switched to autoreconf

.gitignore

@@ -10,3 +10,4 @@ autom4te.cache/
 /depcomp
 src/.deps/
 /src/prokgc
+/examples/Makefile

AUTHORS

@@ -0,0 +1 @@
+Samuel Barreto  first version of all files except kseq.h of course

ChangeLog

@@ -0,0 +1,3 @@
+2017-05-16  Samuel Barreto  <[email protected]>
+
+	* first version of program

configure

@@ -1692,6 +1692,60 @@ $as_echo "$ac_res" >&6; }
   eval $as_lineno_stack; ${as_lineno_stack:+:} unset as_lineno
 
 } # ac_fn_c_check_header_compile
+
+# ac_fn_c_check_type LINENO TYPE VAR INCLUDES
+# -------------------------------------------
+# Tests whether TYPE exists after having included INCLUDES, setting cache
+# variable VAR accordingly.
+ac_fn_c_check_type ()
+{
+  as_lineno=${as_lineno-"$1"} as_lineno_stack=as_lineno_stack=$as_lineno_stack
+  { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $2" >&5
+$as_echo_n "checking for $2... " >&6; }
+if eval \${$3+:} false; then :
+  $as_echo_n "(cached) " >&6
+else
+  eval "$3=no"
+  cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h.  */
+$4
+int
+main ()
+{
+if (sizeof ($2))
+	 return 0;
+  ;
+  return 0;
+}
+_ACEOF
+if ac_fn_c_try_compile "$LINENO"; then :
+  cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h.  */
+$4
+int
+main ()
+{
+if (sizeof (($2)))
+	    return 0;
+  ;
+  return 0;
+}
+_ACEOF
+if ac_fn_c_try_compile "$LINENO"; then :
+
+else
+  eval "$3=yes"
+fi
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+fi
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+fi
+eval ac_res=\$$3
+	       { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_res" >&5
+$as_echo "$ac_res" >&6; }
+  eval $as_lineno_stack; ${as_lineno_stack:+:} unset as_lineno
+
+} # ac_fn_c_check_type
 cat >config.log <<_ACEOF
 This file contains any messages produced by compilers while
 running configure, to aid debugging if configure makes a mistake.
@@ -2045,7 +2099,7 @@ ac_compiler_gnu=$ac_cv_c_compiler_gnu
 
 
 
-ac_config_files="$ac_config_files Makefile src/Makefile examples/Makefile"
+ac_config_files="$ac_config_files Makefile examples/Makefile src/Makefile"
 
 am__api_version='1.15'
 
@@ -4325,8 +4379,197 @@ done
 
 
 # Checks for typedefs, structures, and compiler characteristics.
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for inline" >&5
+$as_echo_n "checking for inline... " >&6; }
+if ${ac_cv_c_inline+:} false; then :
+  $as_echo_n "(cached) " >&6
+else
+  ac_cv_c_inline=no
+for ac_kw in inline __inline__ __inline; do
+  cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h.  */
+#ifndef __cplusplus
+typedef int foo_t;
+static $ac_kw foo_t static_foo () {return 0; }
+$ac_kw foo_t foo () {return 0; }
+#endif
+
+_ACEOF
+if ac_fn_c_try_compile "$LINENO"; then :
+  ac_cv_c_inline=$ac_kw
+fi
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+  test "$ac_cv_c_inline" != no && break
+done
+
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_c_inline" >&5
+$as_echo "$ac_cv_c_inline" >&6; }
+
+case $ac_cv_c_inline in
+  inline | yes) ;;
+  *)
+    case $ac_cv_c_inline in
+      no) ac_val=;;
+      *) ac_val=$ac_cv_c_inline;;
+    esac
+    cat >>confdefs.h <<_ACEOF
+#ifndef __cplusplus
+#define inline $ac_val
+#endif
+_ACEOF
+    ;;
+esac
+
+ac_fn_c_check_type "$LINENO" "size_t" "ac_cv_type_size_t" "$ac_includes_default"
+if test "x$ac_cv_type_size_t" = xyes; then :
+
+else
+
+cat >>confdefs.h <<_ACEOF
+#define size_t unsigned int
+_ACEOF
+
+fi
+
 
