
  eval $as_lineno_stack; ${as_lineno_stack:+:} unset as_lineno

} # ac_fn_c_check_header_compile

# ac_fn_c_try_link LINENO
# -----------------------
# Try to link conftest.$ac_ext, and return whether this succeeded.
ac_fn_c_try_link ()
{
  as_lineno=${as_lineno-"$1"} as_lineno_stack=as_lineno_stack=$as_lineno_stack
  rm -f conftest.$ac_objext conftest.beam conftest$ac_exeext
  if { { ac_try="$ac_link"
case "(($ac_try" in
  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
  *) ac_try_echo=$ac_try;;
esac
eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\""
printf "%s\n" "$ac_try_echo"; } >&5
  (eval "$ac_link") 2>conftest.err
  ac_status=$?
  if test -s conftest.err; then
    grep -v '^ *+' conftest.err >conftest.er1
    cat conftest.er1 >&5
    mv -f conftest.er1 conftest.err
  fi
  printf "%s\n" "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
  test $ac_status = 0; } && {
	 test -z "$ac_c_werror_flag" ||
	 test ! -s conftest.err
       } && test -s conftest$ac_exeext && {
	 test "$cross_compiling" = yes ||
	 test -x conftest$ac_exeext
       }
then :
  ac_retval=0
else case e in #(
  e) printf "%s\n" "$as_me: failed program was:" >&5
sed 's/^/| /' conftest.$ac_ext >&5

	ac_retval=1 ;;
esac
fi
  # Delete the IPA/IPO (Inter Procedural Analysis/Optimization) information
  # created by the PGI compiler (conftest_ipa8_conftest.oo), as it would
  # interfere with the next link command; also delete a directory that is
  # left behind by Apple's compiler.  We do this before executing the actions.
  rm -rf conftest.dSYM conftest_ipa8_conftest.oo
  eval $as_lineno_stack; ${as_lineno_stack:+:} unset as_lineno
  as_fn_set_status $ac_retval

} # ac_fn_c_try_link
ac_configure_args_raw=
for ac_arg
do
  case $ac_arg in
  *\'*)
    ac_arg=`printf "%s\n" "$ac_arg" | sed "s/'/'\\\\\\\\''/g"` ;;
  esac
  as_fn_append ac_configure_args_raw " '$ac_arg'"
done

case $ac_configure_args_raw in
  *$as_nl*)
    ac_safe_unquote= ;;
  *)
    ac_unsafe_z='|&;<>()$`\\"*?[ ''	' # This string ends in space, tab.
    ac_unsafe_a="$ac_unsafe_z#~"
    ac_safe_unquote="s/ '\\([^$ac_unsafe_a][^$ac_unsafe_z]*\\)'/ \\1/g"
    ac_configure_args_raw=`      printf "%s\n" "$ac_configure_args_raw" | sed "$ac_safe_unquote"`;;
esac

cat >config.log <<_ACEOF
This file contains any messages produced by compilers while
running configure, to aid debugging if configure makes a mistake.

It was created by BCFtools $as_me 1.19, which was
generated by GNU Autoconf 2.72d.  Invocation command line was

  $ $0$ac_configure_args_raw

_ACEOF
exec 5>>config.log
{
cat <<_ASUNAME
## --------- ##
## Platform. ##
## --------- ##

hostname = `(hostname || uname -n) 2>/dev/null | sed 1q`
uname -m = `(uname -m) 2>/dev/null || echo unknown`
uname -r = `(uname -r) 2>/dev/null || echo unknown`
uname -s = `(uname -s) 2>/dev/null || echo unknown`
uname -v = `(uname -v) 2>/dev/null || echo unknown`

/usr/bin/uname -p = `(/usr/bin/uname -p) 2>/dev/null || echo unknown`
/bin/uname -X     = `(/bin/uname -X) 2>/dev/null     || echo unknown`

/bin/arch              = `(/bin/arch) 2>/dev/null              || echo unknown`
/usr/bin/arch -k       = `(/usr/bin/arch -k) 2>/dev/null       || echo unknown`
/usr/convex/getsysinfo = `(/usr/convex/getsysinfo) 2>/dev/null || echo unknown`
/usr/bin/hostinfo      = `(/usr/bin/hostinfo) 2>/dev/null      || echo unknown`
/bin/machine           = `(/bin/machine) 2>/dev/null           || echo unknown`
/usr/bin/oslevel       = `(/usr/bin/oslevel) 2>/dev/null       || echo unknown`
/bin/universe          = `(/bin/universe) 2>/dev/null          || echo unknown`

_ASUNAME

as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
for as_dir in $PATH
do
  IFS=$as_save_IFS
  case $as_dir in #(((
    '') as_dir=./ ;;
    */) ;;
    *) as_dir=$as_dir/ ;;
  esac
    printf "%s\n" "PATH: $as_dir"
  done
IFS=$as_save_IFS

} >&5

cat >&5 <<_ACEOF


## ----------- ##
## Core tests. ##
## ----------- ##

_ACEOF


# Keep a trace of the command line.
# Strip out --no-create and --no-recursion so they do not pile up.
# Strip out --silent because we don't want to record it for future runs.
# Also quote any args containing shell meta-characters.
# Make two passes to allow for proper duplicate-argument suppression.
ac_configure_args=
ac_configure_args0=
ac_configure_args1=
ac_must_keep_next=false
for ac_pass in 1 2
do
  for ac_arg
  do
    case $ac_arg in
    -no-create | --no-c* | -n | -no-recursion | --no-r*) continue ;;
    -q | -quiet | --quiet | --quie | --qui | --qu | --q \
    | -silent | --silent | --silen | --sile | --sil)
      continue ;;
    *\'*)
      ac_arg=`printf "%s\n" "$ac_arg" | sed "s/'/'\\\\\\\\''/g"` ;;
    esac
    case $ac_pass in
    1) as_fn_append ac_configure_args0 " '$ac_arg'" ;;
    2)
      as_fn_append ac_configure_args1 " '$ac_arg'"
      if test $ac_must_keep_next = true; then
	ac_must_keep_next=false # Got value, back to normal.
      else
	case $ac_arg in
	  *=* | --config-cache | -C | -disable-* | --disable-* \
	  | -enable-* | --enable-* | -gas | --g* | -nfp | --nf* \
	  | -q | -quiet | --q* | -silent | --sil* | -v | -verb* \
	  | -with-* | --with-* | -without-* | --without-* | --x)
	    case "$ac_configure_args0 " in
	      "$ac_configure_args1"*" '$ac_arg' "* ) continue ;;
	    esac
	    ;;
	  -* ) ac_must_keep_next=true ;;
	esac
      fi
      as_fn_append ac_configure_args " '$ac_arg'"
      ;;
    esac
  done
done
{ ac_configure_args0=; unset ac_configure_args0;}
{ ac_configure_args1=; unset ac_configure_args1;}

# When interrupted or exit'd, cleanup temporary files, and complete
# config.log.  We remove comments because anyway the quotes in there
# would cause problems or look ugly.
# WARNING: Use '\'' to represent an apostrophe within the trap.
# WARNING: Do not start the trap code with a newline, due to a FreeBSD 4.0 bug.
trap 'exit_status=$?
  # Sanitize IFS.
  IFS=" ""	$as_nl"
  # Save into config.log some information that might help in debugging.
  {
    echo

    printf "%s\n" "## ---------------- ##
## Cache variables. ##
## ---------------- ##"
    echo
    # The following way of writing the cache mishandles newlines in values,
(
  for ac_var in `(set) 2>&1 | sed -n '\''s/^\([a-zA-Z_][a-zA-Z0-9_]*\)=.*/\1/p'\''`; do
    eval ac_val=\$$ac_var
    case $ac_val in #(
    *${as_nl}*)
      case $ac_var in #(
      *_cv_*) { printf "%s\n" "$as_me:${as_lineno-$LINENO}: WARNING: cache variable $ac_var contains a newline" >&5
printf "%s\n" "$as_me: WARNING: cache variable $ac_var contains a newline" >&2;} ;;
      esac
      case $ac_var in #(
      _ | IFS | as_nl) ;; #(
      BASH_ARGV | BASH_SOURCE) eval $ac_var= ;; #(
      *) { eval $ac_var=; unset $ac_var;} ;;
      esac ;;
    esac
  done
  (set) 2>&1 |
    case $as_nl`(ac_space='\'' '\''; set) 2>&1` in #(
    *${as_nl}ac_space=\ *)
      sed -n \
	"s/'\''/'\''\\\\'\'''\''/g;
	  s/^\\([_$as_cr_alnum]*_cv_[_$as_cr_alnum]*\\)=\\(.*\\)/\\1='\''\\2'\''/p"
      ;; #(
    *)
      sed -n "/^[_$as_cr_alnum]*_cv_[_$as_cr_alnum]*=/p"
      ;;
    esac |
    sort
)
    echo

    printf "%s\n" "## ----------------- ##
## Output variables. ##
## ----------------- ##"
    echo
    for ac_var in $ac_subst_vars
    do
      eval ac_val=\$$ac_var
      case $ac_val in
      *\'\''*) ac_val=`printf "%s\n" "$ac_val" | sed "s/'\''/'\''\\\\\\\\'\'''\''/g"`;;
      esac
      printf "%s\n" "$ac_var='\''$ac_val'\''"
    done | sort
    echo

    if test -n "$ac_subst_files"; then
      printf "%s\n" "## ------------------- ##
## File substitutions. ##
## ------------------- ##"
      echo
      for ac_var in $ac_subst_files
      do
	eval ac_val=\$$ac_var
	case $ac_val in
	*\'\''*) ac_val=`printf "%s\n" "$ac_val" | sed "s/'\''/'\''\\\\\\\\'\'''\''/g"`;;
	esac
	printf "%s\n" "$ac_var='\''$ac_val'\''"
      done | sort
      echo
    fi

    if test -s confdefs.h; then
      printf "%s\n" "## ----------- ##
## confdefs.h. ##
## ----------- ##"
      echo
      cat confdefs.h
      echo
    fi
    test "$ac_signal" != 0 &&
      printf "%s\n" "$as_me: caught signal $ac_signal"
    printf "%s\n" "$as_me: exit $exit_status"
  } >&5
  rm -f core *.core core.conftest.* &&
    rm -f -r conftest* confdefs* conf$$* $ac_clean_files &&
    exit $exit_status
' 0
for ac_signal in 1 2 13 15; do
  trap 'ac_signal='$ac_signal'; as_fn_exit 1' $ac_signal
done
ac_signal=0

# confdefs.h avoids OS command line length limits that DEFS can exceed.
rm -f -r conftest* confdefs.h

printf "%s\n" "/* confdefs.h */" > confdefs.h

# Predefined preprocessor variables.

printf "%s\n" "#define PACKAGE_NAME \"$PACKAGE_NAME\"" >>confdefs.h

printf "%s\n" "#define PACKAGE_TARNAME \"$PACKAGE_TARNAME\"" >>confdefs.h

printf "%s\n" "#define PACKAGE_VERSION \"$PACKAGE_VERSION\"" >>confdefs.h

printf "%s\n" "#define PACKAGE_STRING \"$PACKAGE_STRING\"" >>confdefs.h

printf "%s\n" "#define PACKAGE_BUGREPORT \"$PACKAGE_BUGREPORT\"" >>confdefs.h

printf "%s\n" "#define PACKAGE_URL \"$PACKAGE_URL\"" >>confdefs.h


# Let the site file select an alternate cache file if it wants to.
# Prefer an explicitly selected file to automatically selected ones.
if test -n "$CONFIG_SITE"; then
  ac_site_files="$CONFIG_SITE"
elif test "x$prefix" != xNONE; then
  ac_site_files="$prefix/share/config.site $prefix/etc/config.site"
else
  ac_site_files="$ac_default_prefix/share/config.site $ac_default_prefix/etc/config.site"
fi

for ac_site_file in $ac_site_files
do
  case $ac_site_file in #(
  */*) :
     ;; #(
  *) :
    ac_site_file=./$ac_site_file ;;
esac
  if test -f "$ac_site_file" && test -r "$ac_site_file"; then
    { printf "%s\n" "$as_me:${as_lineno-$LINENO}: loading site script $ac_site_file" >&5
printf "%s\n" "$as_me: loading site script $ac_site_file" >&6;}
    sed 's/^/| /' "$ac_site_file" >&5
    . "$ac_site_file" \
      || { { printf "%s\n" "$as_me:${as_lineno-$LINENO}: error: in '$ac_pwd':" >&5
printf "%s\n" "$as_me: error: in '$ac_pwd':" >&2;}
as_fn_error $? "failed to load site script $ac_site_file
See 'config.log' for more details" "$LINENO" 5; }
  fi
done

if test -r "$cache_file"; then
  # Some versions of bash will fail to source /dev/null (special files
  # actually), so we avoid doing that.  DJGPP emulates it as a regular file.
  if test /dev/null != "$cache_file" && test -f "$cache_file"; then
    { printf "%s\n" "$as_me:${as_lineno-$LINENO}: loading cache $cache_file" >&5
printf "%s\n" "$as_me: loading cache $cache_file" >&6;}
    case $cache_file in
      [\\/]* | ?:[\\/]* ) . "$cache_file";;
      *)                      . "./$cache_file";;
    esac
  fi
else
  { printf "%s\n" "$as_me:${as_lineno-$LINENO}: creating cache $cache_file" >&5
printf "%s\n" "$as_me: creating cache $cache_file" >&6;}
  >$cache_file
fi

# Test code for whether the C compiler supports C89 (global declarations)
ac_c_conftest_c89_globals='
/* Does the compiler advertise C89 conformance?
   Do not test the value of __STDC__, because some compilers set it to 0
   while being otherwise adequately conformant. */
#if !defined __STDC__
# error "Compiler does not advertise C89 conformance"
#endif

#include <stddef.h>
#include <stdarg.h>
struct stat;
/* Most of the following tests are stolen from RCS 5.7 src/conf.sh.  */
struct buf { int x; };
struct buf * (*rcsopen) (struct buf *, struct stat *, int);
static char *e (char **p, int i)
{
  return p[i];
}
static char *f (char * (*g) (char **, int), char **p, ...)
{
  char *s;
  va_list v;
  va_start (v,p);
  s = g (p, va_arg (v,int));
  va_end (v);
  return s;
}

/* C89 style stringification. */
#define noexpand_stringify(a) #a
const char *stringified = noexpand_stringify(arbitrary+token=sequence);

/* C89 style token pasting.  Exercises some of the corner cases that
   e.g. old MSVC gets wrong, but not very hard. */
#define noexpand_concat(a,b) a##b
#define expand_concat(a,b) noexpand_concat(a,b)
extern int vA;
extern int vbee;
#define aye A
#define bee B
int *pvA = &expand_concat(v,aye);
int *pvbee = &noexpand_concat(v,bee);

/* OSF 4.0 Compaq cc is some sort of almost-ANSI by default.  It has
   function prototypes and stuff, but not \xHH hex character constants.
   These do not provoke an error unfortunately, instead are silently treated
   as an "x".  The following induces an error, until -std is added to get
   proper ANSI mode.  Curiously \x00 != x always comes out true, for an
   array size at least.  It is necessary to write \x00 == 0 to get something
   that is true only with -std.  */
int osf4_cc_array ['\''\x00'\'' == 0 ? 1 : -1];

/* IBM C 6 for AIX is almost-ANSI by default, but it replaces macro parameters
   inside strings and character constants.  */
#define FOO(x) '\''x'\''
int xlc6_cc_array[FOO(a) == '\''x'\'' ? 1 : -1];

int test (int i, double x);
struct s1 {int (*f) (int a);};
struct s2 {int (*f) (double a);};
int pairnames (int, char **, int *(*)(struct buf *, struct stat *, int),
               int, int);'

# Test code for whether the C compiler supports C89 (body of main).
ac_c_conftest_c89_main='
ok |= (argc == 0 || f (e, argv, 0) != argv[0] || f (e, argv, 1) != argv[1]);
'

# Test code for whether the C compiler supports C99 (global declarations)
ac_c_conftest_c99_globals='
// Does the compiler advertise C99 conformance?
#if !defined __STDC_VERSION__ || __STDC_VERSION__ < 199901L
# error "Compiler does not advertise C99 conformance"
#endif

#include <stdbool.h>
extern int puts (const char *);
extern int printf (const char *, ...);
extern int dprintf (int, const char *, ...);
extern void *malloc (size_t);
extern void free (void *);

// Check varargs macros.  These examples are taken from C99 6.10.3.5.
// dprintf is used instead of fprintf to avoid needing to declare
// FILE and stderr.
#define debug(...) dprintf (2, __VA_ARGS__)
#define showlist(...) puts (#__VA_ARGS__)
#define report(test,...) ((test) ? puts (#test) : printf (__VA_ARGS__))
static void
test_varargs_macros (void)
{
  int x = 1234;
  int y = 5678;
  debug ("Flag");
  debug ("X = %d\n", x);
  showlist (The first, second, and third items.);
  report (x>y, "x is %d but y is %d", x, y);
}

// Check long long types.
#define BIG64 18446744073709551615ull
#define BIG32 4294967295ul
#define BIG_OK (BIG64 / BIG32 == 4294967297ull && BIG64 % BIG32 == 0)
#if !BIG_OK
  #error "your preprocessor is broken"
#endif
#if BIG_OK
#else
  #error "your preprocessor is broken"
#endif
static long long int bignum = -9223372036854775807LL;
static unsigned long long int ubignum = BIG64;

struct incomplete_array
{
  int datasize;
  double data[];
};

struct named_init {
  int number;
  const wchar_t *name;
  double average;
};

typedef const char *ccp;

static inline int
test_restrict (ccp restrict text)
{
  // See if C++-style comments work.
  // Iterate through items via the restricted pointer.
  // Also check for declarations in for loops.
  for (unsigned int i = 0; *(text+i) != '\''\0'\''; ++i)
    continue;
  return 0;
}

// Check varargs and va_copy.
static bool
test_varargs (const char *format, ...)
{
  va_list args;
  va_start (args, format);
  va_list args_copy;
  va_copy (args_copy, args);

  const char *str = "";
  int number = 0;
  float fnumber = 0;

  while (*format)
    {
      switch (*format++)
	{
	case '\''s'\'': // string
	  str = va_arg (args_copy, const char *);
	  break;
	case '\''d'\'': // int
	  number = va_arg (args_copy, int);
	  break;
	case '\''f'\'': // float
	  fnumber = va_arg (args_copy, double);
	  break;
	default:
	  break;
	}
    }
  va_end (args_copy);
  va_end (args);

  return *str && number && fnumber;
}
'

# Test code for whether the C compiler supports C99 (body of main).
ac_c_conftest_c99_main='
  // Check bool.
  _Bool success = false;
  success |= (argc != 0);

  // Check restrict.
  if (test_restrict ("String literal") == 0)
    success = true;
  char *restrict newvar = "Another string";

  // Check varargs.
  success &= test_varargs ("s, d'\'' f .", "string", 65, 34.234);
  test_varargs_macros ();

  // Check flexible array members.
  struct incomplete_array *ia =
    malloc (sizeof (struct incomplete_array) + (sizeof (double) * 10));
  ia->datasize = 10;
  for (int i = 0; i < ia->datasize; ++i)
    ia->data[i] = i * 1.234;
  // Work around memory leak warnings.
  free (ia);

  // Check named initializers.
  struct named_init ni = {
    .number = 34,
    .name = L"Test wide string",
    .average = 543.34343,
  };

  ni.number = 58;

  int dynamic_array[ni.number];
  dynamic_array[0] = argv[0][0];
  dynamic_array[ni.number - 1] = 543;

  // work around unused variable warnings
  ok |= (!success || bignum == 0LL || ubignum == 0uLL || newvar[0] == '\''x'\''
	 || dynamic_array[ni.number - 1] != 543);
'

# Test code for whether the C compiler supports C11 (global declarations)
ac_c_conftest_c11_globals='
// Does the compiler advertise C11 conformance?
#if !defined __STDC_VERSION__ || __STDC_VERSION__ < 201112L
# error "Compiler does not advertise C11 conformance"
#endif

// Check _Alignas.
char _Alignas (double) aligned_as_double;
char _Alignas (0) no_special_alignment;
extern char aligned_as_int;
char _Alignas (0) _Alignas (int) aligned_as_int;

// Check _Alignof.
enum
{
  int_alignment = _Alignof (int),
  int_array_alignment = _Alignof (int[100]),
  char_alignment = _Alignof (char)
};
_Static_assert (0 < -_Alignof (int), "_Alignof is signed");

// Check _Noreturn.
int _Noreturn does_not_return (void) { for (;;) continue; }

// Check _Static_assert.
struct test_static_assert
{
  int x;
  _Static_assert (sizeof (int) <= sizeof (long int),
                  "_Static_assert does not work in struct");
  long int y;
};

// Check UTF-8 literals.
#define u8 syntax error!
char const utf8_literal[] = u8"happens to be ASCII" "another string";

// Check duplicate typedefs.
typedef long *long_ptr;
typedef long int *long_ptr;
typedef long_ptr long_ptr;

// Anonymous structures and unions -- taken from C11 6.7.2.1 Example 1.
struct anonymous
{
  union {
    struct { int i; int j; };
    struct { int k; long int l; } w;
  };
  int m;
} v1;
'

