Changeset 2979

Timestamp:

Jan 31, 2013, 8:15:40 AM (10 years ago)

Author:

Peter

Message:

extending test for BamRead::cigar

File:

• branches/0.10-stable/test/bam.cc (modified) (2 diffs)

branches/0.10-stable/test/bam.cc

@@ -52 +52 @@
 using namespace omic;
 
+void test_cigar(test::Suite& suite, const BamRead& b, const BamHeader& hdr)
+{
+  BamRead bam(b);
+
+  suite.out() << "test cigar:\n";
+  suite.out() << bam.cigar_str() << "\n";
+  OutBamFile os("cigar_test.bam", hdr);
+  std::vector<uint32_t> cig;
+
+  bam.cigar(cig);
+  suite.out() << bam.cigar_str() << "\n";
+  suite.add(bam.cigar_str()=="");
+  os.write(bam);
+
+  cig.resize(1);
+  cig[0] = bam_cigar_gen(bam.sequence_length(), BAM_CMATCH);
+  bam.cigar(cig);
+  suite.out() << bam.cigar_str() << "\n";
+  suite.add(bam.cigar_str()=="100M");
+  os.write(bam);
+
+  cig.resize(3);
+  cig[0] = bam_cigar_gen(50, BAM_CMATCH);
+  cig[1] = bam_cigar_gen(2, BAM_CDEL);
+  cig[2] = bam_cigar_gen(50, BAM_CMATCH);
+  bam.cigar(cig);
+  suite.out() << bam.cigar_str() << "\n";
+  suite.add(bam.cigar_str()=="50M2D50M");
+  os.write(bam);
+
+  // check that other elements in data* is preserved
+  if (!suite.add(same_query_name(b, bam)))
+    suite.err() << "error: \n'" << b.name() << "'\n'" << bam.name() << "'\n";
+
+  if (!suite.add(b.sequence()==bam.sequence()))
+    suite.err() << "error: \n'" << b.sequence() << "'\n'"
+                << bam.sequence() << "'\n";
+
+  for (int32_t i=0; i<b.core().l_qseq; ++i)
+    if (bam.qual(i) != b.qual(i)) {
+      suite.err() << "error: qual: " << i << " " << bam.qual(i)
+                  << " not euqal " << b.qual(i) << "\n";
+      suite.add(false);
+    }
+
+  os.close();
+}
+
 void test1(test::Suite& suite)
 {
@@ -68 +116 @@
     suite.add(false);
   }
+  test_cigar(suite, bam, in.header());
 }
 #endif