Changeset 3431

Timestamp:

Oct 26, 2015, 8:09:34 AM (8 years ago)

Author:

Peter

Message:

revert r3426 and some cosmetic changes (refs #794)

Location:

branches/0.13-stable

Files:

• NEWS (modified) (1 diff)
• configure.ac (modified) (2 diffs)
• test/Suite.cc (modified) (1 diff)
• test/Suite.h (modified) (2 diffs)
• test/pileup.cc (modified) (3 diffs)
• yat/utility/config_public.h.in (modified) (1 diff)

branches/0.13-stable/NEWS

@@ -10 +10 @@
   - AveragerWeighted::n(void) now return 0, when object is empty (ticket #802)
   - added support for htslib (see ticket #794)
-      - YAT_HAVE_LIBBAM is defined if linking against libbam (not against libhts)
-      - YAT_BAM_HEADER is only defined when building against libbam
+      - `YAT_HAVE_LIBBAM` is defined if linking against either libbam
+        or libhts. Use #if defined YAT_HAVE_LIBBAM && !defined
+        (YAT_HAVE_HTSLIB) to check that building against libbam.
+      - `YAT_BAM_HEADER` is only defined when building against libbam
   - Container2DIterator is now tagged with
     boost::random_access_traversal_tag (see ticket #803, r3393)

branches/0.13-stable/configure.ac

@@ -385 +385 @@
       AC_MSG_CHECKING([samtools API])
       AC_MSG_RESULT([yes])
-      AC_DEFINE([YAT_HAVE_LIBBAM], [1],
-                [Define to 1 if yat is built against libbam])
-
       LIBS="$BAM_LIBS $LIBS"
       # check if function bam_calend works. Result of this test can be
@@ -401 +398 @@
   ])
   AC_SUBST([HAVE_HTSLIB], [$have_hts])
+
+  AC_DEFINE([YAT_HAVE_LIBBAM], [1],
+            [Define to 1 if yat is built with bam support])
 
   YAT_CHECK_LA_LIBS([

branches/0.13-stable/test/Suite.cc

@@ -46 +46 @@
     if (require_bam) {
 #ifndef YAT_HAVE_LIBBAM
-      out() << "no libbam\n";
+      out() << "no bam support\n";
       exit (EXIT_SKIP);
 #endif

branches/0.13-stable/test/Suite.h

@@ -24 +24 @@
 */
 
+// ensure that config.h always is included first
+#ifndef YAT_VERSION
+#error header 'config.h' not included
+#endif
+
+#include <yat/utility/config_public.h>
+
 #define YAT_TEST_PROLOGUE "\n=== " << __func__ << " ===\n"
 
@@ -30 +37 @@
 
 // SKIP_BAM_TEST is defined if we should skip bam tests
-#ifndef HAVE_LIBBAM
-#define SKIP_BAM_TEST
-#endif
-#ifndef HAVE_SAMTOOLS
+#if !defined (YAT_HAVE_LIBBAM) || !defined (HAVE_SAMTOOLS_EXECUTABLE)
 #define SKIP_BAM_TEST
 #endif

branches/0.13-stable/test/pileup.cc

@@ -23 +23 @@
 
 #include "Suite.h"
+
+#include <yat/utility/config_public.h>
 
 #ifdef YAT_HAVE_LIBBAM
@@ -50 +52 @@
 
 
-#ifdef YAT_HAVE_LIBBAM
 char seq_nt16(size_t x)
 {
@@ -63 +64 @@
 }
 
+#ifdef YAT_HAVE_LIBBAM
 void test1(test::Suite& suite, const std::string& fn)
 {

branches/0.13-stable/yat/utility/config_public.h.in

@@ -44 +44 @@
 #undef YAT_HAVE_HTS_H
 
-/// Define to 1 if yat is built against libbam
+/// Define to 1 if yat is built with bam support
 #undef YAT_HAVE_LIBBAM