# Test code for whether the C compiler supports C11 (body of main).
ac_c_conftest_c11_main='
  _Static_assert ((offsetof (struct anonymous, i)
		   == offsetof (struct anonymous, w.k)),
		  "Anonymous union alignment botch");
  v1.i = 2;
  v1.w.k = 5;
  ok |= v1.i != 5;
'

# Test code for whether the C compiler supports C11 (complete).
ac_c_conftest_c11_program="${ac_c_conftest_c89_globals}
${ac_c_conftest_c99_globals}
${ac_c_conftest_c11_globals}

int
main (int argc, char **argv)
{
  int ok = 0;
  ${ac_c_conftest_c89_main}
  ${ac_c_conftest_c99_main}
  ${ac_c_conftest_c11_main}
  return ok;
}
"

# Test code for whether the C compiler supports C99 (complete).
ac_c_conftest_c99_program="${ac_c_conftest_c89_globals}
${ac_c_conftest_c99_globals}

int
main (int argc, char **argv)
{
  int ok = 0;
  ${ac_c_conftest_c89_main}
  ${ac_c_conftest_c99_main}
  return ok;
}
"

# Test code for whether the C compiler supports C89 (complete).
ac_c_conftest_c89_program="${ac_c_conftest_c89_globals}

int
main (int argc, char **argv)
{
  int ok = 0;
  ${ac_c_conftest_c89_main}
  return ok;
}
"

# Check that the precious variables saved in the cache have kept the same
# value.
ac_cache_corrupted=false
for ac_var in $ac_precious_vars; do
  eval ac_old_set=\$ac_cv_env_${ac_var}_set
  eval ac_new_set=\$ac_env_${ac_var}_set
  eval ac_old_val=\$ac_cv_env_${ac_var}_value
  eval ac_new_val=\$ac_env_${ac_var}_value
  case $ac_old_set,$ac_new_set in
    set,)
      { printf "%s\n" "$as_me:${as_lineno-$LINENO}: error: '$ac_var' was set to '$ac_old_val' in the previous run" >&5
printf "%s\n" "$as_me: error: '$ac_var' was set to '$ac_old_val' in the previous run" >&2;}
      ac_cache_corrupted=: ;;
    ,set)
      { printf "%s\n" "$as_me:${as_lineno-$LINENO}: error: '$ac_var' was not set in the previous run" >&5
printf "%s\n" "$as_me: error: '$ac_var' was not set in the previous run" >&2;}
      ac_cache_corrupted=: ;;
    ,);;
    *)
      if test "x$ac_old_val" != "x$ac_new_val"; then
	# differences in whitespace do not lead to failure.
	ac_old_val_w=`echo x $ac_old_val`
	ac_new_val_w=`echo x $ac_new_val`
	if test "$ac_old_val_w" != "$ac_new_val_w"; then
	  { printf "%s\n" "$as_me:${as_lineno-$LINENO}: error: '$ac_var' has changed since the previous run:" >&5
printf "%s\n" "$as_me: error: '$ac_var' has changed since the previous run:" >&2;}
	  ac_cache_corrupted=:
	else
	  { printf "%s\n" "$as_me:${as_lineno-$LINENO}: warning: ignoring whitespace changes in '$ac_var' since the previous run:" >&5
printf "%s\n" "$as_me: warning: ignoring whitespace changes in '$ac_var' since the previous run:" >&2;}
	  eval $ac_var=\$ac_old_val
	fi
	{ printf "%s\n" "$as_me:${as_lineno-$LINENO}:   former value:  '$ac_old_val'" >&5
printf "%s\n" "$as_me:   former value:  '$ac_old_val'" >&2;}
	{ printf "%s\n" "$as_me:${as_lineno-$LINENO}:   current value: '$ac_new_val'" >&5
printf "%s\n" "$as_me:   current value: '$ac_new_val'" >&2;}
      fi;;
  esac
  # Pass precious variables to config.status.
  if test "$ac_new_set" = set; then
    case $ac_new_val in
    *\'*) ac_arg=$ac_var=`printf "%s\n" "$ac_new_val" | sed "s/'/'\\\\\\\\''/g"` ;;
    *) ac_arg=$ac_var=$ac_new_val ;;
    esac
    case " $ac_configure_args " in
      *" '$ac_arg' "*) ;; # Avoid dups.  Use of quotes ensures accuracy.
      *) as_fn_append ac_configure_args " '$ac_arg'" ;;
    esac
  fi
done
if $ac_cache_corrupted; then
  { printf "%s\n" "$as_me:${as_lineno-$LINENO}: error: in '$ac_pwd':" >&5
printf "%s\n" "$as_me: error: in '$ac_pwd':" >&2;}
  { printf "%s\n" "$as_me:${as_lineno-$LINENO}: error: changes in the environment can compromise the build" >&5
printf "%s\n" "$as_me: error: changes in the environment can compromise the build" >&2;}
  as_fn_error $? "run '${MAKE-make} distclean' and/or 'rm $cache_file'
	    and start over" "$LINENO" 5
fi
## -------------------- ##
## Main body of script. ##
## -------------------- ##

ac_ext=c
ac_cpp='$CPP $CPPFLAGS'
ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
ac_compiler_gnu=$ac_cv_c_compiler_gnu



ac_config_headers="$ac_config_headers config.h"


# ===========================================================================
#      http://www.gnu.org/software/autoconf-archive/ax_with_htslib.html
# ===========================================================================
#
# SYNOPSIS
#
#   AX_WITH_HTSLIB
#
# DESCRIPTION
#
#   This macro checks whether HTSlib <http://www.htslib.org/> is installed
#   or nearby, and adds a --with-htslib=DIR option to the configure script
#   for specifying the location.  It locates either an installation prefix
#   (with 'include' and 'lib' subdirectories) or an HTSlib source tree, as
#   HTSlib is fast-moving and users may wish to use an in-development tree.
#
#   Different checks occur depending on the --with-htslib argument given:
#
#   With --with-htslib=DIR, checks whether DIR is a source tree (including
#     a separate build tree) or contains a working installation.
#   By default, searches for a source tree (with a name matching htslib*)
#     within or alongside $srcdir.  Produces AC_MSG_ERROR if there are
#     several equally-likely candidates.  If there are none, checks for
#     a working default installation.
#   With --with-htslib=system, checks for a working default installation.
#
#   If a source tree is found or specified, it is added to AC_CONFIG_SUBDIRS
#   if either --enable-configure-htslib is set, or where htslib is included
#   in a subdirectory (for packages that want to supply an embedded htslib).
#   Unfortunately this may cause a "you should use literals" warning when
#   autoconf is run.
#
#   The following output variables are set by this macro:
#
#     HTSDIR              Directory containing HTSlib source tree
#     HTSLIB_CPPFLAGS     Preprocessor flags for compiling with HTSlib
#     HTSLIB_LDFLAGS      Linker flags for linking with HTSlib
#
#   The following shell variables may be defined:
#
#     ax_cv_htslib        Set to "yes" if HTSlib was found
#     ax_cv_htslib_which  Set to "source", "install", or "none"
#
# LICENSE
#
#   Copyright (C) 2015, 2017, 2021 Genome Research Ltd
#
#   Copying and distribution of this file, with or without modification, are
#   permitted in any medium without royalty provided the copyright notice
#   and this notice are preserved.  This file is offered as-is, without any
#   warranty.

#serial 3





# SYNOPSIS
#
# HTS_PROG_CC_WERROR(FLAGS_VAR)
#
# Set FLAGS_VAR to the flags needed to make the C compiler treat warnings
# as errors.














ac_ext=c
ac_cpp='$CPP $CPPFLAGS'
ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
ac_compiler_gnu=$ac_cv_c_compiler_gnu
if test -n "$ac_tool_prefix"; then
  # Extract the first word of "${ac_tool_prefix}gcc", so it can be a program name with args.
set dummy ${ac_tool_prefix}gcc; ac_word=$2
{ printf "%s\n" "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
printf %s "checking for $ac_word... " >&6; }
if test ${ac_cv_prog_CC+y}
then :
  printf %s "(cached) " >&6
else case e in #(
  e) if test -n "$CC"; then
  ac_cv_prog_CC="$CC" # Let the user override the test.
else
as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
for as_dir in $PATH
do
  IFS=$as_save_IFS
  case $as_dir in #(((
    '') as_dir=./ ;;
    */) ;;
    *) as_dir=$as_dir/ ;;
  esac
    for ac_exec_ext in '' $ac_executable_extensions; do
  if as_fn_executable_p "$as_dir$ac_word$ac_exec_ext"; then
    ac_cv_prog_CC="${ac_tool_prefix}gcc"
    printf "%s\n" "$as_me:${as_lineno-$LINENO}: found $as_dir$ac_word$ac_exec_ext" >&5
    break 2
  fi
done
  done
IFS=$as_save_IFS

fi ;;
esac
fi
CC=$ac_cv_prog_CC
if test -n "$CC"; then
  { printf "%s\n" "$as_me:${as_lineno-$LINENO}: result: $CC" >&5
printf "%s\n" "$CC" >&6; }
else
  { printf "%s\n" "$as_me:${as_lineno-$LINENO}: result: no" >&5
printf "%s\n" "no" >&6; }
fi


fi
if test -z "$ac_cv_prog_CC"; then
  ac_ct_CC=$CC
  # Extract the first word of "gcc", so it can be a program name with args.
set dummy gcc; ac_word=$2
{ printf "%s\n" "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
printf %s "checking for $ac_word... " >&6; }
if test ${ac_cv_prog_ac_ct_CC+y}
then :
  printf %s "(cached) " >&6
else case e in #(
  e) if test -n "$ac_ct_CC"; then
  ac_cv_prog_ac_ct_CC="$ac_ct_CC" # Let the user override the test.
else
as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
for as_dir in $PATH
do
  IFS=$as_save_IFS
  case $as_dir in #(((
    '') as_dir=./ ;;
    */) ;;
    *) as_dir=$as_dir/ ;;
  esac
    for ac_exec_ext in '' $ac_executable_extensions; do
  if as_fn_executable_p "$as_dir$ac_word$ac_exec_ext"; then
    ac_cv_prog_ac_ct_CC="gcc"
    printf "%s\n" "$as_me:${as_lineno-$LINENO}: found $as_dir$ac_word$ac_exec_ext" >&5
    break 2
  fi
done
  done
IFS=$as_save_IFS

fi ;;
esac
fi
ac_ct_CC=$ac_cv_prog_ac_ct_CC
if test -n "$ac_ct_CC"; then
  { printf "%s\n" "$as_me:${as_lineno-$LINENO}: result: $ac_ct_CC" >&5
printf "%s\n" "$ac_ct_CC" >&6; }
else
  { printf "%s\n" "$as_me:${as_lineno-$LINENO}: result: no" >&5
printf "%s\n" "no" >&6; }
fi

  if test "x$ac_ct_CC" = x; then
    CC=""
  else
    case $cross_compiling:$ac_tool_warned in
yes:)
{ printf "%s\n" "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5
printf "%s\n" "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;}
ac_tool_warned=yes ;;
esac
    CC=$ac_ct_CC
  fi
else
  CC="$ac_cv_prog_CC"
fi

if test -z "$CC"; then
          if test -n "$ac_tool_prefix"; then
    # Extract the first word of "${ac_tool_prefix}cc", so it can be a program name with args.
set dummy ${ac_tool_prefix}cc; ac_word=$2
{ printf "%s\n" "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
printf %s "checking for $ac_word... " >&6; }
if test ${ac_cv_prog_CC+y}
then :
  printf %s "(cached) " >&6
else case e in #(
  e) if test -n "$CC"; then
  ac_cv_prog_CC="$CC" # Let the user override the test.
else
as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
for as_dir in $PATH
do
  IFS=$as_save_IFS
  case $as_dir in #(((
    '') as_dir=./ ;;
    */) ;;
    *) as_dir=$as_dir/ ;;
  esac
    for ac_exec_ext in '' $ac_executable_extensions; do
  if as_fn_executable_p "$as_dir$ac_word$ac_exec_ext"; then
    ac_cv_prog_CC="${ac_tool_prefix}cc"
    printf "%s\n" "$as_me:${as_lineno-$LINENO}: found $as_dir$ac_word$ac_exec_ext" >&5
    break 2
  fi
done
  done
IFS=$as_save_IFS

fi ;;
esac
fi
CC=$ac_cv_prog_CC
if test -n "$CC"; then
  { printf "%s\n" "$as_me:${as_lineno-$LINENO}: result: $CC" >&5
printf "%s\n" "$CC" >&6; }
else
  { printf "%s\n" "$as_me:${as_lineno-$LINENO}: result: no" >&5
printf "%s\n" "no" >&6; }
fi


  fi
fi
if test -z "$CC"; then
  # Extract the first word of "cc", so it can be a program name with args.
set dummy cc; ac_word=$2
{ printf "%s\n" "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
printf %s "checking for $ac_word... " >&6; }
if test ${ac_cv_prog_CC+y}
then :
  printf %s "(cached) " >&6
else case e in #(
  e) if test -n "$CC"; then
  ac_cv_prog_CC="$CC" # Let the user override the test.
else
  ac_prog_rejected=no
as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
for as_dir in $PATH
do
  IFS=$as_save_IFS
  case $as_dir in #(((
    '') as_dir=./ ;;
    */) ;;
    *) as_dir=$as_dir/ ;;
  esac
    for ac_exec_ext in '' $ac_executable_extensions; do
  if as_fn_executable_p "$as_dir$ac_word$ac_exec_ext"; then
    if test "$as_dir$ac_word$ac_exec_ext" = "/usr/ucb/cc"; then
       ac_prog_rejected=yes
       continue
     fi
    ac_cv_prog_CC="cc"
    printf "%s\n" "$as_me:${as_lineno-$LINENO}: found $as_dir$ac_word$ac_exec_ext" >&5
    break 2
  fi
done
  done
IFS=$as_save_IFS

if test $ac_prog_rejected = yes; then
  # We found a bogon in the path, so make sure we never use it.
  set dummy $ac_cv_prog_CC
  shift
  if test $# != 0; then
    # We chose a different compiler from the bogus one.
    # However, it has the same basename, so the bogon will be chosen
    # first if we set CC to just the basename; use the full file name.
    shift
    ac_cv_prog_CC="$as_dir$ac_word${1+' '}$@"
  fi
fi
fi ;;
esac
fi
CC=$ac_cv_prog_CC
if test -n "$CC"; then
  { printf "%s\n" "$as_me:${as_lineno-$LINENO}: result: $CC" >&5
printf "%s\n" "$CC" >&6; }
else
  { printf "%s\n" "$as_me:${as_lineno-$LINENO}: result: no" >&5
printf "%s\n" "no" >&6; }
fi


fi
if test -z "$CC"; then
  if test -n "$ac_tool_prefix"; then
  for ac_prog in cl.exe
  do
    # Extract the first word of "$ac_tool_prefix$ac_prog", so it can be a program name with args.
set dummy $ac_tool_prefix$ac_prog; ac_word=$2
{ printf "%s\n" "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
printf %s "checking for $ac_word... " >&6; }
if test ${ac_cv_prog_CC+y}
then :
  printf %s "(cached) " >&6
else case e in #(
  e) if test -n "$CC"; then
  ac_cv_prog_CC="$CC" # Let the user override the test.
else
as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
for as_dir in $PATH
do
  IFS=$as_save_IFS
  case $as_dir in #(((
    '') as_dir=./ ;;
    */) ;;
    *) as_dir=$as_dir/ ;;
  esac
    for ac_exec_ext in '' $ac_executable_extensions; do
  if as_fn_executable_p "$as_dir$ac_word$ac_exec_ext"; then
    ac_cv_prog_CC="$ac_tool_prefix$ac_prog"
    printf "%s\n" "$as_me:${as_lineno-$LINENO}: found $as_dir$ac_word$ac_exec_ext" >&5
    break 2
  fi
done
  done
IFS=$as_save_IFS

fi ;;
esac
fi
CC=$ac_cv_prog_CC
if test -n "$CC"; then
  { printf "%s\n" "$as_me:${as_lineno-$LINENO}: result: $CC" >&5
printf "%s\n" "$CC" >&6; }
else
  { printf "%s\n" "$as_me:${as_lineno-$LINENO}: result: no" >&5
printf "%s\n" "no" >&6; }
fi


    test -n "$CC" && break
  done
fi
if test -z "$CC"; then
  ac_ct_CC=$CC
  for ac_prog in cl.exe
do
  # Extract the first word of "$ac_prog", so it can be a program name with args.
set dummy $ac_prog; ac_word=$2
{ printf "%s\n" "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
printf %s "checking for $ac_word... " >&6; }
if test ${ac_cv_prog_ac_ct_CC+y}
then :
  printf %s "(cached) " >&6
else case e in #(
  e) if test -n "$ac_ct_CC"; then
  ac_cv_prog_ac_ct_CC="$ac_ct_CC" # Let the user override the test.
else
as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
for as_dir in $PATH
do
  IFS=$as_save_IFS
  case $as_dir in #(((
    '') as_dir=./ ;;
    */) ;;
    *) as_dir=$as_dir/ ;;
  esac
    for ac_exec_ext in '' $ac_executable_extensions; do
  if as_fn_executable_p "$as_dir$ac_word$ac_exec_ext"; then
    ac_cv_prog_ac_ct_CC="$ac_prog"
    printf "%s\n" "$as_me:${as_lineno-$LINENO}: found $as_dir$ac_word$ac_exec_ext" >&5
    break 2
  fi
done
  done
IFS=$as_save_IFS

fi ;;
esac
fi
ac_ct_CC=$ac_cv_prog_ac_ct_CC
if test -n "$ac_ct_CC"; then
  { printf "%s\n" "$as_me:${as_lineno-$LINENO}: result: $ac_ct_CC" >&5
printf "%s\n" "$ac_ct_CC" >&6; }
else
  { printf "%s\n" "$as_me:${as_lineno-$LINENO}: result: no" >&5
printf "%s\n" "no" >&6; }
fi


  test -n "$ac_ct_CC" && break
done

  if test "x$ac_ct_CC" = x; then
    CC=""
  else
    case $cross_compiling:$ac_tool_warned in
yes:)
{ printf "%s\n" "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5
printf "%s\n" "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;}
ac_tool_warned=yes ;;
esac
    CC=$ac_ct_CC
  fi
fi

fi
if test -z "$CC"; then
  if test -n "$ac_tool_prefix"; then
  # Extract the first word of "${ac_tool_prefix}clang", so it can be a program name with args.
set dummy ${ac_tool_prefix}clang; ac_word=$2
{ printf "%s\n" "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
printf %s "checking for $ac_word... " >&6; }
if test ${ac_cv_prog_CC+y}
then :
  printf %s "(cached) " >&6
else case e in #(
  e) if test -n "$CC"; then
  ac_cv_prog_CC="$CC" # Let the user override the test.
else
as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
for as_dir in $PATH
do
  IFS=$as_save_IFS
  case $as_dir in #(((
    '') as_dir=./ ;;
    */) ;;
    *) as_dir=$as_dir/ ;;
  esac
    for ac_exec_ext in '' $ac_executable_extensions; do
  if as_fn_executable_p "$as_dir$ac_word$ac_exec_ext"; then
    ac_cv_prog_CC="${ac_tool_prefix}clang"
    printf "%s\n" "$as_me:${as_lineno-$LINENO}: found $as_dir$ac_word$ac_exec_ext" >&5
    break 2
  fi
done
  done
IFS=$as_save_IFS

fi ;;
esac
fi
CC=$ac_cv_prog_CC
if test -n "$CC"; then
  { printf "%s\n" "$as_me:${as_lineno-$LINENO}: result: $CC" >&5
printf "%s\n" "$CC" >&6; }
else
  { printf "%s\n" "$as_me:${as_lineno-$LINENO}: result: no" >&5
printf "%s\n" "no" >&6; }
fi


fi
if test -z "$ac_cv_prog_CC"; then
  ac_ct_CC=$CC
  # Extract the first word of "clang", so it can be a program name with args.
set dummy clang; ac_word=$2
{ printf "%s\n" "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
printf %s "checking for $ac_word... " >&6; }
if test ${ac_cv_prog_ac_ct_CC+y}
then :
  printf %s "(cached) " >&6
else case e in #(
  e) if test -n "$ac_ct_CC"; then
  ac_cv_prog_ac_ct_CC="$ac_ct_CC" # Let the user override the test.
else
as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
for as_dir in $PATH
do
  IFS=$as_save_IFS
  case $as_dir in #(((
    '') as_dir=./ ;;
    */) ;;
    *) as_dir=$as_dir/ ;;
  esac
    for ac_exec_ext in '' $ac_executable_extensions; do
  if as_fn_executable_p "$as_dir$ac_word$ac_exec_ext"; then
    ac_cv_prog_ac_ct_CC="clang"
    printf "%s\n" "$as_me:${as_lineno-$LINENO}: found $as_dir$ac_word$ac_exec_ext" >&5
    break 2
  fi
done
  done
IFS=$as_save_IFS

fi ;;
esac
fi
ac_ct_CC=$ac_cv_prog_ac_ct_CC
if test -n "$ac_ct_CC"; then
  { printf "%s\n" "$as_me:${as_lineno-$LINENO}: result: $ac_ct_CC" >&5
printf "%s\n" "$ac_ct_CC" >&6; }
else
  { printf "%s\n" "$as_me:${as_lineno-$LINENO}: result: no" >&5
printf "%s\n" "no" >&6; }
fi

  if test "x$ac_ct_CC" = x; then
    CC=""
  else
    case $cross_compiling:$ac_tool_warned in
yes:)
{ printf "%s\n" "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5
printf "%s\n" "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;}
ac_tool_warned=yes ;;
esac
    CC=$ac_ct_CC
  fi
else
  CC="$ac_cv_prog_CC"
fi

fi


test -z "$CC" && { { printf "%s\n" "$as_me:${as_lineno-$LINENO}: error: in '$ac_pwd':" >&5
printf "%s\n" "$as_me: error: in '$ac_pwd':" >&2;}
as_fn_error $? "no acceptable C compiler found in \$PATH
See 'config.log' for more details" "$LINENO" 5; }