 # Checks for library functions.
+for ac_header in stdlib.h
+do :
+  ac_fn_c_check_header_mongrel "$LINENO" "stdlib.h" "ac_cv_header_stdlib_h" "$ac_includes_default"
+if test "x$ac_cv_header_stdlib_h" = xyes; then :
+  cat >>confdefs.h <<_ACEOF
+#define HAVE_STDLIB_H 1
+_ACEOF
+
+fi
+
+done
+
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for GNU libc compatible malloc" >&5
+$as_echo_n "checking for GNU libc compatible malloc... " >&6; }
+if ${ac_cv_func_malloc_0_nonnull+:} false; then :
+  $as_echo_n "(cached) " >&6
+else
+  if test "$cross_compiling" = yes; then :
+  ac_cv_func_malloc_0_nonnull=no
+else
+  cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h.  */
+#if defined STDC_HEADERS || defined HAVE_STDLIB_H
+# include <stdlib.h>
+#else
+char *malloc ();
+#endif
+
+int
+main ()
+{
+return ! malloc (0);
+  ;
+  return 0;
+}
+_ACEOF
+if ac_fn_c_try_run "$LINENO"; then :
+  ac_cv_func_malloc_0_nonnull=yes
+else
+  ac_cv_func_malloc_0_nonnull=no
+fi
+rm -f core *.core core.conftest.* gmon.out bb.out conftest$ac_exeext \
+  conftest.$ac_objext conftest.beam conftest.$ac_ext
+fi
+
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_func_malloc_0_nonnull" >&5
+$as_echo "$ac_cv_func_malloc_0_nonnull" >&6; }
+if test $ac_cv_func_malloc_0_nonnull = yes; then :
+
+$as_echo "#define HAVE_MALLOC 1" >>confdefs.h
+
+else
+  $as_echo "#define HAVE_MALLOC 0" >>confdefs.h
+
+   case " $LIBOBJS " in
+  *" malloc.$ac_objext "* ) ;;
+  *) LIBOBJS="$LIBOBJS malloc.$ac_objext"
+ ;;
+esac
+
+
+$as_echo "#define malloc rpl_malloc" >>confdefs.h
+
+fi
+
+
+for ac_header in stdlib.h
+do :
+  ac_fn_c_check_header_mongrel "$LINENO" "stdlib.h" "ac_cv_header_stdlib_h" "$ac_includes_default"
+if test "x$ac_cv_header_stdlib_h" = xyes; then :
+  cat >>confdefs.h <<_ACEOF
+#define HAVE_STDLIB_H 1
+_ACEOF
+
+fi
+
+done
+
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for GNU libc compatible realloc" >&5
+$as_echo_n "checking for GNU libc compatible realloc... " >&6; }
+if ${ac_cv_func_realloc_0_nonnull+:} false; then :
+  $as_echo_n "(cached) " >&6
+else
+  if test "$cross_compiling" = yes; then :
+  ac_cv_func_realloc_0_nonnull=no
+else
+  cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h.  */
+#if defined STDC_HEADERS || defined HAVE_STDLIB_H
+# include <stdlib.h>
+#else
+char *realloc ();
+#endif
+
+int
+main ()
+{
+return ! realloc (0, 0);
+  ;
+  return 0;
+}
+_ACEOF
+if ac_fn_c_try_run "$LINENO"; then :
+  ac_cv_func_realloc_0_nonnull=yes
+else
+  ac_cv_func_realloc_0_nonnull=no
+fi
+rm -f core *.core core.conftest.* gmon.out bb.out conftest$ac_exeext \
+  conftest.$ac_objext conftest.beam conftest.$ac_ext
+fi
+
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_func_realloc_0_nonnull" >&5
+$as_echo "$ac_cv_func_realloc_0_nonnull" >&6; }
+if test $ac_cv_func_realloc_0_nonnull = yes; then :
+
+$as_echo "#define HAVE_REALLOC 1" >>confdefs.h
+
+else
+  $as_echo "#define HAVE_REALLOC 0" >>confdefs.h
+
+   case " $LIBOBJS " in
+  *" realloc.$ac_objext "* ) ;;
+  *) LIBOBJS="$LIBOBJS realloc.$ac_objext"
+ ;;
+esac
+
+
+$as_echo "#define realloc rpl_realloc" >>confdefs.h
+
+fi
+
+
+
+
 
 cat >confcache <<\_ACEOF
 # This file is a shell script that caches the results of configure
@@ -5070,8 +5313,8 @@ for ac_config_target in $ac_config_targets
 do
   case $ac_config_target in
     "Makefile") CONFIG_FILES="$CONFIG_FILES Makefile" ;;
-    "src/Makefile") CONFIG_FILES="$CONFIG_FILES src/Makefile" ;;
     "examples/Makefile") CONFIG_FILES="$CONFIG_FILES examples/Makefile" ;;
+    "src/Makefile") CONFIG_FILES="$CONFIG_FILES src/Makefile" ;;
     "depfiles") CONFIG_COMMANDS="$CONFIG_COMMANDS depfiles" ;;
 
   *) as_fn_error $? "invalid argument: \`$ac_config_target'" "$LINENO" 5;;

configure.ac

@@ -4,7 +4,7 @@
 AC_PREREQ([2.69])
 AC_INIT(prokgc, 0.0.1, [email protected])
 AC_CONFIG_SRCDIR([src/prokgc.c])
-AC_CONFIG_FILES([Makefile] [src/Makefile] [examples/Makefile])
+AC_CONFIG_FILES([Makefile examples/Makefile src/Makefile])
 AM_INIT_AUTOMAKE
 
 : ${CFLAGS="-g -Wall -O3 -std=gnu99"}
@@ -18,7 +18,13 @@ PKG_CHECK_MODULES([DEPS], [glib-2.0 >= 2.50.0])
 AC_CHECK_HEADERS([stdlib.h string.h])
 
 # Checks for typedefs, structures, and compiler characteristics.
+AC_C_INLINE
+AC_TYPE_SIZE_T
 
 # Checks for library functions.
+AC_FUNC_MALLOC
+AC_FUNC_REALLOC
+
+
 
 AC_OUTPUT

examples/Makefile.am

@@ -0,0 +1,2 @@
+example.csv:
+	prokgc --cds example_cds.fasta --genome example_genome.fasta --taxid 1234