Changeset 2929

Timestamp:

Dec 26, 2012, 2:32:57 AM (9 years ago)

Author:

Peter

Message:

add EXIT_SKIP macro. make test compile also --without-samtools

Location:

branches/0.10-stable/test

Files:

• Suite.h (modified) (1 diff)
• bam_iterator.cc (modified) (5 diffs)
• bam_pair_analyse.cc (modified) (3 diffs)
• bam_region_iterator.cc (modified) (3 diffs)

branches/0.10-stable/test/Suite.h

@@ -25 +25 @@
 
 #define YAT_TEST_PROLOGUE "\n=== " << __func__ << " ===\n"
+
+// used to tell automake that test should be skipped
+#define EXIT_SKIP 77
 
 #include <yat/utility/VectorMutable.h>

branches/0.10-stable/test/bam_iterator.cc

@@ -20 +20 @@
 #include "Suite.h"
 
+#ifdef HAVE_LIBBAM
 #include "yat/omic/BamFile.h"
 #include "yat/omic/BamRead.h"
 #include "yat/omic/BamReadIterator.h"
 #include "yat/omic/BamWriteIterator.h"
+#endif
 
 #include <algorithm>
 #include <cassert>
 #include <fstream>
-#include <iostream>
 #include <string>
 
 using namespace theplu::yat;
+
+void test1(test::Suite& suite);
+
+int main(int argc, char* argv[])
+{
+  test::Suite suite(argc, argv);
+#ifndef HAVE_LIBBAM
+  suite.out() << "no libbam\n";
+  return EXIT_SKIP;
+#endif
+#ifndef HAVE_SAMTOOLS
+  suite.out() << "no samtools\n";
+  return EXIT_SKIP;
+#endif
+  test1(suite);
+  return suite.return_value();
+}
+
+#ifdef HAVE_LIBBAM
 using namespace omic;
 
@@ -79 +99 @@
 };
 
-int main(int argc, char* argv[])
+
+void test1(test::Suite& suite)
 {
-#ifndef HAVE_SAMTOOLS
-  return EXIT_SKIP;
-#endif
-  test::Suite suite(argc, argv);
-
   std::string file = "../../data/foo.sorted.bam";
 
@@ -99 +115 @@
   in.open(file);
   size_t n1 = std::distance(BamReadIterator(in), BamReadIterator());
-  std::cout << "entries in " << file << ": " << n1 << "\n";
+  suite.out() << "entries in " << file << ": " << n1 << "\n";
   in.close();
 
@@ -105 +121 @@
   size_t n2 = std::distance(BamReadIterator(copy), BamReadIterator());
   copy.close();
-  std::cout << "entries in " << outname << ": " << n2 << "\n";
+  suite.out() << "entries in " << outname << ": " << n2 << "\n";
   if (n1!=n2) {
-    std::cout << "error: not same number of entries in copy\n";
-    exit(1);
+    suite.out() << "error: not same number of entries in copy\n";
+    suite.add(false);
   }
 
@@ -115 +131 @@
   if (!std::equal(BamReadIterator(in), BamReadIterator(),
                   BamReadIterator(copy), BamReadEqual())) {
-    std::cout << "error: " << file << " and " << outname << " not equal\n";
-    exit(1);
+    suite.out() << "error: " << file << " and " << outname << " not equal\n";
+    suite.add(false);
   }
   copy.close();
   in.close();
   unlink(outname.c_str());
-  std::cout << "OK\n";
-  return 0;
 }
+#endif

branches/0.10-stable/test/bam_pair_analyse.cc

@@ -20 +20 @@
 #include "Suite.h"
 
+using namespace theplu::yat;
+
+#if HAVE_LIBBAM
 #include "yat/omic/algorithm.h"
 #include "yat/omic/BamRead.h"
 #include "yat/omic/BamReadIterator.h"
+#endif
 
-using namespace theplu::yat;
+void test1(test::Suite& suite);
+
+int main(int argc, char* argv[])
+{
+  test::Suite suite(argc, argv);
+#ifndef HAVE_LIBBAM
+  suite.out() << "no libbam\n";
+  return EXIT_SKIP;
+#endif
+#ifndef HAVE_SAMTOOLS
+  suite.out() << "no samtools available\n";
+  return EXIT_SKIP;
+#endif
+
+#ifdef HAVE_LIBBAM
+  test1(suite);
+#endif
+  return suite.return_value();
+}
+
+
+#ifdef HAVE_LIBBAM
 using namespace omic;
 
@@ -39 +64 @@
 };
 
-
-int main(int argc, char* argv[])
+void test1(test::Suite& suite)
 {
-#ifndef HAVE_SAMTOOLS
-  return EXIT_SKIP;
-#endif
-  test::Suite suite(argc, argv);
-
   std::string file = "../../data/foo.sorted.bam";
 
@@ -54 +73 @@
   Counter counter;
   bam_pair_analyse(iter, end, counter);
-
   suite.out() << counter.n_ << "\n";
-
   suite.add(counter.n_==395);
-
   is.close();
-  return suite.return_value();
 }
+#endif

branches/0.10-stable/test/bam_region_iterator.cc

@@ -20 +20 @@
 #include "Suite.h"
 
+#ifdef HAVE_LIBBAM
 #include "yat/omic/BamReadIterator.h"
 #include "yat/omic/BamWriteIterator.h"
 #include "yat/omic/config_bam.h"
+#endif
 
+#ifdef YAT_BAM_HEADER
 #include YAT_BAM_HEADER
+#endif
 
 #include <algorithm>
@@ -33 +37 @@
 
 using namespace theplu::yat;
-using namespace theplu::yat::omic;
+
+void test1(test::Suite& suite);
+int main(int argc, char* argv[])
+{
+  test::Suite suite(argc, argv);
+#ifndef HAVE_LIBBAM
+  suite.out() << "no libbam\n";
+  return EXIT_SKIP;
+#endif
+#ifndef HAVE_SAMTOOLS
+  suite.out() << "no samtools\n";
+  return EXIT_SKIP;
+#endif
+
+  try {
+    test1(suite);
+  }
+  catch (std::runtime_error& e) {
+    suite.err() << "what: " << e.what() << "\n";
+    suite.add(false);
+  }
+
+  return suite.return_value();
+}
 
 void test1(test::Suite& suite)
 {
+#ifdef HAVE_LIBBAM
+  using namespace omic;
   std::string file = "../../data/foo.sorted.bam";
 
@@ -64 +93 @@
   suite.err() << "count: " << count << "\nexpected: 185\n";
   suite.add(false);
+#endif
 }
-
-
-int main(int argc, char* argv[])
-{
-#ifndef HAVE_SAMTOOLS
-  return EXIT_SKIP;
-#endif
-  test::Suite suite(argc, argv);
-
-  try {
-    test1(suite);
-  }
-  catch (std::runtime_error& e) {
-    suite.err() << "what: " << e.what() << "\n";
-    suite.add(false);
-  }
-
-  return suite.return_value();
-}