# Provide some information about the compiler.
printf "%s\n" "$as_me:${as_lineno-$LINENO}: checking for C compiler version" >&5
set X $ac_compile
ac_compiler=$2
for ac_option in --version -v -V -qversion -version; do
  { { ac_try="$ac_compiler $ac_option >&5"
case "(($ac_try" in
  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
  *) ac_try_echo=$ac_try;;
esac
eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\""
printf "%s\n" "$ac_try_echo"; } >&5
  (eval "$ac_compiler $ac_option >&5") 2>conftest.err
  ac_status=$?
  if test -s conftest.err; then
    sed '10a\
... rest of stderr output deleted ...
         10q' conftest.err >conftest.er1
    cat conftest.er1 >&5
  fi
  rm -f conftest.er1 conftest.err
  printf "%s\n" "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
  test $ac_status = 0; }
done

cat confdefs.h - <<_ACEOF >conftest.$ac_ext
/* end confdefs.h.  */

int
main (void)
{

  ;
  return 0;
}
_ACEOF
ac_clean_files_save=$ac_clean_files
ac_clean_files="$ac_clean_files a.out a.out.dSYM a.exe b.out"
# Try to create an executable without -o first, disregard a.out.
# It will help us diagnose broken compilers, and finding out an intuition
# of exeext.
{ printf "%s\n" "$as_me:${as_lineno-$LINENO}: checking whether the C compiler works" >&5
printf %s "checking whether the C compiler works... " >&6; }
ac_link_default=`printf "%s\n" "$ac_link" | sed 's/ -o *conftest[^ ]*//'`

# The possible output files:
ac_files="a.out conftest.exe conftest a.exe a_out.exe b.out conftest.*"

ac_rmfiles=
for ac_file in $ac_files
do
  case $ac_file in
    *.$ac_ext | *.xcoff | *.tds | *.d | *.pdb | *.xSYM | *.bb | *.bbg | *.map | *.inf | *.dSYM | *.o | *.obj ) ;;
    * ) ac_rmfiles="$ac_rmfiles $ac_file";;
  esac
done
rm -f $ac_rmfiles

if { { ac_try="$ac_link_default"
case "(($ac_try" in
  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
  *) ac_try_echo=$ac_try;;
esac
eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\""
printf "%s\n" "$ac_try_echo"; } >&5
  (eval "$ac_link_default") 2>&5
  ac_status=$?
  printf "%s\n" "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
  test $ac_status = 0; }
then :
  # Autoconf-2.13 could set the ac_cv_exeext variable to 'no'.
# So ignore a value of 'no', otherwise this would lead to 'EXEEXT = no'
# in a Makefile.  We should not override ac_cv_exeext if it was cached,
# so that the user can short-circuit this test for compilers unknown to
# Autoconf.
for ac_file in $ac_files ''
do
  test -f "$ac_file" || continue
  case $ac_file in
    *.$ac_ext | *.xcoff | *.tds | *.d | *.pdb | *.xSYM | *.bb | *.bbg | *.map | *.inf | *.dSYM | *.o | *.obj )
	;;
    [ab].out )
	# We found the default executable, but exeext='' is most
	# certainly right.
	break;;
    *.* )
	if test ${ac_cv_exeext+y} && test "$ac_cv_exeext" != no;
	then :; else
	   ac_cv_exeext=`expr "$ac_file" : '[^.]*\(\..*\)'`
	fi
	# We set ac_cv_exeext here because the later test for it is not
	# safe: cross compilers may not add the suffix if given an '-o'
	# argument, so we may need to know it at that point already.
	# Even if this section looks crufty: it has the advantage of
	# actually working.
	break;;
    * )
	break;;
  esac
done
test "$ac_cv_exeext" = no && ac_cv_exeext=

else case e in #(
  e) ac_file='' ;;
esac
fi
if test -z "$ac_file"
then :
  { printf "%s\n" "$as_me:${as_lineno-$LINENO}: result: no" >&5
printf "%s\n" "no" >&6; }
printf "%s\n" "$as_me: failed program was:" >&5
sed 's/^/| /' conftest.$ac_ext >&5

{ { printf "%s\n" "$as_me:${as_lineno-$LINENO}: error: in '$ac_pwd':" >&5
printf "%s\n" "$as_me: error: in '$ac_pwd':" >&2;}
as_fn_error 77 "C compiler cannot create executables
See 'config.log' for more details" "$LINENO" 5; }
else case e in #(
  e) { printf "%s\n" "$as_me:${as_lineno-$LINENO}: result: yes" >&5
printf "%s\n" "yes" >&6; } ;;
esac
fi
{ printf "%s\n" "$as_me:${as_lineno-$LINENO}: checking for C compiler default output file name" >&5
printf %s "checking for C compiler default output file name... " >&6; }
{ printf "%s\n" "$as_me:${as_lineno-$LINENO}: result: $ac_file" >&5
printf "%s\n" "$ac_file" >&6; }
ac_exeext=$ac_cv_exeext

rm -f -r a.out a.out.dSYM a.exe conftest$ac_cv_exeext b.out
ac_clean_files=$ac_clean_files_save
{ printf "%s\n" "$as_me:${as_lineno-$LINENO}: checking for suffix of executables" >&5
printf %s "checking for suffix of executables... " >&6; }
if { { ac_try="$ac_link"
case "(($ac_try" in
  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
  *) ac_try_echo=$ac_try;;
esac
eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\""
printf "%s\n" "$ac_try_echo"; } >&5
  (eval "$ac_link") 2>&5
  ac_status=$?
  printf "%s\n" "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
  test $ac_status = 0; }
then :
  # If both 'conftest.exe' and 'conftest' are 'present' (well, observable)
# catch 'conftest.exe'.  For instance with Cygwin, 'ls conftest' will
# work properly (i.e., refer to 'conftest.exe'), while it won't with
# 'rm'.
for ac_file in conftest.exe conftest conftest.*; do
  test -f "$ac_file" || continue
  case $ac_file in
    *.$ac_ext | *.xcoff | *.tds | *.d | *.pdb | *.xSYM | *.bb | *.bbg | *.map | *.inf | *.dSYM | *.o | *.obj ) ;;
    *.* ) ac_cv_exeext=`expr "$ac_file" : '[^.]*\(\..*\)'`
	  break;;
    * ) break;;
  esac
done
else case e in #(
  e) { { printf "%s\n" "$as_me:${as_lineno-$LINENO}: error: in '$ac_pwd':" >&5
printf "%s\n" "$as_me: error: in '$ac_pwd':" >&2;}
as_fn_error $? "cannot compute suffix of executables: cannot compile and link
See 'config.log' for more details" "$LINENO" 5; } ;;
esac
fi
rm -f conftest conftest$ac_cv_exeext
{ printf "%s\n" "$as_me:${as_lineno-$LINENO}: result: $ac_cv_exeext" >&5
printf "%s\n" "$ac_cv_exeext" >&6; }

rm -f conftest.$ac_ext
EXEEXT=$ac_cv_exeext
ac_exeext=$EXEEXT
cat confdefs.h - <<_ACEOF >conftest.$ac_ext
/* end confdefs.h.  */
#include <stdio.h>
int
main (void)
{
FILE *f = fopen ("conftest.out", "w");
 if (!f)
  return 1;
 return ferror (f) || fclose (f) != 0;

  ;
  return 0;
}
_ACEOF
ac_clean_files="$ac_clean_files conftest.out"
# Check that the compiler produces executables we can run.  If not, either
# the compiler is broken, or we cross compile.
{ printf "%s\n" "$as_me:${as_lineno-$LINENO}: checking whether we are cross compiling" >&5
printf %s "checking whether we are cross compiling... " >&6; }
if test "$cross_compiling" != yes; then
  { { ac_try="$ac_link"
case "(($ac_try" in
  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
  *) ac_try_echo=$ac_try;;
esac
eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\""
printf "%s\n" "$ac_try_echo"; } >&5
  (eval "$ac_link") 2>&5
  ac_status=$?
  printf "%s\n" "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
  test $ac_status = 0; }
  if { ac_try='./conftest$ac_cv_exeext'
  { { case "(($ac_try" in
  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
  *) ac_try_echo=$ac_try;;
esac
eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\""
printf "%s\n" "$ac_try_echo"; } >&5
  (eval "$ac_try") 2>&5
  ac_status=$?
  printf "%s\n" "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
  test $ac_status = 0; }; }; then
    cross_compiling=no
  else
    if test "$cross_compiling" = maybe; then
	cross_compiling=yes
    else
	{ { printf "%s\n" "$as_me:${as_lineno-$LINENO}: error: in '$ac_pwd':" >&5
printf "%s\n" "$as_me: error: in '$ac_pwd':" >&2;}
as_fn_error 77 "cannot run C compiled programs.
If you meant to cross compile, use '--host'.
See 'config.log' for more details" "$LINENO" 5; }
    fi
  fi
fi
{ printf "%s\n" "$as_me:${as_lineno-$LINENO}: result: $cross_compiling" >&5
printf "%s\n" "$cross_compiling" >&6; }

rm -f conftest.$ac_ext conftest$ac_cv_exeext \
  conftest.o conftest.obj conftest.out
ac_clean_files=$ac_clean_files_save
{ printf "%s\n" "$as_me:${as_lineno-$LINENO}: checking for suffix of object files" >&5
printf %s "checking for suffix of object files... " >&6; }
if test ${ac_cv_objext+y}
then :
  printf %s "(cached) " >&6
else case e in #(
  e) cat confdefs.h - <<_ACEOF >conftest.$ac_ext
/* end confdefs.h.  */

int
main (void)
{

  ;
  return 0;
}
_ACEOF
rm -f conftest.o conftest.obj
if { { ac_try="$ac_compile"
case "(($ac_try" in
  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
  *) ac_try_echo=$ac_try;;
esac
eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\""
printf "%s\n" "$ac_try_echo"; } >&5
  (eval "$ac_compile") 2>&5
  ac_status=$?
  printf "%s\n" "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
  test $ac_status = 0; }
then :
  for ac_file in conftest.o conftest.obj conftest.*; do
  test -f "$ac_file" || continue;
  case $ac_file in
    *.$ac_ext | *.xcoff | *.tds | *.d | *.pdb | *.xSYM | *.bb | *.bbg | *.map | *.inf | *.dSYM ) ;;
    *) ac_cv_objext=`expr "$ac_file" : '.*\.\(.*\)'`
       break;;
  esac
done
else case e in #(
  e) printf "%s\n" "$as_me: failed program was:" >&5
sed 's/^/| /' conftest.$ac_ext >&5

{ { printf "%s\n" "$as_me:${as_lineno-$LINENO}: error: in '$ac_pwd':" >&5
printf "%s\n" "$as_me: error: in '$ac_pwd':" >&2;}
as_fn_error $? "cannot compute suffix of object files: cannot compile
See 'config.log' for more details" "$LINENO" 5; } ;;
esac
fi
rm -f conftest.$ac_cv_objext conftest.$ac_ext ;;
esac
fi
{ printf "%s\n" "$as_me:${as_lineno-$LINENO}: result: $ac_cv_objext" >&5
printf "%s\n" "$ac_cv_objext" >&6; }
OBJEXT=$ac_cv_objext
ac_objext=$OBJEXT
{ printf "%s\n" "$as_me:${as_lineno-$LINENO}: checking whether the compiler supports GNU C" >&5
printf %s "checking whether the compiler supports GNU C... " >&6; }
if test ${ac_cv_c_compiler_gnu+y}
then :
  printf %s "(cached) " >&6
else case e in #(
  e) cat confdefs.h - <<_ACEOF >conftest.$ac_ext
/* end confdefs.h.  */

int
main (void)
{
#ifndef __GNUC__
       choke me
#endif

  ;
  return 0;
}
_ACEOF
if ac_fn_c_try_compile "$LINENO"
then :
  ac_compiler_gnu=yes
else case e in #(
  e) ac_compiler_gnu=no ;;
esac
fi
rm -f core conftest.err conftest.$ac_objext conftest.beam conftest.$ac_ext
ac_cv_c_compiler_gnu=$ac_compiler_gnu
 ;;
esac
fi
{ printf "%s\n" "$as_me:${as_lineno-$LINENO}: result: $ac_cv_c_compiler_gnu" >&5
printf "%s\n" "$ac_cv_c_compiler_gnu" >&6; }
ac_compiler_gnu=$ac_cv_c_compiler_gnu

if test $ac_compiler_gnu = yes; then
  GCC=yes
else
  GCC=
fi
ac_test_CFLAGS=${CFLAGS+y}
ac_save_CFLAGS=$CFLAGS
{ printf "%s\n" "$as_me:${as_lineno-$LINENO}: checking whether $CC accepts -g" >&5
printf %s "checking whether $CC accepts -g... " >&6; }
if test ${ac_cv_prog_cc_g+y}
then :
  printf %s "(cached) " >&6
else case e in #(
  e) ac_save_c_werror_flag=$ac_c_werror_flag
   ac_c_werror_flag=yes
   ac_cv_prog_cc_g=no
   CFLAGS="-g"
   cat confdefs.h - <<_ACEOF >conftest.$ac_ext
/* end confdefs.h.  */

int
main (void)
{

  ;
  return 0;
}
_ACEOF
if ac_fn_c_try_compile "$LINENO"
then :
  ac_cv_prog_cc_g=yes
else case e in #(
  e) CFLAGS=""
      cat confdefs.h - <<_ACEOF >conftest.$ac_ext
/* end confdefs.h.  */

int
main (void)
{

  ;
  return 0;
}
_ACEOF
if ac_fn_c_try_compile "$LINENO"
then :

else case e in #(
  e) ac_c_werror_flag=$ac_save_c_werror_flag
	 CFLAGS="-g"
	 cat confdefs.h - <<_ACEOF >conftest.$ac_ext
/* end confdefs.h.  */

int
main (void)
{

  ;
  return 0;
}
_ACEOF
if ac_fn_c_try_compile "$LINENO"
then :
  ac_cv_prog_cc_g=yes
fi
rm -f core conftest.err conftest.$ac_objext conftest.beam conftest.$ac_ext ;;
esac
fi
rm -f core conftest.err conftest.$ac_objext conftest.beam conftest.$ac_ext ;;
esac
fi
rm -f core conftest.err conftest.$ac_objext conftest.beam conftest.$ac_ext
   ac_c_werror_flag=$ac_save_c_werror_flag ;;
esac
fi
{ printf "%s\n" "$as_me:${as_lineno-$LINENO}: result: $ac_cv_prog_cc_g" >&5
printf "%s\n" "$ac_cv_prog_cc_g" >&6; }
if test $ac_test_CFLAGS; then
  CFLAGS=$ac_save_CFLAGS
elif test $ac_cv_prog_cc_g = yes; then
  if test "$GCC" = yes; then
    CFLAGS="-g -O2"
  else
    CFLAGS="-g"
  fi
else
  if test "$GCC" = yes; then
    CFLAGS="-O2"
  else
    CFLAGS=
  fi
fi
ac_prog_cc_stdc=no
if test x$ac_prog_cc_stdc = xno
then :
  { printf "%s\n" "$as_me:${as_lineno-$LINENO}: checking for $CC option to enable C11 features" >&5
printf %s "checking for $CC option to enable C11 features... " >&6; }
if test ${ac_cv_prog_cc_c11+y}
then :
  printf %s "(cached) " >&6
else case e in #(
  e) ac_cv_prog_cc_c11=no
ac_save_CC=$CC
cat confdefs.h - <<_ACEOF >conftest.$ac_ext
/* end confdefs.h.  */
$ac_c_conftest_c11_program
_ACEOF
for ac_arg in '' -std=gnu11
do
  CC="$ac_save_CC $ac_arg"
  if ac_fn_c_try_compile "$LINENO"
then :
  ac_cv_prog_cc_c11=$ac_arg
fi
rm -f core conftest.err conftest.$ac_objext conftest.beam
  test "x$ac_cv_prog_cc_c11" != "xno" && break
done
rm -f conftest.$ac_ext
CC=$ac_save_CC ;;
esac
fi

if test "x$ac_cv_prog_cc_c11" = xno
then :
  { printf "%s\n" "$as_me:${as_lineno-$LINENO}: result: unsupported" >&5
printf "%s\n" "unsupported" >&6; }
else case e in #(
  e) if test "x$ac_cv_prog_cc_c11" = x
then :
  { printf "%s\n" "$as_me:${as_lineno-$LINENO}: result: none needed" >&5
printf "%s\n" "none needed" >&6; }
else case e in #(
  e) { printf "%s\n" "$as_me:${as_lineno-$LINENO}: result: $ac_cv_prog_cc_c11" >&5
printf "%s\n" "$ac_cv_prog_cc_c11" >&6; }
     CC="$CC $ac_cv_prog_cc_c11" ;;
esac
fi
  ac_cv_prog_cc_stdc=$ac_cv_prog_cc_c11
  ac_prog_cc_stdc=c11 ;;
esac
fi
fi
if test x$ac_prog_cc_stdc = xno
then :
  { printf "%s\n" "$as_me:${as_lineno-$LINENO}: checking for $CC option to enable C99 features" >&5
printf %s "checking for $CC option to enable C99 features... " >&6; }
if test ${ac_cv_prog_cc_c99+y}
then :
  printf %s "(cached) " >&6
else case e in #(
  e) ac_cv_prog_cc_c99=no
ac_save_CC=$CC
cat confdefs.h - <<_ACEOF >conftest.$ac_ext
/* end confdefs.h.  */
$ac_c_conftest_c99_program
_ACEOF
for ac_arg in '' -std=gnu99 -std=c99 -c99 -qlanglvl=extc1x -qlanglvl=extc99 -AC99 -D_STDC_C99=
do
  CC="$ac_save_CC $ac_arg"
  if ac_fn_c_try_compile "$LINENO"
then :
  ac_cv_prog_cc_c99=$ac_arg
fi
rm -f core conftest.err conftest.$ac_objext conftest.beam
  test "x$ac_cv_prog_cc_c99" != "xno" && break
done
rm -f conftest.$ac_ext
CC=$ac_save_CC ;;
esac
fi

if test "x$ac_cv_prog_cc_c99" = xno
then :
  { printf "%s\n" "$as_me:${as_lineno-$LINENO}: result: unsupported" >&5
printf "%s\n" "unsupported" >&6; }
else case e in #(
  e) if test "x$ac_cv_prog_cc_c99" = x
then :
  { printf "%s\n" "$as_me:${as_lineno-$LINENO}: result: none needed" >&5
printf "%s\n" "none needed" >&6; }
else case e in #(
  e) { printf "%s\n" "$as_me:${as_lineno-$LINENO}: result: $ac_cv_prog_cc_c99" >&5
printf "%s\n" "$ac_cv_prog_cc_c99" >&6; }
     CC="$CC $ac_cv_prog_cc_c99" ;;
esac
fi
  ac_cv_prog_cc_stdc=$ac_cv_prog_cc_c99
  ac_prog_cc_stdc=c99 ;;
esac
fi
fi
if test x$ac_prog_cc_stdc = xno
then :
  { printf "%s\n" "$as_me:${as_lineno-$LINENO}: checking for $CC option to enable C89 features" >&5
printf %s "checking for $CC option to enable C89 features... " >&6; }
if test ${ac_cv_prog_cc_c89+y}
then :
  printf %s "(cached) " >&6
else case e in #(
  e) ac_cv_prog_cc_c89=no
ac_save_CC=$CC
cat confdefs.h - <<_ACEOF >conftest.$ac_ext
/* end confdefs.h.  */
$ac_c_conftest_c89_program
_ACEOF
for ac_arg in '' -qlanglvl=extc89 -qlanglvl=ansi -std -Ae "-Aa -D_HPUX_SOURCE" "-Xc -D__EXTENSIONS__"
do
  CC="$ac_save_CC $ac_arg"
  if ac_fn_c_try_compile "$LINENO"
then :
  ac_cv_prog_cc_c89=$ac_arg
fi
rm -f core conftest.err conftest.$ac_objext conftest.beam
  test "x$ac_cv_prog_cc_c89" != "xno" && break
done
rm -f conftest.$ac_ext
CC=$ac_save_CC ;;
esac
fi

if test "x$ac_cv_prog_cc_c89" = xno
then :
  { printf "%s\n" "$as_me:${as_lineno-$LINENO}: result: unsupported" >&5
printf "%s\n" "unsupported" >&6; }
else case e in #(
  e) if test "x$ac_cv_prog_cc_c89" = x
then :
  { printf "%s\n" "$as_me:${as_lineno-$LINENO}: result: none needed" >&5
printf "%s\n" "none needed" >&6; }
else case e in #(
  e) { printf "%s\n" "$as_me:${as_lineno-$LINENO}: result: $ac_cv_prog_cc_c89" >&5
printf "%s\n" "$ac_cv_prog_cc_c89" >&6; }
     CC="$CC $ac_cv_prog_cc_c89" ;;
esac
fi
  ac_cv_prog_cc_stdc=$ac_cv_prog_cc_c89
  ac_prog_cc_stdc=c89 ;;
esac
fi
fi

ac_ext=c
ac_cpp='$CPP $CPPFLAGS'
ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
ac_compiler_gnu=$ac_cv_c_compiler_gnu


