Changeset 3302

Timestamp:

Aug 20, 2014, 8:55:24 AM (9 years ago)

Author:

Peter

Message:

add test for BamRead::end(). Use samtools' bam_calend if HAVE_BAM_CALEND is #defined. refs #810

Location:

branches/0.12-stable

Files:

• test/bam.cc (modified) (2 diffs)
• yat/omic/BamRead.cc (modified) (1 diff)
• yat/omic/BamRead.h (modified) (1 diff)

branches/0.12-stable/test/bam.cc

@@ -120 +120 @@
 
 
+void test_end(test::Suite& suite, BamRead bam)
+{
+  suite.out() << "test end:\n";
+  suite.out() << bam.pos() << "-" << bam.end() << " " << bam.cigar_str()
+              << "\n";
+  uint32_t end = bam.end();
+  if (!suite.add(end==24093)) {
+    suite.err() << "error: incorrect end: " << end << "\n";
+  }
+
+  // change the cigar to include a DIFF and EQUAL
+  utility::Aligner::Cigar cig;
+  cig.push_back(BAM_CEQUAL, 55);
+  cig.push_back(BAM_CDIFF, 1);
+  cig.push_back(BAM_CEQUAL, 44);
+  bam.cigar(cig);
+  suite.out() << bam.pos() << "-" << bam.end() << " " << bam.cigar_str()
+              << "\n";
+  end = bam.end();
+  if (!suite.add(end==24093)) {
+    suite.err() << "error: incorrect end: " << end << "\n";
+  }
+}
+
+
 void test_sequence(test::Suite& suite, const BamRead& b)
 {
@@ -234 +259 @@
   in.read(bam);
   // test that functions are implemented
-  bam.end();
+  test_end(suite, bam);
   bam.flag();
   bam.mpos();

branches/0.12-stable/yat/omic/BamRead.cc

@@ -112 +112 @@
   uint32_t BamRead::calend(const bam1_core_t *c, const uint32_t *cigar) const
   {
+#ifdef HAVE_BAM_CALEND
+    return bam_calend(&core(), bam1_cigar(bam_));
+#endif
     int k, end = c->pos;
     for (k = 0; k < c->n_cigar; ++k) {

branches/0.12-stable/yat/omic/BamRead.h

@@ -309 +309 @@
     friend class OutBamFile;
     friend class BamReadIterator;
-    // FIXME guard out this
     uint32_t calend(const bam1_core_t *c, const uint32_t *cigar) const;
   };