Changeset 3068

Timestamp:

Aug 1, 2013, 5:16:44 AM (10 years ago)

Author:

Peter

Message:

Fixes #766

Replace #defines HAVE_BAM_H (and friends) in
yat/utility/config_public.h with #defines YAT_HAVE_BAM_H (and
friends). Update logic in yat/omic/config_bam.h accordingly as well as
test code in libbam detection.

Location:

trunk

Files:

• NEWS (modified) (1 diff)
• m4/yat_check_libbam.m4 (modified) (6 diffs)
• yat/omic/config_bam.h (modified) (1 diff)
• yat/utility/config_public.h.in (modified) (1 diff)

trunk/NEWS

@@ -11 +11 @@
   - tTest::score(void) is now declared const (ticket #755)
   - BamReadIterator(4) will now throw if region is invalid (ticket #764)
+  - #defines HAVE_BAM_H, HAVE_BAM_BAM_H, and HAVE_SAMTOOLS_BAM_H have been
+    replaced with corresponding macros with prefix 'YAT_' (see ticket #766)
 
   A complete list of closed tickets can be found here [[br]]

trunk/m4/yat_check_libbam.m4

@@ -1 +1 @@
 ## $Id$
 #
-# serial 2 (yat 0.10.2)
+# serial 3 (yat 0.11)
 #
 #
@@ -28 +28 @@
 yat_bam_header=no
 # check how to #include <bam.h>
-AC_CHECK_HEADERS([bam/bam.h bam.h samtools/bam.h bam.h],
-                 [yat_bam_header=yes; break])
+m4_map_args_w([bam/bam.h bam.h samtools/bam.h],
+              [_YAT_CHECK_HEADER_BAM(], [)
+])
 AS_IF([test x$yat_bam_header = xyes], [$1], [$2])
 ]) # YAT_CHECK_HEADER_BAM
+
+
+# _YAT_CHECK_HEADER_BAM
+# =====================
+# Private macro used in YAT_CHECK_HEADER_BAM
+AC_DEFUN([_YAT_CHECK_HEADER_BAM],
+[
+AS_IF([test x$yat_bam_header = xno], [dnl
+  AC_CHECK_HEADER([$1], [
+    AC_DEFINE_UNQUOTED(AS_TR_CPP([YAT_HAVE_$1]), [1],
+                       [Define to 1 if you have <$1> header file])
+    yat_bam_header=yes;
+  ])
+])
+]) # _YAT_CHECK_HEADER_BAM
 
 
@@ -39 +55 @@
 AC_DEFUN([YAT_CHECK_LIBBAM],
 [
-AC_REQUIRE([YAT_CHECK_HEADER_BAM])
 BAM_LIBS=no
 AC_MSG_CHECKING([for library containing bam_header_destroy])
@@ -64 +79 @@
 save_LIBS=$LIBS
 LIBS="$1 $LIBS"
-AC_LINK_IFELSE([AC_LANG_PROGRAM([@%:@if HAVE_BAM_H
-                                 @%:@ include <bam.h>
-                                 @%:@elif HAVE_BAM_BAM_H
-                                 @%:@ include <bam/bam.h>
-                                 @%:@elif HAVE_SAMTOOLS_BAM_H
-                                 @%:@ include <samtools/bam.h>
-                                 @%:@endif
-                                ],[
+AC_LINK_IFELSE([AC_LANG_PROGRAM([_YAT_BAM_INCLUDES],
+                                [
                                  bam_header_t* hdr = bam_header_init();
                                  bam_header_destroy(hdr);
@@ -86 +95 @@
 [
 AC_MSG_CHECKING([for bam_nt16_rev_table])
-AC_LINK_IFELSE([AC_LANG_PROGRAM(
-                 [@%:@if HAVE_BAM_H
-                  @%:@ include <bam.h>
-                  @%:@elif HAVE_BAM_BAM_H
-                  @%:@ include <bam/bam.h>
-                  @%:@elif HAVE_SAMTOOLS_BAM_H
-                  @%:@ include <samtools/bam.h>
-                  @%:@endif
-                 ],[
-                  char c = bam_nt16_rev_table@<:@7@:>@;
-                 ])
+AC_LINK_IFELSE([AC_LANG_PROGRAM([_YAT_BAM_INCLUDES],
+                  [char c = bam_nt16_rev_table@<:@7@:>@;])
                ],[
                  AC_MSG_RESULT([yes])
@@ -105 +105 @@
                ])
 ]) # YAT_BAM_NT16_REV_TABLE
+
+
+# _YAT_BAM_INCLUDES
+# =================
+# Private macro that expand PP magic we see in 'yat/omic/bam_config.h'
+AC_DEFUN([_YAT_BAM_INCLUDES],
+[AC_REQUIRE([YAT_CHECK_HEADER_BAM])
+@%:@if YAT_HAVE_BAM_H
+@%:@ include <bam.h>
+@%:@elif YAT_HAVE_BAM_BAM_H
+@%:@ include <bam/bam.h>
+@%:@elif YAT_HAVE_SAMTOOLS_BAM_H
+@%:@ include <samtools/bam.h>
+@%:@endif
+]) # _YAT_BAM_HEADER

trunk/yat/omic/config_bam.h

@@ -34 +34 @@
 #include "yat/utility/config_public.h"
 
-#ifdef HAVE_BAM_H
+#ifdef YAT_HAVE_BAM_H
 # define YAT_BAM_HEADER "bam.h"
 # define YAT_SAM_HEADER "sam.h"
 #else
-# ifdef HAVE_BAM_BAM_H
+# ifdef YAT_HAVE_BAM_BAM_H
 #  define YAT_BAM_HEADER "bam/bam.h"
 #  define YAT_SAM_HEADER "bam/sam.h"
 # else
-#  ifdef HAVE_SAMTOOLS_BAM_H
+#  ifdef YAT_HAVE_SAMTOOLS_BAM_H
 #   define YAT_BAM_HEADER "samtools/bam.h"
 #   define YAT_SAM_HEADER "samtools/sam.h"

trunk/yat/utility/config_public.h.in

@@ -29 +29 @@
 
 /// Define to 1 if you have the <bam/bam.h> header file.
-#undef HAVE_BAM_BAM_H
+#undef YAT_HAVE_BAM_BAM_H
 
 /// Define to 1 if you have the <bam.h> header file.
-#undef HAVE_BAM_H
+#undef YAT_HAVE_BAM_H
 
 /// Define to 1 if you have the <samtools/bam.h> header file.
-#undef HAVE_SAMTOOLS_BAM_H
+#undef YAT_HAVE_SAMTOOLS_BAM_H
 
 /// Define if compiler supports deprecated attribute, as in g++ 4.0