Changeset 3031 for trunk/test/bam.cc

Timestamp:

Apr 27, 2013, 1:24:13 PM (10 years ago)

Author:

Peter

Message:

new function BamRead::sequence(2). refs #746

File:

• trunk/test/bam.cc (modified) (2 diffs)

trunk/test/bam.cc

@@ -120 +120 @@
 }
 
+
+void test_sequence(test::Suite& suite, const BamRead& b)
+{
+  suite.out() << "test sequence\n";
+  BamRead bam(b);
+  std::string seq = b.sequence();
+  std::vector<uint8_t> qual;
+  qual.reserve(seq.size());
+  for (size_t i=0; i<seq.size(); ++i)
+    qual.push_back(bam.qual(i));
+  assert(seq.size()==100);
+  bam.sequence(seq, qual);
+
+  if (bam.sequence()!=seq) {
+    suite.add(false);
+    suite.err() << "incorrect sequence:" << bam.sequence() << "\n";
+    suite.err() << "expected: " << seq << "\n";
+  }
+
+  // just for consistency
+  std::vector<uint32_t> cig;
+  bam.cigar(cig);
+  bam.core().flag &= ~BAM_FUNMAP;
+
+  // trim off one base
+  seq.resize(seq.size()-1);
+  qual.resize(qual.size()-1);
+  bam.sequence(seq, qual);
+
+  if (bam.sequence()!=seq) {
+    suite.add(false);
+    suite.err() << "incorrect sequence:" << bam.sequence() << "\n";
+    suite.err() << "expected: " << seq << "\n";
+  }
+
+  // extend sequence
+  seq.resize(120, 'A');
+  qual.resize(120, 0);
+  bam.sequence(seq, qual);
+  if (bam.sequence()!=seq) {
+    suite.add(false);
+    suite.err() << "incorrect sequence:" << bam.sequence() << "\n";
+    suite.err() << "expected: " << seq << "\n";
+  }
+}
+
+
 void test1(test::Suite& suite)
 {
@@ -165 +212 @@
   test_cigar(suite, bam, in.header());
   test_aux(suite, bam);
-}
-#endif
+  test_sequence(suite, bam);
+}
+#endif