{ printf "%s\n" "$as_me:${as_lineno-$LINENO}: checking for grep that handles long lines and -e" >&5
printf %s "checking for grep that handles long lines and -e... " >&6; }
if test ${ac_cv_path_GREP+y}
then :
  printf %s "(cached) " >&6
else case e in #(
  e) if test -z "$GREP"; then
  ac_path_GREP_found=false
  # Loop through the user's path and test for each of PROGNAME-LIST
  as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
for as_dir in $PATH$PATH_SEPARATOR/usr/xpg4/bin
do
  IFS=$as_save_IFS
  case $as_dir in #(((
    '') as_dir=./ ;;
    */) ;;
    *) as_dir=$as_dir/ ;;
  esac
    for ac_prog in grep ggrep
   do
    for ac_exec_ext in '' $ac_executable_extensions; do
      ac_path_GREP="$as_dir$ac_prog$ac_exec_ext"
      as_fn_executable_p "$ac_path_GREP" || continue
# Check for GNU ac_path_GREP and select it if it is found.
  # Check for GNU $ac_path_GREP
case `"$ac_path_GREP" --version 2>&1` in #(
*GNU*)
  ac_cv_path_GREP="$ac_path_GREP" ac_path_GREP_found=:;;
#(
*)
  ac_count=0
  printf %s 0123456789 >"conftest.in"
  while :
  do
    cat "conftest.in" "conftest.in" >"conftest.tmp"
    mv "conftest.tmp" "conftest.in"
    cp "conftest.in" "conftest.nl"
    printf "%s\n" 'GREP' >> "conftest.nl"
    "$ac_path_GREP" -e 'GREP$' -e '-(cannot match)-' < "conftest.nl" >"conftest.out" 2>/dev/null || break
    diff "conftest.out" "conftest.nl" >/dev/null 2>&1 || break
    as_fn_arith $ac_count + 1 && ac_count=$as_val
    if test $ac_count -gt ${ac_path_GREP_max-0}; then
      # Best one so far, save it but keep looking for a better one
      ac_cv_path_GREP="$ac_path_GREP"
      ac_path_GREP_max=$ac_count
    fi
    # 10*(2^10) chars as input seems more than enough
    test $ac_count -gt 10 && break
  done
  rm -f conftest.in conftest.tmp conftest.nl conftest.out;;
esac

      $ac_path_GREP_found && break 3
    done
  done
  done
IFS=$as_save_IFS
  if test -z "$ac_cv_path_GREP"; then
    as_fn_error $? "no acceptable grep could be found in $PATH$PATH_SEPARATOR/usr/xpg4/bin" "$LINENO" 5
  fi
else
  ac_cv_path_GREP=$GREP
fi
 ;;
esac
fi
{ printf "%s\n" "$as_me:${as_lineno-$LINENO}: result: $ac_cv_path_GREP" >&5
printf "%s\n" "$ac_cv_path_GREP" >&6; }
 GREP="$ac_cv_path_GREP"



  # Check whether --enable-warnings was given.
if test ${enable_warnings+y}
then :
  enableval=$enable_warnings;
else case e in #(
  e) enable_warnings=yes ;;
esac
fi


  if test "x$enable_warnings" != xno
then :



    ansi=""
    if test "x$ansi" = "x"
then :
  msg="for C compiler warning flags"
else case e in #(
  e) msg="for C compiler warning and ANSI conformance flags" ;;
esac
fi

    { printf "%s\n" "$as_me:${as_lineno-$LINENO}: checking $msg" >&5
printf %s "checking $msg... " >&6; }
    if test ${hts_cv_prog_cc_warnings+y}
then :
  printf %s "(cached) " >&6
else case e in #(
  e)       hts_cv_prog_cc_warnings=""
      if test "x$CC" != "x"
then :

        cat > conftest.c <<EOF
int main(int argc, char **argv) { return 0; }
EOF



        # Tests for flags to enable C compiler warnings
        # GCC compatible
        if test "x$GCC" = "xyes" &&
               "$CC" -c -Wall conftest.c > /dev/null 2>&1 &&
               test -f conftest.o
then :
            if test "x$ansi" = "x"
then :
  hts_cv_prog_cc_warnings="-Wall"
else case e in #(
  e) hts_cv_prog_cc_warnings="-Wall -ansi -pedantic" ;;
esac
fi

elif # Sun Studio or Solaris C compiler
        "$CC" -V 2>&1 | $GREP -i -E "WorkShop|Sun C" > /dev/null 2>&1 &&
         "$CC" -c -v -Xc conftest.c > /dev/null 2>&1 &&
         test -f conftest.o
then :
          if test "x$ansi" = "x"
then :
  hts_cv_prog_cc_warnings="-v"
else case e in #(
  e) hts_cv_prog_cc_warnings="-v -Xc" ;;
esac
fi

elif # Digital Unix C compiler
        "$CC" -V 2>&1 | $GREP -i "Digital UNIX Compiler" > /dev/null 2>&1 &&
         "$CC" -c -verbose -w0 -warnprotos -std1 conftest.c > /dev/null 2>&1 &&
         test -f conftest.o
then :
             if test "x$ansi" = "x"
then :
  hts_cv_prog_cc_warnings="-verbose -w0 -warnprotos"
else case e in #(
  e) hts_cv_prog_cc_warnings="-verbose -w0 -warnprotos -std1" ;;
esac
fi

elif # C for AIX Compiler
        "$CC" 2>&1 | $GREP -i "C for AIX Compiler" > /dev/null 2>&1 &&
         "$CC" -c -qlanglvl=ansi -qinfo=all conftest.c > /dev/null 2>&1 &&
         test -f conftest.o
then :
          if test "x$ansi" = "x"
then :
  hts_cv_prog_cc_warnings="-qsrcmsg -qinfo=all:noppt:noppc:noobs:nocnd"
else case e in #(
  e) hts_cv_prog_cc_warnings="-qsrcmsg -qinfo=all:noppt:noppc:noobs:nocnd -qlanglvl=ansi" ;;
esac
fi

elif # IRIX C compiler
        "$CC" -version 2>&1 | $GREP -i "MIPSpro Compilers" > /dev/null 2>&1 &&
         "$CC" -c -fullwarn -ansi -ansiE conftest.c > /dev/null 2>&1 &&
         test -f conftest.o
then :
             if test "x$ansi" = "x"
then :
  hts_cv_prog_cc_warnings="-fullwarn"
else case e in #(
  e) hts_cv_prog_cc_warnings="-fullwarn -ansi -ansiE" ;;
esac
fi

elif # HP-UX C compiler
        what "$CC" 2>&1 | $GREP -i "HP C Compiler" > /dev/null 2>&1 &&
         "$CC" -c -Aa +w1 conftest.c > /dev/null 2>&1 &&
         test -f conftest.o
then :
          if test "x$ansi" = "x"
then :
  hts_cv_prog_cc_warnings="+w1"
else case e in #(
  e) hts_cv_prog_cc_warnings="+w1 -Aa" ;;
esac
fi

elif # The NEC SX series (Super-UX 10) C compiler
        "$CC" -V 2>&1 | $GREP "/SX" > /dev/null 2>&1 &&
         "$CC" -c -pvctl,fullmsg -Xc conftest.c > /dev/null 2>&1 &&
         test -f conftest.o
then :

        if test "x$ansi" = "x"
then :
  hts_cv_prog_cc_warnings="-pvctl,fullmsg"
else case e in #(
  e) hts_cv_prog_cc_warnings="-pvctl,fullmsg -Xc" ;;
esac
fi

elif # The Cray C compiler (Unicos)
        "$CC" -V 2>&1 | $GREP -i "Cray" > /dev/null 2>&1 &&
         "$CC" -c -h msglevel_2 conftest.c > /dev/null 2>&1 &&
         test -f conftest.o
then :
          if test "x$ansi" = "x"
then :
  hts_cv_prog_cc_warnings="-h#msglevel_2"
else case e in #(
  e) hts_cv_prog_cc_warnings="-h#msglevel_2,conform" ;;
esac
fi

elif # The Tiny C Compiler
        "$CC" -v 2>&1 | $GREP "tcc version" > /dev/null &&
         "$CC" -Wall -c conftest.c > /dev/null 2>&1 &&
         test -f conftest.o
then :
           hts_cv_prog_cc_warnings="-Wall"

fi
        rm -f conftest.*

fi
     ;;
esac
fi


    if test "x$hts_cv_prog_cc_warnings" != "x"
then :

ac_arg_result=`echo "$hts_cv_prog_cc_warnings" | tr '#' ' '`
{ printf "%s\n" "$as_me:${as_lineno-$LINENO}: result: $ac_arg_result" >&5
printf "%s\n" "$ac_arg_result" >&6; }

ac_arg_needed=""
for ac_arg in $hts_cv_prog_cc_warnings
do
  ac_arg_sp=`echo "$ac_arg" | tr '#' ' '`
  case " $CFLAGS " in #(
  *" $ac_arg_sp "*) :
     ;; #(
  *) :
    ac_arg_needed="$ac_arg_all $ac_arg_sp" ;;
esac
done
CFLAGS="$ac_arg_needed $CFLAGS"
else case e in #(
  e)       { printf "%s\n" "$as_me:${as_lineno-$LINENO}: result: unknown" >&5
printf "%s\n" "unknown" >&6; }
     ;;
esac
fi

fi


  # Check whether --enable-werror was given.
if test ${enable_werror+y}
then :
  enableval=$enable_werror; enable_werror=yes
fi


  if test "x$enable_werror" = xyes
then :

    { printf "%s\n" "$as_me:${as_lineno-$LINENO}: checking for C compiler flags to error on warnings" >&5
printf %s "checking for C compiler flags to error on warnings... " >&6; }
    if test ${hts_cv_prog_cc_werror+y}
then :
  printf %s "(cached) " >&6
else case e in #(
  e)       hts_cv_prog_cc_werror=""
      if test "x$CC" != "x"
then :

        cat > conftest.c <<EOF
int main(int argc, char **argv) { return 0; }
EOF

        if 	 # Tests for flags to make the C compiler treat warnings as errors
         # GCC compatible
         test "x$GCC" = "xyes" &&
          "$CC" -c -Werror conftest.c > /dev/null 2>&1 &&
          test -f conftest.o
then :
  hts_cv_prog_cc_werror="-Werror"
elif # Sun Studio or Solaris C compiler
         "$CC" -V 2>&1 | $GREP -i -E "WorkShop|Sun C" > /dev/null 2>&1 &&
          "$CC" -c -errwarn=%all conftest.c > /dev/null 2>&1 &&
          test -f conftest.o
then :
  hts_cv_prog_cc_werror="-errwarn=%all"
elif # The Tiny C Compiler
         "$CC" -v 2>&1 | $GREP "tcc version" > /dev/null &&
          "$CC" -Wall -c conftest.c > /dev/null 2>&1 &&
          test -f conftest.o
then :
  hts_cv_prog_cc_werror="-Werror"

fi
        rm -f conftest.*

fi
     ;;
esac
fi

    if test "x$hts_cv_prog_cc_werror" != x
then :

      { printf "%s\n" "$as_me:${as_lineno-$LINENO}: result: $hts_cv_prog_cc_werror" >&5
printf "%s\n" "$hts_cv_prog_cc_werror" >&6; }
      if test "xhts_late_cflags" != x
then :
  eval hts_late_cflags="$hts_cv_prog_cc_werror"
fi

else case e in #(
  e)       { printf "%s\n" "$as_me:${as_lineno-$LINENO}: result: unknown" >&5
printf "%s\n" "unknown" >&6; }
     ;;
esac
fi

fi



# Check whether --enable-largefile was given.
if test ${enable_largefile+y}
then :
  enableval=$enable_largefile;
fi
if test "$enable_largefile,$enable_year2038" != no,no
then :
  { printf "%s\n" "$as_me:${as_lineno-$LINENO}: checking for $CC option to enable large file support" >&5
printf %s "checking for $CC option to enable large file support... " >&6; }
if test ${ac_cv_sys_largefile_opts+y}
then :
  printf %s "(cached) " >&6
else case e in #(
  e) ac_save_CC="$CC"
  ac_opt_found=no
  for ac_opt in "none needed" "-D_FILE_OFFSET_BITS=64" "-D_LARGE_FILES=1" "-n32"; do
    if test x"$ac_opt" != x"none needed"
then :
  CC="$ac_save_CC $ac_opt"
fi
    cat confdefs.h - <<_ACEOF >conftest.$ac_ext
/* end confdefs.h.  */
#include <sys/types.h>
#ifndef FTYPE
# define FTYPE off_t
#endif
 /* Check that FTYPE can represent 2**63 - 1 correctly.
    We can't simply define LARGE_FTYPE to be 9223372036854775807,
    since some C++ compilers masquerading as C compilers
    incorrectly reject 9223372036854775807.  */
#define LARGE_FTYPE (((FTYPE) 1 << 31 << 31) - 1 + ((FTYPE) 1 << 31 << 31))
  int FTYPE_is_large[(LARGE_FTYPE % 2147483629 == 721
		       && LARGE_FTYPE % 2147483647 == 1)
		      ? 1 : -1];
int
main (void)
{

  ;
  return 0;
}
_ACEOF
if ac_fn_c_try_compile "$LINENO"
then :
  if test x"$ac_opt" = x"none needed"
then :
  # GNU/Linux s390x and alpha need _FILE_OFFSET_BITS=64 for wide ino_t.
	 CC="$CC -DFTYPE=ino_t"
	 if ac_fn_c_try_compile "$LINENO"
then :

else case e in #(
  e) CC="$CC -D_FILE_OFFSET_BITS=64"
	    if ac_fn_c_try_compile "$LINENO"
then :
  ac_opt='-D_FILE_OFFSET_BITS=64'
fi
rm -f core conftest.err conftest.$ac_objext conftest.beam ;;
esac
fi
rm -f core conftest.err conftest.$ac_objext conftest.beam
fi
      ac_cv_sys_largefile_opts=$ac_opt
      ac_opt_found=yes
fi
rm -f core conftest.err conftest.$ac_objext conftest.beam conftest.$ac_ext
    test $ac_opt_found = no || break
  done
  CC="$ac_save_CC"

  test $ac_opt_found = yes || ac_cv_sys_largefile_opts="support not detected" ;;
esac
fi
{ printf "%s\n" "$as_me:${as_lineno-$LINENO}: result: $ac_cv_sys_largefile_opts" >&5
printf "%s\n" "$ac_cv_sys_largefile_opts" >&6; }

ac_have_largefile=yes
case $ac_cv_sys_largefile_opts in #(
  "none needed") :
     ;; #(
  "supported through gnulib") :
     ;; #(
  "support not detected") :
    ac_have_largefile=no ;; #(
  "-D_FILE_OFFSET_BITS=64") :

printf "%s\n" "#define _FILE_OFFSET_BITS 64" >>confdefs.h
 ;; #(
  "-D_LARGE_FILES=1") :

printf "%s\n" "#define _LARGE_FILES 1" >>confdefs.h
 ;; #(
  "-n32") :
    CC="$CC -n32" ;; #(
  *) :
    as_fn_error $? "internal error: bad value for \$ac_cv_sys_largefile_opts" "$LINENO" 5 ;;
esac

if test "$enable_year2038" != no
then :
  { printf "%s\n" "$as_me:${as_lineno-$LINENO}: checking for $CC option for timestamps after 2038" >&5
printf %s "checking for $CC option for timestamps after 2038... " >&6; }
if test ${ac_cv_sys_year2038_opts+y}
then :
  printf %s "(cached) " >&6
else case e in #(
  e) ac_save_CPPFLAGS="$CPPFLAGS"
  ac_opt_found=no
  for ac_opt in "none needed" "-D_TIME_BITS=64" "-D__MINGW_USE_VC2005_COMPAT" "-U_USE_32_BIT_TIME_T -D__MINGW_USE_VC2005_COMPAT"; do
    if test x"$ac_opt" != x"none needed"
then :
  CPPFLAGS="$ac_save_CPPFLAGS $ac_opt"
fi
    cat confdefs.h - <<_ACEOF >conftest.$ac_ext
/* end confdefs.h.  */

  #include <time.h>
  /* Check that time_t can represent 2**32 - 1 correctly.  */
  #define LARGE_TIME_T \\
    ((time_t) (((time_t) 1 << 30) - 1 + 3 * ((time_t) 1 << 30)))
  int verify_time_t_range[(LARGE_TIME_T / 65537 == 65535
                           && LARGE_TIME_T % 65537 == 0)
                          ? 1 : -1];

int
main (void)
{

  ;
  return 0;
}
_ACEOF
if ac_fn_c_try_compile "$LINENO"
then :
  ac_cv_sys_year2038_opts="$ac_opt"
      ac_opt_found=yes
fi
rm -f core conftest.err conftest.$ac_objext conftest.beam conftest.$ac_ext
    test $ac_opt_found = no || break
  done
  CPPFLAGS="$ac_save_CPPFLAGS"
  test $ac_opt_found = yes || ac_cv_sys_year2038_opts="support not detected" ;;
esac
fi
{ printf "%s\n" "$as_me:${as_lineno-$LINENO}: result: $ac_cv_sys_year2038_opts" >&5
printf "%s\n" "$ac_cv_sys_year2038_opts" >&6; }

ac_have_year2038=yes
case $ac_cv_sys_year2038_opts in #(
  "none needed") :
     ;; #(
  "support not detected") :
    ac_have_year2038=no ;; #(
  "-D_TIME_BITS=64") :

printf "%s\n" "#define _TIME_BITS 64" >>confdefs.h
 ;; #(
  "-D__MINGW_USE_VC2005_COMPAT") :

printf "%s\n" "#define __MINGW_USE_VC2005_COMPAT 1" >>confdefs.h
 ;; #(
  "-U_USE_32_BIT_TIME_T"*) :
    { { printf "%s\n" "$as_me:${as_lineno-$LINENO}: error: in '$ac_pwd':" >&5
printf "%s\n" "$as_me: error: in '$ac_pwd':" >&2;}
as_fn_error $? "the 'time_t' type is currently forced to be 32-bit. It
will stop working after mid-January 2038. Remove
_USE_32BIT_TIME_T from the compiler flags.
See 'config.log' for more details" "$LINENO" 5; } ;; #(
  *) :
    as_fn_error $? "internal error: bad value for \$ac_cv_sys_year2038_opts" "$LINENO" 5 ;;
esac

fi

fi

# Check whether --enable-bcftools-plugins was given.
if test ${enable_bcftools_plugins+y}
then :
  enableval=$enable_bcftools_plugins;
else case e in #(
  e) enable_bcftools_plugins=yes ;;
esac
fi




# Check whether --with-bcf-plugin-dir was given.
if test ${with_bcf_plugin_dir+y}
then :
  withval=$with_bcf_plugin_dir; case $withval in
     yes|no) as_fn_error $? "no directory specified for --with-plugin-dir" "$LINENO" 5 ;;
   esac
else case e in #(
  e) with_bcf_plugin_dir='$(libexecdir)/bcftools' ;;
esac
fi

bcf_plugindir=$with_bcf_plugin_dir



# Check whether --with-bcf-plugin-path was given.
if test ${with_bcf_plugin_path+y}
then :
  withval=$with_bcf_plugin_path; case $withval in
     yes) as_fn_error $? "no path specified for --with-bcf-plugin-path" "$LINENO" 5 ;;
     no)  with_bcf_plugin_path= ;;
   esac
else case e in #(
  e) with_bcf_plugin_path=$with_bcf_plugin_dir ;;
esac
fi

bcf_pluginpath=$with_bcf_plugin_path


# Check whether --enable-perl-filters was given.
if test ${enable_perl_filters+y}
then :
  enableval=$enable_perl_filters;
else case e in #(
  e) enable_perl_filters=no ;;
esac
fi



# Check whether --enable-libgsl was given.
if test ${enable_libgsl+y}
then :
  enableval=$enable_libgsl;
else case e in #(
  e) enable_libgsl=no ;;
esac
fi



# Check whether --with-cblas was given.
if test ${with_cblas+y}
then :
  withval=$with_cblas; case $withval in #(
  no) :
    as_fn_error $? "no library name specified for --with-cblas" "$LINENO" 5 ;; #(
  *) :
     ;;
esac
else case e in #(
  e) with_cblas=yes ;;
esac
fi





# Check whether --with-htslib was given.
if test ${with_htslib+y}
then :
  withval=$with_htslib;
else case e in #(
  e) with_htslib=search ;;
esac
fi

