@@ -596,6 +596,42 @@ fi

 rmdir .tst 2>/dev/null

 AC_SUBST([am__leading_dot])])

+# Add --enable-maintainer-mode option to configure.         -*- Autoconf -*-

+# From Jim Meyering

+

+# Copyright (C) 1996-2013 Free Software Foundation, Inc.

+#

+# This file is free software; the Free Software Foundation

+# gives unlimited permission to copy and/or distribute it,

+# with or without modifications, as long as this notice is preserved.

+

+# AM_MAINTAINER_MODE([DEFAULT-MODE])

+# ----------------------------------

+# Control maintainer-specific portions of Makefiles.

+# Default is to disable them, unless 'enable' is passed literally.

+# For symmetry, 'disable' may be passed as well.  Anyway, the user

+# can override the default with the --enable/--disable switch.

+AC_DEFUN([AM_MAINTAINER_MODE],

+[m4_case(m4_default([$1], [disable]),

+       [enable], [m4_define([am_maintainer_other], [disable])],

+       [disable], [m4_define([am_maintainer_other], [enable])],

+       [m4_define([am_maintainer_other], [enable])

+        m4_warn([syntax], [unexpected argument to AM@&t@_MAINTAINER_MODE: $1])])

+AC_MSG_CHECKING([whether to enable maintainer-specific portions of Makefiles])

+  dnl maintainer-mode's default is 'disable' unless 'enable' is passed

+  AC_ARG_ENABLE([maintainer-mode],

+    [AS_HELP_STRING([--]am_maintainer_other[-maintainer-mode],

+      am_maintainer_other[ make rules and dependencies not useful

+      (and sometimes confusing) to the casual installer])],

+    [USE_MAINTAINER_MODE=$enableval],

+    [USE_MAINTAINER_MODE=]m4_if(am_maintainer_other, [enable], [no], [yes]))

+  AC_MSG_RESULT([$USE_MAINTAINER_MODE])

+  AM_CONDITIONAL([MAINTAINER_MODE], [test $USE_MAINTAINER_MODE = yes])

+  MAINT=$MAINTAINER_MODE_TRUE

+  AC_SUBST([MAINT])dnl

+]

+)

+

 # Check to see how 'make' treats includes.	            -*- Autoconf -*-

 # Copyright (C) 2001-2013 Free Software Foundation, Inc.

@@ -676,6 +676,9 @@ MAINTAINER_FALSE

 MAINTAINER_TRUE

 FULLDIST_FALSE

 FULLDIST_TRUE

+MAINT

+MAINTAINER_MODE_FALSE

+MAINTAINER_MODE_TRUE

 AM_BACKSLASH

 AM_DEFAULT_VERBOSITY

 AM_DEFAULT_V

@@ -776,6 +779,7 @@ enable_option_checking

 enable_largefile

 enable_dependency_tracking

 enable_silent_rules

+enable_maintainer_mode

 enable_fulldist

 enable_maintainer

 enable_shared

@@ -1429,6 +1433,9 @@ Optional Features:

                           speeds up one-time build

   --enable-silent-rules   less verbose build output (undo: "make V=1")

   --disable-silent-rules  verbose build output (undo: "make V=0")

+  --disable-maintainer-mode

+                          disable make rules and dependencies not useful (and

+                          sometimes confusing) to the casual installer

   --enable-fulldist       For use by program maintainer

   --enable-maintainer     For use by program maintainer

   --enable-shared[=PKGS]  build shared libraries [default=yes]

@@ -4421,6 +4428,29 @@ fi

+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether to enable maintainer-specific portions of Makefiles" >&5

+$as_echo_n "checking whether to enable maintainer-specific portions of Makefiles... " >&6; }

+    # Check whether --enable-maintainer-mode was given.

+if test "${enable_maintainer_mode+set}" = set; then :

+  enableval=$enable_maintainer_mode; USE_MAINTAINER_MODE=$enableval

+else

+  USE_MAINTAINER_MODE=yes

+fi

+

+  { $as_echo "$as_me:${as_lineno-$LINENO}: result: $USE_MAINTAINER_MODE" >&5

+$as_echo "$USE_MAINTAINER_MODE" >&6; }

+   if test $USE_MAINTAINER_MODE = yes; then

+  MAINTAINER_MODE_TRUE=

+  MAINTAINER_MODE_FALSE='#'

+else

+  MAINTAINER_MODE_TRUE='#'

+  MAINTAINER_MODE_FALSE=

+fi

+

+  MAINT=$MAINTAINER_MODE_TRUE

+

+

+

  if test "x$enable_fulldist" = xyes; then

   FULLDIST_TRUE=

   FULLDIST_FALSE='#'

@@ -16597,6 +16627,10 @@ else

   am__EXEEXT_FALSE=

 fi

+if test -z "${MAINTAINER_MODE_TRUE}" && test -z "${MAINTAINER_MODE_FALSE}"; then

+  as_fn_error $? "conditional \"MAINTAINER_MODE\" was never defined.

+Usually this means the macro was only invoked conditionally." "$LINENO" 5

+fi

 if test -z "${FULLDIST_TRUE}" && test -z "${FULLDIST_FALSE}"; then

   as_fn_error $? "conditional \"FULLDIST\" was never defined.

 Usually this means the macro was only invoked conditionally." "$LINENO" 5

@@ -596,6 +596,42 @@ fi

 rmdir .tst 2>/dev/null

 AC_SUBST([am__leading_dot])])

+# Add --enable-maintainer-mode option to configure.         -*- Autoconf -*-

+# From Jim Meyering

+

+# Copyright (C) 1996-2013 Free Software Foundation, Inc.