# Check whether --enable-configure-htslib was given.
if test ${enable_configure_htslib+y}
then :
  enableval=$enable_configure_htslib;
else case e in #(
  e) enable_configure_htslib=only_in_subdir ;;
esac
fi


case $with_htslib in
yes|search)
  { printf "%s\n" "$as_me:${as_lineno-$LINENO}: checking location of HTSlib source tree" >&5
printf %s "checking location of HTSlib source tree... " >&6; }
  case $srcdir in
    .) srcp= ;;
    *) srcp=$srcdir/ ;;
  esac
  found=
  for dir in ${srcp}htslib* -- ${srcp}../htslib -- ${srcp}../htslib*
  do
    if test "$dir" = "--"; then
      test -n "$found" && break
    elif test -f "$dir/hts.c" && test -f "$dir/htslib/hts.h"; then
      found="${found}1"
      HTSDIR=$dir
    fi
  done
  if test -z "$found"; then
    { printf "%s\n" "$as_me:${as_lineno-$LINENO}: result: none found" >&5
printf "%s\n" "none found" >&6; }
    ax_cv_htslib_which=system
  elif test "$found" = 1; then
    { printf "%s\n" "$as_me:${as_lineno-$LINENO}: result: $HTSDIR" >&5
printf "%s\n" "$HTSDIR" >&6; }
    ax_cv_htslib_which=source
    if test "x$enable_configure_htslib" = "xonly_in_subdir" ; then
      case $HTSDIR in
        "${srcp}htslib"*) enable_configure_htslib=yes ;;
        *) ;;
      esac
    fi
  else
    { printf "%s\n" "$as_me:${as_lineno-$LINENO}: result: several directories found" >&5
printf "%s\n" "several directories found" >&6; }
    as_fn_error $? "use --with-htslib=DIR to select which HTSlib to use" "$LINENO" 5
  fi
  ;;
no) ax_cv_htslib_which=none ;;
system) ax_cv_htslib_which=system ;;
*)
  HTSDIR=$with_htslib
  if test -f "$HTSDIR/hts.c" && test -f "$HTSDIR/htslib/hts.h"; then
    ax_cv_htslib_which=source
  elif test -f "$HTSDIR/htslib_vars.mk"; then
    ax_cv_htslib_which=build
  else
    ax_cv_htslib_which=install
  fi
  ;;
esac

case $ax_cv_htslib_which in
source)
  ax_cv_htslib=yes
  HTSLIB_CPPFLAGS="-I$HTSDIR"
  HTSLIB_LDFLAGS="-L$HTSDIR"
  if test "x$enable_configure_htslib" = "xyes"; then
    # We can't use a literal, because $HTSDIR is user-provided and variable
    subdirs="$subdirs $HTSDIR"

  fi
  ;;
build)
  ax_cv_htslib=yes
  ax_cv_htslib_which=source
  # Ensure this is fully expanded, as the caller might not be using @HTSDIR@
  HTSSRCDIR=$(sed -n 's:\$(HTSDIR):'$HTSDIR':
                      s/^HTSSRCDIR *= *//p' "$HTSDIR/htslib_vars.mk")
  HTSLIB_CPPFLAGS="-I$HTSSRCDIR"
  HTSLIB_LDFLAGS="-L$HTSDIR"
  ;;
system)
  ac_fn_c_check_header_compile "$LINENO" "htslib/sam.h" "ac_cv_header_htslib_sam_h" ";
"
if test "x$ac_cv_header_htslib_sam_h" = xyes
then :
  { printf "%s\n" "$as_me:${as_lineno-$LINENO}: checking for hts_version in -lhts" >&5
printf %s "checking for hts_version in -lhts... " >&6; }
if test ${ac_cv_lib_hts_hts_version+y}
then :
  printf %s "(cached) " >&6
else case e in #(
  e) ac_check_lib_save_LIBS=$LIBS
LIBS="-lhts  $LIBS"
cat confdefs.h - <<_ACEOF >conftest.$ac_ext
/* end confdefs.h.  */

/* Override any GCC internal prototype to avoid an error.
   Use char because int might match the return type of a GCC
   builtin and then its argument prototype would still apply.
   The 'extern "C"' is for builds by C++ compilers;
   although this is not generally supported in C code supporting it here
   has little cost and some practical benefit (sr 110532).  */
#ifdef __cplusplus
extern "C"
#endif
char hts_version (void);
int
main (void)
{
return hts_version ();
  ;
  return 0;
}
_ACEOF
if ac_fn_c_try_link "$LINENO"
then :
  ac_cv_lib_hts_hts_version=yes
else case e in #(
  e) ac_cv_lib_hts_hts_version=no ;;
esac
fi
rm -f core conftest.err conftest.$ac_objext conftest.beam \
    conftest$ac_exeext conftest.$ac_ext
LIBS=$ac_check_lib_save_LIBS ;;
esac
fi
{ printf "%s\n" "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_hts_hts_version" >&5
printf "%s\n" "$ac_cv_lib_hts_hts_version" >&6; }
if test "x$ac_cv_lib_hts_hts_version" = xyes
then :
  ax_cv_htslib=yes
else case e in #(
  e) ax_cv_htslib=no ;;
esac
fi

else case e in #(
  e) ax_cv_htslib=no ;;
esac
fi

  ax_cv_htslib_which=install
  HTSDIR=
  HTSLIB_CPPFLAGS=
  HTSLIB_LDFLAGS=
  ;;
install)
  ax_saved_CPPFLAGS=$CPPFLAGS
  ax_saved_LDFLAGS=$LDFLAGS
  HTSLIB_CPPFLAGS="-I$HTSDIR/include"
  HTSLIB_LDFLAGS="-L$HTSDIR/lib"
  CPPFLAGS="$CPPFLAGS $HTSLIB_CPPFLAGS"
  LDFLAGS="$LDFLAGS $HTSLIB_LDFLAGS"
  ac_fn_c_check_header_compile "$LINENO" "htslib/sam.h" "ac_cv_header_htslib_sam_h" ";
"
if test "x$ac_cv_header_htslib_sam_h" = xyes
then :
  { printf "%s\n" "$as_me:${as_lineno-$LINENO}: checking for hts_version in -lhts" >&5
printf %s "checking for hts_version in -lhts... " >&6; }
if test ${ac_cv_lib_hts_hts_version+y}
then :
  printf %s "(cached) " >&6
else case e in #(
  e) ac_check_lib_save_LIBS=$LIBS
LIBS="-lhts  $LIBS"
cat confdefs.h - <<_ACEOF >conftest.$ac_ext
/* end confdefs.h.  */

/* Override any GCC internal prototype to avoid an error.
   Use char because int might match the return type of a GCC
   builtin and then its argument prototype would still apply.
   The 'extern "C"' is for builds by C++ compilers;
   although this is not generally supported in C code supporting it here
   has little cost and some practical benefit (sr 110532).  */
#ifdef __cplusplus
extern "C"
#endif
char hts_version (void);
int
main (void)
{
return hts_version ();
  ;
  return 0;
}
_ACEOF
if ac_fn_c_try_link "$LINENO"
then :
  ac_cv_lib_hts_hts_version=yes
else case e in #(
  e) ac_cv_lib_hts_hts_version=no ;;
esac
fi
rm -f core conftest.err conftest.$ac_objext conftest.beam \
    conftest$ac_exeext conftest.$ac_ext
LIBS=$ac_check_lib_save_LIBS ;;
esac
fi
{ printf "%s\n" "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_hts_hts_version" >&5
printf "%s\n" "$ac_cv_lib_hts_hts_version" >&6; }
if test "x$ac_cv_lib_hts_hts_version" = xyes
then :
  ax_cv_htslib=yes
else case e in #(
  e) ax_cv_htslib=no ;;
esac
fi

else case e in #(
  e) ax_cv_htslib=no ;;
esac
fi

  HTSDIR=
  CPPFLAGS=$ax_saved_CPPFLAGS
  LDFLAGS=$ax_saved_LDFLAGS
  ;;
none)
  ax_cv_htslib=no
  ;;
esac




if test "$ax_cv_htslib" != yes; then
  as_fn_error $? "HTSlib development files not found

BCFtools uses HTSlib to parse bioinformatics file formats etc.  Building it
requires an unpacked HTSlib source tree (which will be built in conjunction
with bcftools) or a previously-installed HTSlib.  In either case you may
need to configure --with-htslib=DIR to locate the appropriate HTSlib.

FAILED.  You must supply an HTSlib in order to build bcftools successfully." "$LINENO" 5
fi

if test "$ax_cv_htslib_which" = source; then
  Hsource=
  Hinstall='#'
else
  Hsource='#'
  Hinstall=
fi



if test "$enable_bcftools_plugins" != "no"
then :
    { printf "%s\n" "$as_me:${as_lineno-$LINENO}: checking shared library type" >&5
printf %s "checking shared library type... " >&6; }
  test -n "$host_alias" || host_alias=unknown-`uname -s`
  case $host_alias in #(
  *-cygwin* | *-CYGWIN*) :
          host_result="Cygwin DLL"
      PLATFORM=CYGWIN
      PLUGIN_EXT=.cygdll
      HTSLIB_DLL=libhts.dll.a
	   ;; #(
  *-msys* | *-MSYS* | *-mingw* | *-MINGW*) :
          host_result="MSYS dll"
      PLATFORM=MSYS
      PLUGIN_EXT=.dll
      HTSLIB_DLL=hts.dll.a
      # This also sets __USE_MINGW_ANSI_STDIO which in turn makes PRId64,
      # %lld and %z printf formats work.  It also enforces the snprintf to
      # be C99 compliant so it returns the correct values (in kstring.c).
      CPPFLAGS="$CPPFLAGS -D_XOPEN_SOURCE=600" ;; #(
  *-darwin* | *-Darwin*) :
          host_result="Darwin dylib"
      PLATFORM=Darwin
      PLUGIN_EXT=.so ;; #(
  *) :
          host_result="plain .so"
      PLATFORM=default
      PLUGIN_EXT=.so ;; #(
  *) :
     ;;
esac
  { printf "%s\n" "$as_me:${as_lineno-$LINENO}: result: $host_result" >&5
printf "%s\n" "$host_result" >&6; }



printf "%s\n" "#define PLUGIN_EXT \"$PLUGIN_EXT\"" >>confdefs.h



printf "%s\n" "#define ENABLE_BCF_PLUGINS 1" >>confdefs.h


  case $PLUGIN_EXT in #(
  *cygdll | *so) :
    { printf "%s\n" "$as_me:${as_lineno-$LINENO}: checking for library containing dlopen" >&5
printf %s "checking for library containing dlopen... " >&6; }
if test ${ac_cv_search_dlopen+y}
then :
  printf %s "(cached) " >&6
else case e in #(
  e) ac_func_search_save_LIBS=$LIBS
cat confdefs.h - <<_ACEOF >conftest.$ac_ext
/* end confdefs.h.  */

/* Override any GCC internal prototype to avoid an error.
   Use char because int might match the return type of a GCC
   builtin and then its argument prototype would still apply.
   The 'extern "C"' is for builds by C++ compilers;
   although this is not generally supported in C code supporting it here
   has little cost and some practical benefit (sr 110532).  */
#ifdef __cplusplus
extern "C"
#endif
char dlopen (void);
int
main (void)
{
return dlopen ();
  ;
  return 0;
}
_ACEOF
for ac_lib in '' dl
do
  if test -z "$ac_lib"; then
    ac_res="none required"
  else
    ac_res=-l$ac_lib
    LIBS="-l$ac_lib  $ac_func_search_save_LIBS"
  fi
  if ac_fn_c_try_link "$LINENO"
then :
  ac_cv_search_dlopen=$ac_res
fi
rm -f core conftest.err conftest.$ac_objext conftest.beam \
    conftest$ac_exeext
  if test ${ac_cv_search_dlopen+y}
then :
  break
fi
done
if test ${ac_cv_search_dlopen+y}
then :

else case e in #(
  e) ac_cv_search_dlopen=no ;;
esac
fi
rm conftest.$ac_ext
LIBS=$ac_func_search_save_LIBS ;;
esac
fi
{ printf "%s\n" "$as_me:${as_lineno-$LINENO}: result: $ac_cv_search_dlopen" >&5
printf "%s\n" "$ac_cv_search_dlopen" >&6; }
ac_res=$ac_cv_search_dlopen
if test "$ac_res" != no
then :
  test "$ac_res" = "none required" || LIBS="$ac_res $LIBS"

else case e in #(
  e) as_fn_error $? "dlopen() not found
Plugin support requires dynamic linking facilities from the operating system.
Either configure with --disable-bcftools-plugins or resolve this error to
build bcftools." "$LINENO" 5 ;;
esac
fi
 ;; #(
  *dll) :
    { printf "%s\n" "$as_me:${as_lineno-$LINENO}: checking for library containing LoadLibraryA" >&5
printf %s "checking for library containing LoadLibraryA... " >&6; }
if test ${ac_cv_search_LoadLibraryA+y}
then :
  printf %s "(cached) " >&6
else case e in #(
  e) ac_func_search_save_LIBS=$LIBS
cat confdefs.h - <<_ACEOF >conftest.$ac_ext
/* end confdefs.h.  */

/* Override any GCC internal prototype to avoid an error.
   Use char because int might match the return type of a GCC
   builtin and then its argument prototype would still apply.
   The 'extern "C"' is for builds by C++ compilers;
   although this is not generally supported in C code supporting it here
   has little cost and some practical benefit (sr 110532).  */
#ifdef __cplusplus
extern "C"
#endif
char LoadLibraryA (void);
int
main (void)
{
return LoadLibraryA ();
  ;
  return 0;
}
_ACEOF
for ac_lib in ''
do
  if test -z "$ac_lib"; then
    ac_res="none required"
  else
    ac_res=-l$ac_lib
    LIBS="-l$ac_lib  $ac_func_search_save_LIBS"
  fi
  if ac_fn_c_try_link "$LINENO"
then :
  ac_cv_search_LoadLibraryA=$ac_res
fi
rm -f core conftest.err conftest.$ac_objext conftest.beam \
    conftest$ac_exeext
  if test ${ac_cv_search_LoadLibraryA+y}
then :
  break
fi
done
if test ${ac_cv_search_LoadLibraryA+y}
then :

else case e in #(
  e) ac_cv_search_LoadLibraryA=no ;;
esac
fi
rm conftest.$ac_ext
LIBS=$ac_func_search_save_LIBS ;;
esac
fi
{ printf "%s\n" "$as_me:${as_lineno-$LINENO}: result: $ac_cv_search_LoadLibraryA" >&5
printf "%s\n" "$ac_cv_search_LoadLibraryA" >&6; }
ac_res=$ac_cv_search_LoadLibraryA
if test "$ac_res" != no
then :
  test "$ac_res" = "none required" || LIBS="$ac_res $LIBS"

else case e in #(
  e) as_fn_error $? "LoadLibraryA() not found
Plugin support requires dynamic linking facilities from the operating system.
Either configure with --disable-bcftools-plugins or resolve this error to
build bcftools." "$LINENO" 5 ;;
esac
fi
 ;; #(
  *) :
     ;;
esac

  { printf "%s\n" "$as_me:${as_lineno-$LINENO}: checking if the compiler accepts -rdynamic" >&5
printf %s "checking if the compiler accepts -rdynamic... " >&6; }
  save_CFLAGS=$CFLAGS
  CFLAGS="$CFLAGS -rdynamic"
  cat confdefs.h - <<_ACEOF >conftest.$ac_ext
/* end confdefs.h.  */

int
main (void)
{

  ;
  return 0;
}
_ACEOF
if ac_fn_c_try_link "$LINENO"
then :
  cc_rdynamic=yes
else case e in #(
  e) cc_rdynamic=no ;;
esac
fi
rm -f core conftest.err conftest.$ac_objext conftest.beam \
    conftest$ac_exeext conftest.$ac_ext
  CFLAGS=$save_CFLAGS
  { printf "%s\n" "$as_me:${as_lineno-$LINENO}: result: $cc_rdynamic" >&5
printf "%s\n" "$cc_rdynamic" >&6; }
  if test "$cc_rdynamic" = "yes"
then :
      CC_RDYNAMIC_OPT=-rdynamic
else case e in #(
  e) CC_RDYNAMIC_OPT= ;;
esac
fi


fi
save_LIBS=$LIBS
zlib_devel=ok
ac_fn_c_check_header_compile "$LINENO" "zlib.h" "ac_cv_header_zlib_h" ";
"
if test "x$ac_cv_header_zlib_h" = xyes
then :

else case e in #(
  e) zlib_devel=missing ;;
esac
fi

{ printf "%s\n" "$as_me:${as_lineno-$LINENO}: checking for inflate in -lz" >&5
printf %s "checking for inflate in -lz... " >&6; }
if test ${ac_cv_lib_z_inflate+y}
then :
  printf %s "(cached) " >&6
else case e in #(
  e) ac_check_lib_save_LIBS=$LIBS
LIBS="-lz  $LIBS"
cat confdefs.h - <<_ACEOF >conftest.$ac_ext
/* end confdefs.h.  */

/* Override any GCC internal prototype to avoid an error.
   Use char because int might match the return type of a GCC
   builtin and then its argument prototype would still apply.
   The 'extern "C"' is for builds by C++ compilers;
   although this is not generally supported in C code supporting it here
   has little cost and some practical benefit (sr 110532).  */
#ifdef __cplusplus
extern "C"
#endif
char inflate (void);
int
main (void)
{
return inflate ();
  ;
  return 0;
}
_ACEOF
if ac_fn_c_try_link "$LINENO"
then :
  ac_cv_lib_z_inflate=yes
else case e in #(
  e) ac_cv_lib_z_inflate=no ;;
esac
fi
rm -f core conftest.err conftest.$ac_objext conftest.beam \
    conftest$ac_exeext conftest.$ac_ext
LIBS=$ac_check_lib_save_LIBS ;;
esac
fi
{ printf "%s\n" "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_z_inflate" >&5
printf "%s\n" "$ac_cv_lib_z_inflate" >&6; }
if test "x$ac_cv_lib_z_inflate" = xyes
then :
  printf "%s\n" "#define HAVE_LIBZ 1" >>confdefs.h

  LIBS="-lz $LIBS"

else case e in #(
  e) zlib_devel=missing ;;
esac
fi

LIBS=$save_LIBS

if test $zlib_devel != ok; then
  as_fn_error $? "zlib development files not found

BCFtools uses compression routines from the zlib library <http://zlib.net>.
Building bcftools requires zlib development files to be installed on the build
machine; you may need to ensure a package such as zlib1g-dev (on Debian or
Ubuntu Linux) or zlib-devel (on RPM-based Linux distributions) is installed.