+#

+# This file is free software; the Free Software Foundation

+# gives unlimited permission to copy and/or distribute it,

+# with or without modifications, as long as this notice is preserved.

+

+# AM_MAINTAINER_MODE([DEFAULT-MODE])

+# ----------------------------------

+# Control maintainer-specific portions of Makefiles.

+# Default is to disable them, unless 'enable' is passed literally.

+# For symmetry, 'disable' may be passed as well.  Anyway, the user

+# can override the default with the --enable/--disable switch.

+AC_DEFUN([AM_MAINTAINER_MODE],

+[m4_case(m4_default([$1], [disable]),

+       [enable], [m4_define([am_maintainer_other], [disable])],

+       [disable], [m4_define([am_maintainer_other], [enable])],

+       [m4_define([am_maintainer_other], [enable])

+        m4_warn([syntax], [unexpected argument to AM@&t@_MAINTAINER_MODE: $1])])

+AC_MSG_CHECKING([whether to enable maintainer-specific portions of Makefiles])

+  dnl maintainer-mode's default is 'disable' unless 'enable' is passed

+  AC_ARG_ENABLE([maintainer-mode],

+    [AS_HELP_STRING([--]am_maintainer_other[-maintainer-mode],

+      am_maintainer_other[ make rules and dependencies not useful

+      (and sometimes confusing) to the casual installer])],

+    [USE_MAINTAINER_MODE=$enableval],

+    [USE_MAINTAINER_MODE=]m4_if(am_maintainer_other, [enable], [no], [yes]))

+  AC_MSG_RESULT([$USE_MAINTAINER_MODE])

+  AM_CONDITIONAL([MAINTAINER_MODE], [test $USE_MAINTAINER_MODE = yes])

+  MAINT=$MAINTAINER_MODE_TRUE

+  AC_SUBST([MAINT])dnl

+]

+)

+

 # Check to see how 'make' treats includes.	            -*- Autoconf -*-

 # Copyright (C) 2001-2013 Free Software Foundation, Inc.

@@ -684,6 +684,9 @@ MAINTAINER_FALSE

 MAINTAINER_TRUE

 FULLDIST_FALSE

 FULLDIST_TRUE

+MAINT

+MAINTAINER_MODE_FALSE

+MAINTAINER_MODE_TRUE

 AM_BACKSLASH

 AM_DEFAULT_VERBOSITY

 AM_DEFAULT_V

@@ -786,6 +789,7 @@ enable_option_checking

 enable_largefile

 enable_dependency_tracking

 enable_silent_rules

+enable_maintainer_mode

 enable_fulldist

 enable_maintainer

 enable_static_linking

@@ -1437,6 +1441,9 @@ Optional Features:

                           speeds up one-time build

   --enable-silent-rules   less verbose build output (undo: "make V=1")

   --disable-silent-rules  verbose build output (undo: "make V=0")

+  --disable-maintainer-mode

+                          disable make rules and dependencies not useful (and

+                          sometimes confusing) to the casual installer

   --enable-fulldist       For use by program maintainer

   --enable-maintainer     For use by program maintainer

   --enable-static-linking Link binaries statically (default=no)

@@ -4425,6 +4432,29 @@ fi

+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether to enable maintainer-specific portions of Makefiles" >&5

+$as_echo_n "checking whether to enable maintainer-specific portions of Makefiles... " >&6; }

+    # Check whether --enable-maintainer-mode was given.

+if test "${enable_maintainer_mode+set}" = set; then :

+  enableval=$enable_maintainer_mode; USE_MAINTAINER_MODE=$enableval

+else

+  USE_MAINTAINER_MODE=yes

+fi

+

+  { $as_echo "$as_me:${as_lineno-$LINENO}: result: $USE_MAINTAINER_MODE" >&5

+$as_echo "$USE_MAINTAINER_MODE" >&6; }

+   if test $USE_MAINTAINER_MODE = yes; then

+  MAINTAINER_MODE_TRUE=

+  MAINTAINER_MODE_FALSE='#'

+else

+  MAINTAINER_MODE_TRUE='#'

+  MAINTAINER_MODE_FALSE=

+fi

+

+  MAINT=$MAINTAINER_MODE_TRUE

+

+

+

  if test "x$enable_fulldist" = xyes; then

   FULLDIST_TRUE=

   FULLDIST_FALSE='#'

@@ -15427,6 +15457,10 @@ else

   am__EXEEXT_FALSE=

 fi

+if test -z "${MAINTAINER_MODE_TRUE}" && test -z "${MAINTAINER_MODE_FALSE}"; then

+  as_fn_error $? "conditional \"MAINTAINER_MODE\" was never defined.

+Usually this means the macro was only invoked conditionally." "$LINENO" 5

+fi

 if test -z "${FULLDIST_TRUE}" && test -z "${FULLDIST_FALSE}"; then

   as_fn_error $? "conditional \"FULLDIST\" was never defined.

 Usually this means the macro was only invoked conditionally." "$LINENO" 5

@@ -93,7 +93,7 @@

 #define HAVE_RINT 1

 /* Define to 1 if you have a working Samtools library. */

-#define HAVE_SAMTOOLS 1

+/* #undef HAVE_SAMTOOLS */

 /* Define to 1 if you have the `sigaction' function. */

 #define HAVE_SIGACTION 1