FAILED.  This error must be resolved in order to build bcftools successfully." "$LINENO" 5
fi

if test "$enable_libgsl" != "no"
then :
    gsl_devel=ok
  save_LIBS="$LIBS"  GSL_LIBS=
  ac_fn_c_check_header_compile "$LINENO" "gsl/gsl_version.h" "ac_cv_header_gsl_gsl_version_h" ";
"
if test "x$ac_cv_header_gsl_gsl_version_h" = xyes
then :

else case e in #(
  e) gsl_devel=missing ;;
esac
fi

  if test "$gsl_devel" != "missing"
then :
      case $with_cblas in #(
  yes) :
    { printf "%s\n" "$as_me:${as_lineno-$LINENO}: checking for library containing cblas_dgemm" >&5
printf %s "checking for library containing cblas_dgemm... " >&6; }
if test ${ac_cv_search_cblas_dgemm+y}
then :
  printf %s "(cached) " >&6
else case e in #(
  e) ac_func_search_save_LIBS=$LIBS
cat confdefs.h - <<_ACEOF >conftest.$ac_ext
/* end confdefs.h.  */

/* Override any GCC internal prototype to avoid an error.
   Use char because int might match the return type of a GCC
   builtin and then its argument prototype would still apply.
   The 'extern "C"' is for builds by C++ compilers;
   although this is not generally supported in C code supporting it here
   has little cost and some practical benefit (sr 110532).  */
#ifdef __cplusplus
extern "C"
#endif
char cblas_dgemm (void);
int
main (void)
{
return cblas_dgemm ();
  ;
  return 0;
}
_ACEOF
for ac_lib in '' cblas gslcblas
do
  if test -z "$ac_lib"; then
    ac_res="none required"
  else
    ac_res=-l$ac_lib
    LIBS="-l$ac_lib  $ac_func_search_save_LIBS"
  fi
  if ac_fn_c_try_link "$LINENO"
then :
  ac_cv_search_cblas_dgemm=$ac_res
fi
rm -f core conftest.err conftest.$ac_objext conftest.beam \
    conftest$ac_exeext
  if test ${ac_cv_search_cblas_dgemm+y}
then :
  break
fi
done
if test ${ac_cv_search_cblas_dgemm+y}
then :

else case e in #(
  e) ac_cv_search_cblas_dgemm=no ;;
esac
fi
rm conftest.$ac_ext
LIBS=$ac_func_search_save_LIBS ;;
esac
fi
{ printf "%s\n" "$as_me:${as_lineno-$LINENO}: result: $ac_cv_search_cblas_dgemm" >&5
printf "%s\n" "$ac_cv_search_cblas_dgemm" >&6; }
ac_res=$ac_cv_search_cblas_dgemm
if test "$ac_res" != no
then :
  test "$ac_res" = "none required" || LIBS="$ac_res $LIBS"
  GSL_LIBS="$ac_cv_search_cblas_dgemm"
else case e in #(
  e) gsl_devel=missing ;;
esac
fi
 ;; #(
  *) :
    as_ac_Lib=`printf "%s\n" "ac_cv_lib_$with_cblas""_cblas_dgemm" | sed "$as_sed_sh"`
{ printf "%s\n" "$as_me:${as_lineno-$LINENO}: checking for cblas_dgemm in -l$with_cblas" >&5
printf %s "checking for cblas_dgemm in -l$with_cblas... " >&6; }
if eval test \${$as_ac_Lib+y}
then :
  printf %s "(cached) " >&6
else case e in #(
  e) ac_check_lib_save_LIBS=$LIBS
LIBS="-l$with_cblas  $LIBS"
cat confdefs.h - <<_ACEOF >conftest.$ac_ext
/* end confdefs.h.  */

/* Override any GCC internal prototype to avoid an error.
   Use char because int might match the return type of a GCC
   builtin and then its argument prototype would still apply.
   The 'extern "C"' is for builds by C++ compilers;
   although this is not generally supported in C code supporting it here
   has little cost and some practical benefit (sr 110532).  */
#ifdef __cplusplus
extern "C"
#endif
char cblas_dgemm (void);
int
main (void)
{
return cblas_dgemm ();
  ;
  return 0;
}
_ACEOF
if ac_fn_c_try_link "$LINENO"
then :
  eval "$as_ac_Lib=yes"
else case e in #(
  e) eval "$as_ac_Lib=no" ;;
esac
fi
rm -f core conftest.err conftest.$ac_objext conftest.beam \
    conftest$ac_exeext conftest.$ac_ext
LIBS=$ac_check_lib_save_LIBS ;;
esac
fi
eval ac_res=\$$as_ac_Lib
	       { printf "%s\n" "$as_me:${as_lineno-$LINENO}: result: $ac_res" >&5
printf "%s\n" "$ac_res" >&6; }
if eval test \"x\$"$as_ac_Lib"\" = x"yes"
then :
  GSL_LIBS="-l$with_cblas"
else case e in #(
  e) gsl_devel=missing ;;
esac
fi
 ;;
esac

fi
  if test "$gsl_devel" != "missing"
then :
      { printf "%s\n" "$as_me:${as_lineno-$LINENO}: checking for gsl_multifit_gradient in -lgsl" >&5
printf %s "checking for gsl_multifit_gradient in -lgsl... " >&6; }
if test ${ac_cv_lib_gsl_gsl_multifit_gradient+y}
then :
  printf %s "(cached) " >&6
else case e in #(
  e) ac_check_lib_save_LIBS=$LIBS
LIBS="-lgsl $GSL_LIBS $LIBS"
cat confdefs.h - <<_ACEOF >conftest.$ac_ext
/* end confdefs.h.  */

/* Override any GCC internal prototype to avoid an error.
   Use char because int might match the return type of a GCC
   builtin and then its argument prototype would still apply.
   The 'extern "C"' is for builds by C++ compilers;
   although this is not generally supported in C code supporting it here
   has little cost and some practical benefit (sr 110532).  */
#ifdef __cplusplus
extern "C"
#endif
char gsl_multifit_gradient (void);
int
main (void)
{
return gsl_multifit_gradient ();
  ;
  return 0;
}
_ACEOF
if ac_fn_c_try_link "$LINENO"
then :
  ac_cv_lib_gsl_gsl_multifit_gradient=yes
else case e in #(
  e) ac_cv_lib_gsl_gsl_multifit_gradient=no ;;
esac
fi
rm -f core conftest.err conftest.$ac_objext conftest.beam \
    conftest$ac_exeext conftest.$ac_ext
LIBS=$ac_check_lib_save_LIBS ;;
esac
fi
{ printf "%s\n" "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_gsl_gsl_multifit_gradient" >&5
printf "%s\n" "$ac_cv_lib_gsl_gsl_multifit_gradient" >&6; }
if test "x$ac_cv_lib_gsl_gsl_multifit_gradient" = xyes
then :
  GSL_LIBS="-lgsl $GSL_LIBS"
else case e in #(
  e) gsl_devel=missing ;;
esac
fi


fi

  if test "$gsl_devel" != "ok"
then :
      as_fn_error $? "libgsl development files not found

The bcftools polysomy command uses routines from the GNU Scientific library
<https://www.gnu.org/software/gsl/>.  Building BCFtools with libgsl enabled
requires libgsl development files to be installed on the build machine; you
may need to ensure a package such as libgsl0-dev (on Debian or Ubuntu linux)
or gsl-devel (on RPM-based Linux distributions) is installed.

Either configure with --disable-libgsl or resolve this error to build bcftools.
    " "$LINENO" 5

fi

  LIBS="$save_LIBS"
  USE_GPL=1



fi

if test "$enable_perl_filters" != "no"
then :
      save_LIBS="$LIBS"
    if ! perl -MExtUtils::Embed -e ccopts -e ldopts >/dev/null 2>&1; then
       as_fn_error $? "Cannot \`perl -MExtUtils::Embed -e ccopts -e ldopts\`" "$LINENO" 5
    fi

printf "%s\n" "#define ENABLE_PERL_FILTERS 1" >>confdefs.h

    PERL_CCOPTS="`perl -MExtUtils::Embed -e ccopts`"
    PERL_LIBS="`perl -MExtUtils::Embed -e ldopts`"
        if test "x$PLATFORM" = "xDarwin"; then
        PERL_CCOPTS="`perl -MExtUtils::Embed -e ccopts | sed 's,-arch i386,,'`"
        PERL_LIBS="`perl -MExtUtils::Embed -e ldopts | sed 's,-arch i386,,'`"
    fi



        { printf "%s\n" "$as_me:${as_lineno-$LINENO}: checking for library containing Perl_call_pv" >&5
printf %s "checking for library containing Perl_call_pv... " >&6; }
if test ${ac_cv_search_Perl_call_pv+y}
then :
  printf %s "(cached) " >&6
else case e in #(
  e) ac_func_search_save_LIBS=$LIBS
cat confdefs.h - <<_ACEOF >conftest.$ac_ext
/* end confdefs.h.  */

/* Override any GCC internal prototype to avoid an error.
   Use char because int might match the return type of a GCC
   builtin and then its argument prototype would still apply.
   The 'extern "C"' is for builds by C++ compilers;
   although this is not generally supported in C code supporting it here
   has little cost and some practical benefit (sr 110532).  */
#ifdef __cplusplus
extern "C"
#endif
char Perl_call_pv (void);
int
main (void)
{
return Perl_call_pv ();
  ;
  return 0;
}
_ACEOF
for ac_lib in '' perl
do
  if test -z "$ac_lib"; then
    ac_res="none required"
  else
    ac_res=-l$ac_lib
    LIBS="-l$ac_lib $PERL_CCOPTS $PERL_LIBS $ac_func_search_save_LIBS"
  fi
  if ac_fn_c_try_link "$LINENO"
then :
  ac_cv_search_Perl_call_pv=$ac_res
fi
rm -f core conftest.err conftest.$ac_objext conftest.beam \
    conftest$ac_exeext
  if test ${ac_cv_search_Perl_call_pv+y}
then :
  break
fi
done
if test ${ac_cv_search_Perl_call_pv+y}
then :

else case e in #(
  e) ac_cv_search_Perl_call_pv=no ;;
esac
fi
rm conftest.$ac_ext
LIBS=$ac_func_search_save_LIBS ;;
esac
fi
{ printf "%s\n" "$as_me:${as_lineno-$LINENO}: result: $ac_cv_search_Perl_call_pv" >&5
printf "%s\n" "$ac_cv_search_Perl_call_pv" >&6; }
ac_res=$ac_cv_search_Perl_call_pv
if test "$ac_res" != no
then :
  test "$ac_res" = "none required" || LIBS="$ac_res $LIBS"

else case e in #(
  e)
        as_fn_error $? "Unable to find the Perl_call_pv() function for perl filters" "$LINENO" 5
     ;;
esac
fi

    LIBS="$save_LIBS"

fi

if test "x$hts_late_cflags" != x
then :
  CFLAGS="$CFLAGS $hts_late_cflags"
fi

{ printf "%s\n" "$as_me:${as_lineno-$LINENO}: checking for library containing regcomp" >&5
printf %s "checking for library containing regcomp... " >&6; }
if test ${ac_cv_search_regcomp+y}
then :
  printf %s "(cached) " >&6
else case e in #(
  e) ac_func_search_save_LIBS=$LIBS
cat confdefs.h - <<_ACEOF >conftest.$ac_ext
/* end confdefs.h.  */

/* Override any GCC internal prototype to avoid an error.
   Use char because int might match the return type of a GCC
   builtin and then its argument prototype would still apply.
   The 'extern "C"' is for builds by C++ compilers;
   although this is not generally supported in C code supporting it here
   has little cost and some practical benefit (sr 110532).  */
#ifdef __cplusplus
extern "C"
#endif
char regcomp (void);
int
main (void)
{
return regcomp ();
  ;
  return 0;
}
_ACEOF
for ac_lib in '' regex
do
  if test -z "$ac_lib"; then
    ac_res="none required"
  else
    ac_res=-l$ac_lib
    LIBS="-l$ac_lib  $ac_func_search_save_LIBS"
  fi
  if ac_fn_c_try_link "$LINENO"
then :
  ac_cv_search_regcomp=$ac_res
fi
rm -f core conftest.err conftest.$ac_objext conftest.beam \
    conftest$ac_exeext
  if test ${ac_cv_search_regcomp+y}
then :
  break
fi
done
if test ${ac_cv_search_regcomp+y}
then :

else case e in #(
  e) ac_cv_search_regcomp=no ;;
esac
fi
rm conftest.$ac_ext
LIBS=$ac_func_search_save_LIBS ;;
esac
fi
{ printf "%s\n" "$as_me:${as_lineno-$LINENO}: result: $ac_cv_search_regcomp" >&5
printf "%s\n" "$ac_cv_search_regcomp" >&6; }
ac_res=$ac_cv_search_regcomp
if test "$ac_res" != no
then :
  test "$ac_res" = "none required" || LIBS="$ac_res $LIBS"
  libregex=needed
fi


test -n "$host_alias" || host_alias=unknown-`uname -s`
case $host_alias in
  *-msys* | *-MSYS* | *-mingw* | *-MINGW*)
    host_result="MSYS dll"
    PLATFORM=MSYS
    PLUGIN_EXT=.dll
    # This also sets __USE_MINGW_ANSI_STDIO which in turn makes PRId64,
    # %lld and %z printf formats work.  It also enforces the snprintf to
    # be C99 compliant so it returns the correct values (in kstring.c).
    CPPFLAGS="$CPPFLAGS -D_XOPEN_SOURCE=600"
    ;;
esac

ac_config_files="$ac_config_files config.mk"

cat >confcache <<\_ACEOF
# This file is a shell script that caches the results of configure
# tests run on this system so they can be shared between configure
# scripts and configure runs, see configure's option --config-cache.
# It is not useful on other systems.  If it contains results you don't
# want to keep, you may remove or edit it.
#
# config.status only pays attention to the cache file if you give it
# the --recheck option to rerun configure.
#
# 'ac_cv_env_foo' variables (set or unset) will be overridden when
# loading this file, other *unset* 'ac_cv_foo' will be assigned the
# following values.

_ACEOF

# The following way of writing the cache mishandles newlines in values,
# but we know of no workaround that is simple, portable, and efficient.
# So, we kill variables containing newlines.
# Ultrix sh set writes to stderr and can't be redirected directly,
# and sets the high bit in the cache file unless we assign to the vars.
(
  for ac_var in `(set) 2>&1 | sed -n 's/^\([a-zA-Z_][a-zA-Z0-9_]*\)=.*/\1/p'`; do
    eval ac_val=\$$ac_var
    case $ac_val in #(
    *${as_nl}*)
      case $ac_var in #(
      *_cv_*) { printf "%s\n" "$as_me:${as_lineno-$LINENO}: WARNING: cache variable $ac_var contains a newline" >&5
printf "%s\n" "$as_me: WARNING: cache variable $ac_var contains a newline" >&2;} ;;
      esac
      case $ac_var in #(
      _ | IFS | as_nl) ;; #(
      BASH_ARGV | BASH_SOURCE) eval $ac_var= ;; #(
      *) { eval $ac_var=; unset $ac_var;} ;;
      esac ;;
    esac
  done

  (set) 2>&1 |
    case $as_nl`(ac_space=' '; set) 2>&1` in #(
    *${as_nl}ac_space=\ *)
      # 'set' does not quote correctly, so add quotes: double-quote
      # substitution turns \\\\ into \\, and sed turns \\ into \.
      sed -n \
	"s/'/'\\\\''/g;
	  s/^\\([_$as_cr_alnum]*_cv_[_$as_cr_alnum]*\\)=\\(.*\\)/\\1='\\2'/p"
      ;; #(
    *)
      # 'set' quotes correctly as required by POSIX, so do not add quotes.
      sed -n "/^[_$as_cr_alnum]*_cv_[_$as_cr_alnum]*=/p"
      ;;
    esac |
    sort
) |
  sed '
     /^ac_cv_env_/b end
     t clear
     :clear
     s/^\([^=]*\)=\(.*[{}].*\)$/test ${\1+y} || &/
     t end
     s/^\([^=]*\)=\(.*\)$/\1=${\1=\2}/
     :end' >>confcache
if diff "$cache_file" confcache >/dev/null 2>&1; then :; else
  if test -w "$cache_file"; then
    if test "x$cache_file" != "x/dev/null"; then
      { printf "%s\n" "$as_me:${as_lineno-$LINENO}: updating cache $cache_file" >&5
printf "%s\n" "$as_me: updating cache $cache_file" >&6;}
      if test ! -f "$cache_file" || test -h "$cache_file"; then
	cat confcache >"$cache_file"
      else
        case $cache_file in #(
        */* | ?:*)
	  mv -f confcache "$cache_file"$$ &&
	  mv -f "$cache_file"$$ "$cache_file" ;; #(
        *)
	  mv -f confcache "$cache_file" ;;
	esac
      fi
    fi
  else
    { printf "%s\n" "$as_me:${as_lineno-$LINENO}: not updating unwritable cache $cache_file" >&5
printf "%s\n" "$as_me: not updating unwritable cache $cache_file" >&6;}
  fi
fi
rm -f confcache

test "x$prefix" = xNONE && prefix=$ac_default_prefix
# Let make expand exec_prefix.
test "x$exec_prefix" = xNONE && exec_prefix='${prefix}'

DEFS=-DHAVE_CONFIG_H

ac_libobjs=
ac_ltlibobjs=
U=
for ac_i in : $LIBOBJS; do test "x$ac_i" = x: && continue
  # 1. Remove the extension, and $U if already installed.
  ac_script='s/\$U\././;s/\.o$//;s/\.obj$//'
  ac_i=`printf "%s\n" "$ac_i" | sed "$ac_script"`
  # 2. Prepend LIBOBJDIR.  When used with automake>=1.10 LIBOBJDIR
  #    will be set to the directory where LIBOBJS objects are built.
  as_fn_append ac_libobjs " \${LIBOBJDIR}$ac_i\$U.$ac_objext"
  as_fn_append ac_ltlibobjs " \${LIBOBJDIR}$ac_i"'$U.lo'
done
LIBOBJS=$ac_libobjs

LTLIBOBJS=$ac_ltlibobjs


# Check whether --enable-year2038 was given.
if test ${enable_year2038+y}
then :
  enableval=$enable_year2038;
fi


: "${CONFIG_STATUS=./config.status}"
ac_write_fail=0
ac_clean_files_save=$ac_clean_files
ac_clean_files="$ac_clean_files $CONFIG_STATUS"
{ printf "%s\n" "$as_me:${as_lineno-$LINENO}: creating $CONFIG_STATUS" >&5
printf "%s\n" "$as_me: creating $CONFIG_STATUS" >&6;}
as_write_fail=0
cat >$CONFIG_STATUS <<_ASEOF || as_write_fail=1
#! $SHELL
# Generated by $as_me.
# Run this file to recreate the current configuration.
# Compiler output produced by configure, useful for debugging
# configure, is in config.log if it exists.

debug=false
ac_cs_recheck=false
ac_cs_silent=false

SHELL=\${CONFIG_SHELL-$SHELL}
export SHELL
_ASEOF
cat >>$CONFIG_STATUS <<\_ASEOF || as_write_fail=1
## -------------------- ##
## M4sh Initialization. ##
## -------------------- ##

# Be more Bourne compatible
DUALCASE=1; export DUALCASE # for MKS sh
if test ${ZSH_VERSION+y} && (emulate sh) >/dev/null 2>&1
then :
  emulate sh
  NULLCMD=:
  # Pre-4.2 versions of Zsh do word splitting on ${1+"$@"}, which
  # is contrary to our usage.  Disable this feature.
  alias -g '${1+"$@"}'='"$@"'
  setopt NO_GLOB_SUBST
else case e in #(
  e) case `(set -o) 2>/dev/null` in #(
  *posix*) :
    set -o posix ;; #(
  *) :
     ;;
esac ;;
esac
fi



# Reset variables that may have inherited troublesome values from
# the environment.

# IFS needs to be set, to space, tab, and newline, in precisely that order.
# (If _AS_PATH_WALK were called with IFS unset, it would have the
# side effect of setting IFS to empty, thus disabling word splitting.)
# Quoting is to prevent editors from complaining about space-tab.
as_nl='
'
export as_nl
IFS=" ""	$as_nl"

PS1='$ '
PS2='> '
PS4='+ '

# Ensure predictable behavior from utilities with locale-dependent output.
LC_ALL=C
export LC_ALL
LANGUAGE=C
export LANGUAGE

# We cannot yet rely on "unset" to work, but we need these variables
# to be unset--not just set to an empty or harmless value--now, to
# avoid bugs in old shells (e.g. pre-3.0 UWIN ksh).  This construct
# also avoids known problems related to "unset" and subshell syntax
# in other old shells (e.g. bash 2.01 and pdksh 5.2.14).
for as_var in BASH_ENV ENV MAIL MAILPATH CDPATH
do eval test \${$as_var+y} \
  && ( (unset $as_var) || exit 1) >/dev/null 2>&1 && unset $as_var || :
done

# Ensure that fds 0, 1, and 2 are open.
if (exec 3>&0) 2>/dev/null; then :; else exec 0</dev/null; fi
if (exec 3>&1) 2>/dev/null; then :; else exec 1>/dev/null; fi
if (exec 3>&2)            ; then :; else exec 2>/dev/null; fi

# The user is always right.
if ${PATH_SEPARATOR+false} :; then
  PATH_SEPARATOR=:
  (PATH='/bin;/bin'; FPATH=$PATH; sh -c :) >/dev/null 2>&1 && {
    (PATH='/bin:/bin'; FPATH=$PATH; sh -c :) >/dev/null 2>&1 ||
      PATH_SEPARATOR=';'
  }
fi


# Find who we are.  Look in the path if we contain no directory separator.
as_myself=
case $0 in #((
  *[\\/]* ) as_myself=$0 ;;
  *) as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
for as_dir in $PATH
do
  IFS=$as_save_IFS
  case $as_dir in #(((
    '') as_dir=./ ;;
    */) ;;
    *) as_dir=$as_dir/ ;;
  esac
    test -r "$as_dir$0" && as_myself=$as_dir$0 && break
  done
IFS=$as_save_IFS

     ;;
esac
# We did not find ourselves, most probably we were run as 'sh COMMAND'
# in which case we are not to be found in the path.
if test "x$as_myself" = x; then
  as_myself=$0
fi
if test ! -f "$as_myself"; then
  printf "%s\n" "$as_myself: error: cannot find myself; rerun with an absolute file name" >&2
  exit 1
fi



# as_fn_error STATUS ERROR [LINENO LOG_FD]
# ----------------------------------------
# Output "`basename $0`: error: ERROR" to stderr. If LINENO and LOG_FD are
# provided, also output the error to LOG_FD, referencing LINENO. Then exit the
# script with STATUS, using 1 if that was 0.
as_fn_error ()
{
  as_status=$1; test $as_status -eq 0 && as_status=1
  if test "$4"; then
    as_lineno=${as_lineno-"$3"} as_lineno_stack=as_lineno_stack=$as_lineno_stack
    printf "%s\n" "$as_me:${as_lineno-$LINENO}: error: $2" >&$4
  fi
  printf "%s\n" "$as_me: error: $2" >&2
  as_fn_exit $as_status
} # as_fn_error


# as_fn_set_status STATUS
# -----------------------
# Set $? to STATUS, without forking.
as_fn_set_status ()
{
  return $1
} # as_fn_set_status

# as_fn_exit STATUS
# -----------------
# Exit the shell with STATUS, even in a "trap 0" or "set -e" context.
as_fn_exit ()
{
  set +e
  as_fn_set_status $1
  exit $1
} # as_fn_exit

# as_fn_unset VAR
# ---------------
# Portably unset VAR.
as_fn_unset ()
{
  { eval $1=; unset $1;}
}
as_unset=as_fn_unset

# as_fn_append VAR VALUE
# ----------------------
# Append the text in VALUE to the end of the definition contained in VAR. Take
# advantage of any shell optimizations that allow amortized linear growth over
# repeated appends, instead of the typical quadratic growth present in naive
# implementations.
if (eval "as_var=1; as_var+=2; test x\$as_var = x12") 2>/dev/null
then :
  eval 'as_fn_append ()
  {
    eval $1+=\$2
  }'
else case e in #(
  e) as_fn_append ()
  {
    eval $1=\$$1\$2
  } ;;
esac
fi # as_fn_append

# as_fn_arith ARG...
# ------------------
# Perform arithmetic evaluation on the ARGs, and store the result in the
# global $as_val. Take advantage of shells that can avoid forks. The arguments
# must be portable across $(()) and expr.
if (eval "test \$(( 1 + 1 )) = 2") 2>/dev/null
then :
  eval 'as_fn_arith ()
  {
    as_val=$(( $* ))
  }'
else case e in #(
  e) as_fn_arith ()
  {
    as_val=`expr "$@" || test $? -eq 1`
  } ;;
esac
fi # as_fn_arith


if expr a : '\(a\)' >/dev/null 2>&1 &&
   test "X`expr 00001 : '.*\(...\)'`" = X001; then
  as_expr=expr
else
  as_expr=false
fi

if (basename -- /) >/dev/null 2>&1 && test "X`basename -- / 2>&1`" = "X/"; then
  as_basename=basename
else
  as_basename=false
fi

if (as_dir=`dirname -- /` && test "X$as_dir" = X/) >/dev/null 2>&1; then
  as_dirname=dirname
else
  as_dirname=false
fi

as_me=`$as_basename -- "$0" ||
$as_expr X/"$0" : '.*/\([^/][^/]*\)/*$' \| \
	 X"$0" : 'X\(//\)$' \| \
	 X"$0" : 'X\(/\)' \| . 2>/dev/null ||
printf "%s\n" X/"$0" |
    sed '/^.*\/\([^/][^/]*\)\/*$/{
	    s//\1/
	    q
	  }
	  /^X\/\(\/\/\)$/{
	    s//\1/
	    q
	  }
	  /^X\/\(\/\).*/{
	    s//\1/
	    q
	  }
	  s/.*/./; q'`

# Avoid depending upon Character Ranges.
as_cr_letters='abcdefghijklmnopqrstuvwxyz'
as_cr_LETTERS='ABCDEFGHIJKLMNOPQRSTUVWXYZ'
as_cr_Letters=$as_cr_letters$as_cr_LETTERS
as_cr_digits='0123456789'
as_cr_alnum=$as_cr_Letters$as_cr_digits


# Determine whether it's possible to make 'echo' print without a newline.
# These variables are no longer used directly by Autoconf, but are AC_SUBSTed
# for compatibility with existing Makefiles.
ECHO_C= ECHO_N= ECHO_T=
case `echo -n x` in #(((((
-n*)
  case `echo 'xy\c'` in
  *c*) ECHO_T='	';;	# ECHO_T is single tab character.
  xy)  ECHO_C='\c';;
  *)   echo `echo ksh88 bug on AIX 6.1` > /dev/null
       ECHO_T='	';;
  esac;;
*)
  ECHO_N='-n';;
esac

# For backward compatibility with old third-party macros, we provide
# the shell variables $as_echo and $as_echo_n.  New code should use
# AS_ECHO(["message"]) and AS_ECHO_N(["message"]), respectively.
as_echo='printf %s\n'
as_echo_n='printf %s'

rm -f conf$$ conf$$.exe conf$$.file
if test -d conf$$.dir; then
  rm -f conf$$.dir/conf$$.file
else
  rm -f conf$$.dir
  mkdir conf$$.dir 2>/dev/null
fi
if (echo >conf$$.file) 2>/dev/null; then
  if ln -s conf$$.file conf$$ 2>/dev/null; then
    as_ln_s='ln -s'
    # ... but there are two gotchas:
    # 1) On MSYS, both 'ln -s file dir' and 'ln file dir' fail.
    # 2) DJGPP < 2.04 has no symlinks; 'ln -s' creates a wrapper executable.
    # In both cases, we have to default to 'cp -pR'.
    ln -s conf$$.file conf$$.dir 2>/dev/null && test ! -f conf$$.exe ||
      as_ln_s='cp -pR'
  elif ln conf$$.file conf$$ 2>/dev/null; then
    as_ln_s=ln
  else
    as_ln_s='cp -pR'
  fi
else
  as_ln_s='cp -pR'
fi
rm -f conf$$ conf$$.exe conf$$.dir/conf$$.file conf$$.file
rmdir conf$$.dir 2>/dev/null


# as_fn_mkdir_p
# -------------
# Create "$as_dir" as a directory, including parents if necessary.
as_fn_mkdir_p ()
{

  case $as_dir in #(
  -*) as_dir=./$as_dir;;
  esac
  test -d "$as_dir" || eval $as_mkdir_p || {
    as_dirs=
    while :; do
      case $as_dir in #(
      *\'*) as_qdir=`printf "%s\n" "$as_dir" | sed "s/'/'\\\\\\\\''/g"`;; #'(
      *) as_qdir=$as_dir;;
      esac
      as_dirs="'$as_qdir' $as_dirs"
      as_dir=`$as_dirname -- "$as_dir" ||
$as_expr X"$as_dir" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \
	 X"$as_dir" : 'X\(//\)[^/]' \| \
	 X"$as_dir" : 'X\(//\)$' \| \
	 X"$as_dir" : 'X\(/\)' \| . 2>/dev/null ||
printf "%s\n" X"$as_dir" |
    sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{
	    s//\1/
	    q
	  }
	  /^X\(\/\/\)[^/].*/{
	    s//\1/
	    q
	  }
	  /^X\(\/\/\)$/{
	    s//\1/
	    q
	  }
	  /^X\(\/\).*/{
	    s//\1/
	    q
	  }
	  s/.*/./; q'`
      test -d "$as_dir" && break
    done
    test -z "$as_dirs" || eval "mkdir $as_dirs"
  } || test -d "$as_dir" || as_fn_error $? "cannot create directory $as_dir"


} # as_fn_mkdir_p
if mkdir -p . 2>/dev/null; then
  as_mkdir_p='mkdir -p "$as_dir"'
else
  test -d ./-p && rmdir ./-p
  as_mkdir_p=false
fi


# as_fn_executable_p FILE
# -----------------------
# Test if FILE is an executable regular file.
as_fn_executable_p ()
{
  test -f "$1" && test -x "$1"
} # as_fn_executable_p
as_test_x='test -x'
as_executable_p=as_fn_executable_p

# Sed expression to map a string onto a valid CPP name.
as_sed_cpp="y%*$as_cr_letters%P$as_cr_LETTERS%;s%[^_$as_cr_alnum]%_%g"
as_tr_cpp="eval sed '$as_sed_cpp'" # deprecated

# Sed expression to map a string onto a valid variable name.
as_sed_sh="y%*+%pp%;s%[^_$as_cr_alnum]%_%g"
as_tr_sh="eval sed '$as_sed_sh'" # deprecated


exec 6>&1
## ----------------------------------- ##
## Main body of $CONFIG_STATUS script. ##
## ----------------------------------- ##
_ASEOF
test $as_write_fail = 0 && chmod +x $CONFIG_STATUS || ac_write_fail=1

cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
# Save the log message, to keep $0 and so on meaningful, and to
# report actual input values of CONFIG_FILES etc. instead of their
# values after options handling.
ac_log="
This file was extended by BCFtools $as_me 1.19, which was
generated by GNU Autoconf 2.72d.  Invocation command line was

  CONFIG_FILES    = $CONFIG_FILES
  CONFIG_HEADERS  = $CONFIG_HEADERS
  CONFIG_LINKS    = $CONFIG_LINKS
  CONFIG_COMMANDS = $CONFIG_COMMANDS
  $ $0 $@

on `(hostname || uname -n) 2>/dev/null | sed 1q`
"

_ACEOF

case $ac_config_files in *"
"*) set x $ac_config_files; shift; ac_config_files=$*;;
esac

case $ac_config_headers in *"
"*) set x $ac_config_headers; shift; ac_config_headers=$*;;
esac


cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
# Files that config.status was made for.
config_files="$ac_config_files"
config_headers="$ac_config_headers"

_ACEOF

cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
ac_cs_usage="\
'$as_me' instantiates files and other configuration actions
from templates according to the current configuration.  Unless the files
and actions are specified as TAGs, all are instantiated by default.

Usage: $0 [OPTION]... [TAG]...

  -h, --help       print this help, then exit
  -V, --version    print version number and configuration settings, then exit
      --config     print configuration, then exit
  -q, --quiet, --silent
                   do not print progress messages
  -d, --debug      don't remove temporary files
      --recheck    update $as_me by reconfiguring in the same conditions
      --file=FILE[:TEMPLATE]
                   instantiate the configuration file FILE
      --header=FILE[:TEMPLATE]
                   instantiate the configuration header FILE

Configuration files:
$config_files

Configuration headers:
$config_headers

Report bugs to <samtools-help@lists.sourceforge.net>.
BCFtools home page: <http://www.htslib.org/>."

_ACEOF
ac_cs_config=`printf "%s\n" "$ac_configure_args" | sed "$ac_safe_unquote"`
ac_cs_config_escaped=`printf "%s\n" "$ac_cs_config" | sed "s/^ //; s/'/'\\\\\\\\''/g"`
cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
ac_cs_config='$ac_cs_config_escaped'
ac_cs_version="\\
BCFtools config.status 1.19
configured by $0, generated by GNU Autoconf 2.72d,
  with options \\"\$ac_cs_config\\"

Copyright (C) 2023 Free Software Foundation, Inc.
This config.status script is free software; the Free Software Foundation
gives unlimited permission to copy, distribute and modify it."

ac_pwd='$ac_pwd'
srcdir='$srcdir'
test -n "\$AWK" || AWK=awk
_ACEOF

cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
# The default lists apply if the user does not specify any file.
ac_need_defaults=:
while test $# != 0
do
  case $1 in
  --*=?*)
    ac_option=`expr "X$1" : 'X\([^=]*\)='`
    ac_optarg=`expr "X$1" : 'X[^=]*=\(.*\)'`
    ac_shift=:
    ;;
  --*=)
    ac_option=`expr "X$1" : 'X\([^=]*\)='`
    ac_optarg=
    ac_shift=:
    ;;
  *)
    ac_option=$1
    ac_optarg=$2
    ac_shift=shift
    ;;
  esac

  case $ac_option in
  # Handling of the options.
  -recheck | --recheck | --rechec | --reche | --rech | --rec | --re | --r)
    ac_cs_recheck=: ;;
  --version | --versio | --versi | --vers | --ver | --ve | --v | -V )
    printf "%s\n" "$ac_cs_version"; exit ;;
  --config | --confi | --conf | --con | --co | --c )
    printf "%s\n" "$ac_cs_config"; exit ;;
  --debug | --debu | --deb | --de | --d | -d )
    debug=: ;;
  --file | --fil | --fi | --f )
    $ac_shift
    case $ac_optarg in
    *\'*) ac_optarg=`printf "%s\n" "$ac_optarg" | sed "s/'/'\\\\\\\\''/g"` ;;
    '') as_fn_error $? "missing file argument" ;;
    esac
    as_fn_append CONFIG_FILES " '$ac_optarg'"
    ac_need_defaults=false;;
  --header | --heade | --head | --hea )
    $ac_shift
    case $ac_optarg in
    *\'*) ac_optarg=`printf "%s\n" "$ac_optarg" | sed "s/'/'\\\\\\\\''/g"` ;;
    esac
    as_fn_append CONFIG_HEADERS " '$ac_optarg'"
    ac_need_defaults=false;;
  --he | --h)
    # Conflict between --help and --header
    as_fn_error $? "ambiguous option: '$1'
Try '$0 --help' for more information.";;
  --help | --hel | -h )
    printf "%s\n" "$ac_cs_usage"; exit ;;
  -q | -quiet | --quiet | --quie | --qui | --qu | --q \
  | -silent | --silent | --silen | --sile | --sil | --si | --s)
    ac_cs_silent=: ;;

  # This is an error.
  -*) as_fn_error $? "unrecognized option: '$1'
Try '$0 --help' for more information." ;;

  *) as_fn_append ac_config_targets " $1"
     ac_need_defaults=false ;;

  esac
  shift
done

ac_configure_extra_args=

if $ac_cs_silent; then
  exec 6>/dev/null
  ac_configure_extra_args="$ac_configure_extra_args --silent"
fi

_ACEOF
cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
if \$ac_cs_recheck; then
  set X $SHELL '$0' $ac_configure_args \$ac_configure_extra_args --no-create --no-recursion
  shift
  \printf "%s\n" "running CONFIG_SHELL=$SHELL \$*" >&6
  CONFIG_SHELL='$SHELL'
  export CONFIG_SHELL
  exec "\$@"
fi

_ACEOF
cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
exec 5>>config.log
{
  echo
  sed 'h;s/./-/g;s/^.../## /;s/...$/ ##/;p;x;p;x' <<_ASBOX
## Running $as_me. ##
_ASBOX
  printf "%s\n" "$ac_log"
} >&5

_ACEOF
cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
_ACEOF

cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1

# Handling of arguments.
for ac_config_target in $ac_config_targets
do
  case $ac_config_target in
    "config.h") CONFIG_HEADERS="$CONFIG_HEADERS config.h" ;;
    "config.mk") CONFIG_FILES="$CONFIG_FILES config.mk" ;;

  *) as_fn_error $? "invalid argument: '$ac_config_target'" "$LINENO" 5;;
  esac
done


# If the user did not use the arguments to specify the items to instantiate,
# then the envvar interface is used.  Set only those that are not.
# We use the long form for the default assignment because of an extremely
# bizarre bug on SunOS 4.1.3.
if $ac_need_defaults; then
  test ${CONFIG_FILES+y} || CONFIG_FILES=$config_files
  test ${CONFIG_HEADERS+y} || CONFIG_HEADERS=$config_headers
fi

# Have a temporary directory for convenience.  Make it in the build tree
# simply because there is no reason against having it here, and in addition,
# creating and moving files from /tmp can sometimes cause problems.
# Hook for its removal unless debugging.
# Note that there is a small window in which the directory will not be cleaned:
# after its creation but before its name has been assigned to '$tmp'.
$debug ||
{
  tmp= ac_tmp=
  trap 'exit_status=$?
  : "${ac_tmp:=$tmp}"
  { test ! -d "$ac_tmp" || rm -fr "$ac_tmp"; } && exit $exit_status
' 0
  trap 'as_fn_exit 1' 1 2 13 15
}
# Create a (secure) tmp directory for tmp files.

{
  tmp=`(umask 077 && mktemp -d "./confXXXXXX") 2>/dev/null` &&
  test -d "$tmp"
}  ||
{
  tmp=./conf$$-$RANDOM
  (umask 077 && mkdir "$tmp")
} || as_fn_error $? "cannot create a temporary directory in ." "$LINENO" 5
ac_tmp=$tmp

# Set up the scripts for CONFIG_FILES section.
# No need to generate them if there are no CONFIG_FILES.
# This happens for instance with './config.status config.h'.
if test -n "$CONFIG_FILES"; then


ac_cr=`echo X | tr X '\015'`
# On cygwin, bash can eat \r inside `` if the user requested igncr.
# But we know of no other shell where ac_cr would be empty at this
# point, so we can use a bashism as a fallback.
if test "x$ac_cr" = x; then
  eval ac_cr=\$\'\\r\'
fi
ac_cs_awk_cr=`$AWK 'BEGIN { print "a\rb" }' </dev/null 2>/dev/null`
if test "$ac_cs_awk_cr" = "a${ac_cr}b"; then
  ac_cs_awk_cr='\\r'
else
  ac_cs_awk_cr=$ac_cr
fi

echo 'BEGIN {' >"$ac_tmp/subs1.awk" &&
_ACEOF


{
  echo "cat >conf$$subs.awk <<_ACEOF" &&
  echo "$ac_subst_vars" | sed 's/.*/&!$&$ac_delim/' &&
  echo "_ACEOF"
} >conf$$subs.sh ||
  as_fn_error $? "could not make $CONFIG_STATUS" "$LINENO" 5
ac_delim_num=`echo "$ac_subst_vars" | grep -c '^'`
ac_delim='%!_!# '
for ac_last_try in false false false false false :; do
  . ./conf$$subs.sh ||
    as_fn_error $? "could not make $CONFIG_STATUS" "$LINENO" 5

  ac_delim_n=`sed -n "s/.*$ac_delim\$/X/p" conf$$subs.awk | grep -c X`
  if test $ac_delim_n = $ac_delim_num; then
    break
  elif $ac_last_try; then
    as_fn_error $? "could not make $CONFIG_STATUS" "$LINENO" 5
  else
    ac_delim="$ac_delim!$ac_delim _$ac_delim!! "
  fi
done
rm -f conf$$subs.sh

cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
cat >>"\$ac_tmp/subs1.awk" <<\\_ACAWK &&
_ACEOF
sed -n '
h
s/^/S["/; s/!.*/"]=/
p
g
s/^[^!]*!//
:repl
t repl
s/'"$ac_delim"'$//
t delim
:nl
h
s/\(.\{148\}\)..*/\1/
t more1
s/["\\]/\\&/g; s/^/"/; s/$/\\n"\\/
p
n
b repl
:more1
s/["\\]/\\&/g; s/^/"/; s/$/"\\/
p
g
s/.\{148\}//
t nl
:delim
h
s/\(.\{148\}\)..*/\1/
t more2
s/["\\]/\\&/g; s/^/"/; s/$/"/
p
b
:more2
s/["\\]/\\&/g; s/^/"/; s/$/"\\/
p
g
s/.\{148\}//
t delim
' <conf$$subs.awk | sed '
/^[^""]/{
  N
  s/\n//
}
' >>$CONFIG_STATUS || ac_write_fail=1
rm -f conf$$subs.awk
cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
_ACAWK
cat >>"\$ac_tmp/subs1.awk" <<_ACAWK &&
  for (key in S) S_is_set[key] = 1
  FS = ""

}
{
  line = $ 0
  nfields = split(line, field, "@")
  substed = 0
  len = length(field[1])
  for (i = 2; i < nfields; i++) {
    key = field[i]
    keylen = length(key)
    if (S_is_set[key]) {
      value = S[key]
      line = substr(line, 1, len) "" value "" substr(line, len + keylen + 3)
      len += length(value) + length(field[++i])
      substed = 1
    } else
      len += 1 + keylen
  }

  print line
}

_ACAWK
_ACEOF
cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
if sed "s/$ac_cr//" < /dev/null > /dev/null 2>&1; then
  sed "s/$ac_cr\$//; s/$ac_cr/$ac_cs_awk_cr/g"
else
  cat
fi < "$ac_tmp/subs1.awk" > "$ac_tmp/subs.awk" \
  || as_fn_error $? "could not setup config files machinery" "$LINENO" 5
_ACEOF

# VPATH may cause trouble with some makes, so we remove sole $(srcdir),
# ${srcdir} and @srcdir@ entries from VPATH if srcdir is ".", strip leading and
# trailing colons and then remove the whole line if VPATH becomes empty
# (actually we leave an empty line to preserve line numbers).
if test "x$srcdir" = x.; then
  ac_vpsub='/^[	 ]*VPATH[	 ]*=[	 ]*/{
h
s///
s/^/:/
s/[	 ]*$/:/
s/:\$(srcdir):/:/g
s/:\${srcdir}:/:/g
s/:@srcdir@:/:/g
s/^:*//
s/:*$//
x
s/\(=[	 ]*\).*/\1/
G
s/\n//
s/^[^=]*=[	 ]*$//
}'
fi

cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
fi # test -n "$CONFIG_FILES"

# Set up the scripts for CONFIG_HEADERS section.
# No need to generate them if there are no CONFIG_HEADERS.
# This happens for instance with './config.status Makefile'.
if test -n "$CONFIG_HEADERS"; then
cat >"$ac_tmp/defines.awk" <<\_ACAWK ||
BEGIN {
_ACEOF

# Transform confdefs.h into an awk script 'defines.awk', embedded as
# here-document in config.status, that substitutes the proper values into
# config.h.in to produce config.h.

# Create a delimiter string that does not exist in confdefs.h, to ease
# handling of long lines.
ac_delim='%!_!# '
for ac_last_try in false false :; do
  ac_tt=`sed -n "/$ac_delim/p" confdefs.h`
  if test -z "$ac_tt"; then
    break
  elif $ac_last_try; then
    as_fn_error $? "could not make $CONFIG_HEADERS" "$LINENO" 5
  else
    ac_delim="$ac_delim!$ac_delim _$ac_delim!! "
  fi
done

# For the awk script, D is an array of macro values keyed by name,
# likewise P contains macro parameters if any.  Preserve backslash
# newline sequences.

ac_word_re=[_$as_cr_Letters][_$as_cr_alnum]*
sed -n '
s/.\{148\}/&'"$ac_delim"'/g
t rset
:rset
s/^[	 ]*#[	 ]*define[	 ][	 ]*/ /
t def
d
:def
s/\\$//
t bsnl
s/["\\]/\\&/g
s/^ \('"$ac_word_re"'\)\(([^()]*)\)[	 ]*\(.*\)/P["\1"]="\2"\
D["\1"]=" \3"/p
s/^ \('"$ac_word_re"'\)[	 ]*\(.*\)/D["\1"]=" \2"/p
d
:bsnl
s/["\\]/\\&/g
s/^ \('"$ac_word_re"'\)\(([^()]*)\)[	 ]*\(.*\)/P["\1"]="\2"\
D["\1"]=" \3\\\\\\n"\\/p
t cont
s/^ \('"$ac_word_re"'\)[	 ]*\(.*\)/D["\1"]=" \2\\\\\\n"\\/p
t cont
d
:cont
n
s/.\{148\}/&'"$ac_delim"'/g
t clear
:clear
s/\\$//
t bsnlc
s/["\\]/\\&/g; s/^/"/; s/$/"/p
d
:bsnlc
s/["\\]/\\&/g; s/^/"/; s/$/\\\\\\n"\\/p
b cont
' <confdefs.h | sed '
s/'"$ac_delim"'/"\\\
"/g' >>$CONFIG_STATUS || ac_write_fail=1

cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
  for (key in D) D_is_set[key] = 1
  FS = ""
}
/^[\t ]*#[\t ]*(define|undef)[\t ]+$ac_word_re([\t (]|\$)/ {
  line = \$ 0
  split(line, arg, " ")
  if (arg[1] == "#") {
    defundef = arg[2]
    mac1 = arg[3]
  } else {
    defundef = substr(arg[1], 2)
    mac1 = arg[2]
  }
  split(mac1, mac2, "(") #)
  macro = mac2[1]
  prefix = substr(line, 1, index(line, defundef) - 1)
  if (D_is_set[macro]) {
    # Preserve the white space surrounding the "#".
    print prefix "define", macro P[macro] D[macro]
    next
  } else {
    # Replace #undef with comments.  This is necessary, for example,
    # in the case of _POSIX_SOURCE, which is predefined and required
    # on some systems where configure will not decide to define it.
    if (defundef == "undef") {
      print "/*", prefix defundef, macro, "*/"
      next
    }
  }
}
{ print }
_ACAWK
_ACEOF
cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
  as_fn_error $? "could not setup config headers machinery" "$LINENO" 5
fi # test -n "$CONFIG_HEADERS"


eval set X "  :F $CONFIG_FILES  :H $CONFIG_HEADERS    "
shift
for ac_tag
do
  case $ac_tag in
  :[FHLC]) ac_mode=$ac_tag; continue;;
  esac
  case $ac_mode$ac_tag in
  :[FHL]*:*);;
  :L* | :C*:*) as_fn_error $? "invalid tag '$ac_tag'" "$LINENO" 5;;
  :[FH]-) ac_tag=-:-;;
  :[FH]*) ac_tag=$ac_tag:$ac_tag.in;;
  esac
  ac_save_IFS=$IFS
  IFS=:
  set x $ac_tag
  IFS=$ac_save_IFS
  shift
  ac_file=$1
  shift

  case $ac_mode in
  :L) ac_source=$1;;
  :[FH])
    ac_file_inputs=
    for ac_f
    do
      case $ac_f in
      -) ac_f="$ac_tmp/stdin";;
      *) # Look for the file first in the build tree, then in the source tree
	 # (if the path is not absolute).  The absolute path cannot be DOS-style,
	 # because $ac_f cannot contain ':'.
	 test -f "$ac_f" ||
	   case $ac_f in
	   [\\/$]*) false;;
	   *) test -f "$srcdir/$ac_f" && ac_f="$srcdir/$ac_f";;
	   esac ||
	   as_fn_error 1 "cannot find input file: '$ac_f'" "$LINENO" 5;;
      esac
      case $ac_f in *\'*) ac_f=`printf "%s\n" "$ac_f" | sed "s/'/'\\\\\\\\''/g"`;; esac
      as_fn_append ac_file_inputs " '$ac_f'"
    done

    # Let's still pretend it is 'configure' which instantiates (i.e., don't
    # use $as_me), people would be surprised to read:
    #    /* config.h.  Generated by config.status.  */
    configure_input='Generated from '`
	  printf "%s\n" "$*" | sed 's|^[^:]*/||;s|:[^:]*/|, |g'
	`' by configure.'
    if test x"$ac_file" != x-; then
      configure_input="$ac_file.  $configure_input"
      { printf "%s\n" "$as_me:${as_lineno-$LINENO}: creating $ac_file" >&5
printf "%s\n" "$as_me: creating $ac_file" >&6;}
    fi
    # Neutralize special characters interpreted by sed in replacement strings.
    case $configure_input in #(
    *\&* | *\|* | *\\* )
       ac_sed_conf_input=`printf "%s\n" "$configure_input" |
       sed 's/[\\\\&|]/\\\\&/g'`;; #(
    *) ac_sed_conf_input=$configure_input;;
    esac

    case $ac_tag in
    *:-:* | *:-) cat >"$ac_tmp/stdin" \
      || as_fn_error $? "could not create $ac_file" "$LINENO" 5 ;;
    esac
    ;;
  esac

  ac_dir=`$as_dirname -- "$ac_file" ||
$as_expr X"$ac_file" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \
	 X"$ac_file" : 'X\(//\)[^/]' \| \
	 X"$ac_file" : 'X\(//\)$' \| \
	 X"$ac_file" : 'X\(/\)' \| . 2>/dev/null ||
printf "%s\n" X"$ac_file" |
    sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{
	    s//\1/
	    q
	  }
	  /^X\(\/\/\)[^/].*/{
	    s//\1/
	    q
	  }
	  /^X\(\/\/\)$/{
	    s//\1/
	    q
	  }
	  /^X\(\/\).*/{
	    s//\1/
	    q
	  }
	  s/.*/./; q'`
  as_dir="$ac_dir"; as_fn_mkdir_p
  ac_builddir=.

case "$ac_dir" in
.) ac_dir_suffix= ac_top_builddir_sub=. ac_top_build_prefix= ;;
*)
  ac_dir_suffix=/`printf "%s\n" "$ac_dir" | sed 's|^\.[\\/]||'`
  # A ".." for each directory in $ac_dir_suffix.
  ac_top_builddir_sub=`printf "%s\n" "$ac_dir_suffix" | sed 's|/[^\\/]*|/..|g;s|/||'`
  case $ac_top_builddir_sub in
  "") ac_top_builddir_sub=. ac_top_build_prefix= ;;
  *)  ac_top_build_prefix=$ac_top_builddir_sub/ ;;
  esac ;;
esac
ac_abs_top_builddir=$ac_pwd
ac_abs_builddir=$ac_pwd$ac_dir_suffix
# for backward compatibility:
ac_top_builddir=$ac_top_build_prefix

case $srcdir in
  .)  # We are building in place.
    ac_srcdir=.
    ac_top_srcdir=$ac_top_builddir_sub
    ac_abs_top_srcdir=$ac_pwd ;;
  [\\/]* | ?:[\\/]* )  # Absolute name.
    ac_srcdir=$srcdir$ac_dir_suffix;
    ac_top_srcdir=$srcdir
    ac_abs_top_srcdir=$srcdir ;;
  *) # Relative name.
    ac_srcdir=$ac_top_build_prefix$srcdir$ac_dir_suffix
    ac_top_srcdir=$ac_top_build_prefix$srcdir
    ac_abs_top_srcdir=$ac_pwd/$srcdir ;;
esac
ac_abs_srcdir=$ac_abs_top_srcdir$ac_dir_suffix


  case $ac_mode in
  :F)
  #
  # CONFIG_FILE
  #

_ACEOF

cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
# If the template does not know about datarootdir, expand it.
# FIXME: This hack should be removed a few years after 2.60.
ac_datarootdir_hack=; ac_datarootdir_seen=
ac_sed_dataroot='
/datarootdir/ {
  p
  q
}
/@datadir@/p
/@docdir@/p
/@infodir@/p
/@localedir@/p
/@mandir@/p'
case `eval "sed -n \"\$ac_sed_dataroot\" $ac_file_inputs"` in
*datarootdir*) ac_datarootdir_seen=yes;;
*@datadir@*|*@docdir@*|*@infodir@*|*@localedir@*|*@mandir@*)
  { printf "%s\n" "$as_me:${as_lineno-$LINENO}: WARNING: $ac_file_inputs seems to ignore the --datarootdir setting" >&5
printf "%s\n" "$as_me: WARNING: $ac_file_inputs seems to ignore the --datarootdir setting" >&2;}
_ACEOF
cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
  ac_datarootdir_hack='
  s&@datadir@&$datadir&g
  s&@docdir@&$docdir&g
  s&@infodir@&$infodir&g
  s&@localedir@&$localedir&g
  s&@mandir@&$mandir&g
  s&\\\${datarootdir}&$datarootdir&g' ;;
esac
_ACEOF

# Neutralize VPATH when '$srcdir' = '.'.
# Shell code in configure.ac might set extrasub.
# FIXME: do we really want to maintain this feature?
cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
ac_sed_extra="$ac_vpsub
$extrasub
_ACEOF
cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
:t
/@[a-zA-Z_][a-zA-Z_0-9]*@/!b
s|@configure_input@|$ac_sed_conf_input|;t t
s&@top_builddir@&$ac_top_builddir_sub&;t t
s&@top_build_prefix@&$ac_top_build_prefix&;t t
s&@srcdir@&$ac_srcdir&;t t
s&@abs_srcdir@&$ac_abs_srcdir&;t t
s&@top_srcdir@&$ac_top_srcdir&;t t
s&@abs_top_srcdir@&$ac_abs_top_srcdir&;t t
s&@builddir@&$ac_builddir&;t t
s&@abs_builddir@&$ac_abs_builddir&;t t
s&@abs_top_builddir@&$ac_abs_top_builddir&;t t
$ac_datarootdir_hack
"
eval sed \"\$ac_sed_extra\" "$ac_file_inputs" | $AWK -f "$ac_tmp/subs.awk" \
  >$ac_tmp/out || as_fn_error $? "could not create $ac_file" "$LINENO" 5

test -z "$ac_datarootdir_hack$ac_datarootdir_seen" &&
  { ac_out=`sed -n '/\${datarootdir}/p' "$ac_tmp/out"`; test -n "$ac_out"; } &&
  { ac_out=`sed -n '/^[	 ]*datarootdir[	 ]*:*=/p' \
      "$ac_tmp/out"`; test -z "$ac_out"; } &&
  { printf "%s\n" "$as_me:${as_lineno-$LINENO}: WARNING: $ac_file contains a reference to the variable 'datarootdir'
which seems to be undefined.  Please make sure it is defined" >&5
printf "%s\n" "$as_me: WARNING: $ac_file contains a reference to the variable 'datarootdir'
which seems to be undefined.  Please make sure it is defined" >&2;}

  rm -f "$ac_tmp/stdin"
  case $ac_file in
  -) cat "$ac_tmp/out" && rm -f "$ac_tmp/out";;
  *) rm -f "$ac_file" && mv "$ac_tmp/out" "$ac_file";;
  esac \
  || as_fn_error $? "could not create $ac_file" "$LINENO" 5
 ;;
  :H)
  #
  # CONFIG_HEADER
  #
  if test x"$ac_file" != x-; then
    {
      printf "%s\n" "/* $configure_input  */" >&1 \
      && eval '$AWK -f "$ac_tmp/defines.awk"' "$ac_file_inputs"
    } >"$ac_tmp/config.h" \
      || as_fn_error $? "could not create $ac_file" "$LINENO" 5
    if diff "$ac_file" "$ac_tmp/config.h" >/dev/null 2>&1; then
      { printf "%s\n" "$as_me:${as_lineno-$LINENO}: $ac_file is unchanged" >&5
printf "%s\n" "$as_me: $ac_file is unchanged" >&6;}
    else
      rm -f "$ac_file"
      mv "$ac_tmp/config.h" "$ac_file" \
	|| as_fn_error $? "could not create $ac_file" "$LINENO" 5
    fi
  else
    printf "%s\n" "/* $configure_input  */" >&1 \
      && eval '$AWK -f "$ac_tmp/defines.awk"' "$ac_file_inputs" \
      || as_fn_error $? "could not create -" "$LINENO" 5
  fi
 ;;


  esac

done # for ac_tag


as_fn_exit 0
_ACEOF
ac_clean_files=$ac_clean_files_save

test $ac_write_fail = 0 ||
  as_fn_error $? "write failure creating $CONFIG_STATUS" "$LINENO" 5


# configure is writing to config.log, and then calls config.status.
# config.status does its own redirection, appending to config.log.
# Unfortunately, on DOS this fails, as config.log is still kept open
# by configure, so config.status won't be able to write to it; its
# output is simply discarded.  So we exec the FD to /dev/null,
# effectively closing config.log, so it can be properly (re)opened and
# appended to by config.status.  When coming back to configure, we
# need to make the FD available again.
if test "$no_create" != yes; then
  ac_cs_success=:
  ac_config_status_args=
  test "$silent" = yes &&
    ac_config_status_args="$ac_config_status_args --quiet"
  exec 5>/dev/null
  $SHELL $CONFIG_STATUS $ac_config_status_args || ac_cs_success=false
  exec 5>>config.log
  # Use ||, not &&, to avoid exiting from the if with $? = 1, which
  # would make configure fail if this is the last instruction.
  $ac_cs_success || as_fn_exit 1
fi

#
# CONFIG_SUBDIRS section.
#
if test "$no_recursion" != yes; then

  # Remove --cache-file, --srcdir, and --disable-option-checking arguments
  # so they do not pile up.
  ac_sub_configure_args=
  ac_prev=
  eval "set x $ac_configure_args"
  shift
  for ac_arg
  do
    if test -n "$ac_prev"; then
      ac_prev=
      continue
    fi
    case $ac_arg in
    -cache-file | --cache-file | --cache-fil | --cache-fi \
    | --cache-f | --cache- | --cache | --cach | --cac | --ca | --c)
      ac_prev=cache_file ;;
    -cache-file=* | --cache-file=* | --cache-fil=* | --cache-fi=* \
    | --cache-f=* | --cache-=* | --cache=* | --cach=* | --cac=* | --ca=* \
    | --c=*)
      ;;
    --config-cache | -C)
      ;;
    -srcdir | --srcdir | --srcdi | --srcd | --src | --sr)
      ac_prev=srcdir ;;
    -srcdir=* | --srcdir=* | --srcdi=* | --srcd=* | --src=* | --sr=*)
      ;;
    -prefix | --prefix | --prefi | --pref | --pre | --pr | --p)
      ac_prev=prefix ;;
    -prefix=* | --prefix=* | --prefi=* | --pref=* | --pre=* | --pr=* | --p=*)
      ;;
    --disable-option-checking)
      ;;
    *)
      case $ac_arg in
      *\'*) ac_arg=`printf "%s\n" "$ac_arg" | sed "s/'/'\\\\\\\\''/g"` ;;
      esac
      as_fn_append ac_sub_configure_args " '$ac_arg'" ;;
    esac
  done

  # Always prepend --prefix to ensure using the same prefix
  # in subdir configurations.
  ac_arg="--prefix=$prefix"
  case $ac_arg in
  *\'*) ac_arg=`printf "%s\n" "$ac_arg" | sed "s/'/'\\\\\\\\''/g"` ;;
  esac
  ac_sub_configure_args="'$ac_arg' $ac_sub_configure_args"

  # Pass --silent
  if test "$silent" = yes; then
    ac_sub_configure_args="--silent $ac_sub_configure_args"
  fi

  # Always prepend --disable-option-checking to silence warnings, since
  # different subdirs can have different --enable and --with options.
  ac_sub_configure_args="--disable-option-checking $ac_sub_configure_args"

  ac_popdir=`pwd`
  for ac_dir in : $subdirs; do test "x$ac_dir" = x: && continue

    # Do not complain, so a configure script can configure whichever
    # parts of a large source tree are present.
    test -d "$srcdir/$ac_dir" || continue

    ac_msg="=== configuring in $ac_dir (`pwd`/$ac_dir)"
    printf "%s\n" "$as_me:${as_lineno-$LINENO}: $ac_msg" >&5
    printf "%s\n" "$ac_msg" >&6
    as_dir="$ac_dir"; as_fn_mkdir_p
    ac_builddir=.

case "$ac_dir" in
.) ac_dir_suffix= ac_top_builddir_sub=. ac_top_build_prefix= ;;
*)
  ac_dir_suffix=/`printf "%s\n" "$ac_dir" | sed 's|^\.[\\/]||'`
  # A ".." for each directory in $ac_dir_suffix.
  ac_top_builddir_sub=`printf "%s\n" "$ac_dir_suffix" | sed 's|/[^\\/]*|/..|g;s|/||'`
  case $ac_top_builddir_sub in
  "") ac_top_builddir_sub=. ac_top_build_prefix= ;;
  *)  ac_top_build_prefix=$ac_top_builddir_sub/ ;;
  esac ;;
esac
ac_abs_top_builddir=$ac_pwd
ac_abs_builddir=$ac_pwd$ac_dir_suffix
# for backward compatibility:
ac_top_builddir=$ac_top_build_prefix

case $srcdir in
  .)  # We are building in place.
    ac_srcdir=.
    ac_top_srcdir=$ac_top_builddir_sub
    ac_abs_top_srcdir=$ac_pwd ;;
  [\\/]* | ?:[\\/]* )  # Absolute name.
    ac_srcdir=$srcdir$ac_dir_suffix;
    ac_top_srcdir=$srcdir
    ac_abs_top_srcdir=$srcdir ;;
  *) # Relative name.
    ac_srcdir=$ac_top_build_prefix$srcdir$ac_dir_suffix
    ac_top_srcdir=$ac_top_build_prefix$srcdir
    ac_abs_top_srcdir=$ac_pwd/$srcdir ;;
esac
ac_abs_srcdir=$ac_abs_top_srcdir$ac_dir_suffix


    cd "$ac_dir"

    # Check for configure.gnu first; this name is used for a wrapper for
    # Metaconfig's "Configure" on case-insensitive file systems.
    if test -f "$ac_srcdir/configure.gnu"; then
      ac_sub_configure=$ac_srcdir/configure.gnu
    elif test -f "$ac_srcdir/configure"; then
      ac_sub_configure=$ac_srcdir/configure
    else
      { printf "%s\n" "$as_me:${as_lineno-$LINENO}: WARNING: no configuration information is in $ac_dir" >&5
printf "%s\n" "$as_me: WARNING: no configuration information is in $ac_dir" >&2;}
      ac_sub_configure=
    fi

    # The recursion is here.
    if test -n "$ac_sub_configure"; then
      # Make the cache file name correct relative to the subdirectory.
      case $cache_file in
      [\\/]* | ?:[\\/]* ) ac_sub_cache_file=$cache_file ;;
      *) # Relative name.
	ac_sub_cache_file=$ac_top_build_prefix$cache_file ;;
      esac

      { printf "%s\n" "$as_me:${as_lineno-$LINENO}: running $SHELL $ac_sub_configure $ac_sub_configure_args --cache-file=$ac_sub_cache_file --srcdir=$ac_srcdir" >&5
printf "%s\n" "$as_me: running $SHELL $ac_sub_configure $ac_sub_configure_args --cache-file=$ac_sub_cache_file --srcdir=$ac_srcdir" >&6;}
      # The eval makes quoting arguments work.
      eval "\$SHELL \"\$ac_sub_configure\" $ac_sub_configure_args \
	   --cache-file=\"\$ac_sub_cache_file\" --srcdir=\"\$ac_srcdir\"" ||
	as_fn_error $? "$ac_sub_configure failed for $ac_dir" "$LINENO" 5
    fi

    cd "$ac_popdir"
  done
fi
if test -n "$ac_unrecognized_opts" && test "$enable_option_checking" != no; then
  { printf "%s\n" "$as_me:${as_lineno-$LINENO}: WARNING: unrecognized options: $ac_unrecognized_opts" >&5
printf "%s\n" "$as_me: WARNING: unrecognized options: $ac_unrecognized_opts" >&2;}
fi


if test "x$USE_GPL" != "x"
then :
    { printf "%s\n" "$as_me:${as_lineno-$LINENO}: License has been changed to GPL.

Linking against the GNU scientific library requires that the resulting
binary is licensed using the GNU General Public License.  In particular,
this means you will have to follow the terms of this license in order
to distribute binary copies.  For more information see the INSTALL file.

Text of the GNU General Public License can be found in the LICENSE file,
or at http://www.gnu.org/copyleft/gpl.html

Information on the GNU Scientific Library, including the rationale for
its choice of license can be found at https://www.gnu.org/software/gsl/
" >&5
printf "%s\n" "$as_me: License has been changed to GPL.

Linking against the GNU scientific library requires that the resulting
binary is licensed using the GNU General Public License.  In particular,
this means you will have to follow the terms of this license in order
to distribute binary copies.  For more information see the INSTALL file.

Text of the GNU General Public License can be found in the LICENSE file,
or at http://www.gnu.org/copyleft/gpl.html

Information on the GNU Scientific Library, including the rationale for
its choice of license can be found at https://www.gnu.org/software/gsl/
" >&6;}
fi

