Sam: add uber off-by-1 test

broadinstitute · Aug 20, 2014 · 703f0cd · 703f0cd
1 parent a3a6f42
commit 703f0cd
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Showing 4 changed files with 9 additions and 5 deletions.
diff --git a/gamgee/cigar.cpp b/gamgee/cigar.cpp
@@ -113,7 +113,6 @@ CigarElement Cigar::parse_next_cigar_element (stringstream& cigar_stream) {
   if ( cigar_stream.fail() || int(element_op) >= 128 )
     throw invalid_argument(string("Error parsing cigar string: ") + cigar_stream.str());
   const auto encoded_op = cigar_op_parse_table[element_op];
-  printf("parsed length: %d, op: %d, econded_op: %d\n", element_length, element_op, encoded_op);
   if ( encoded_op < 0 )
     throw invalid_argument(string("Unrecognized operator ") + char(element_op) + " in cigar string: " + cigar_stream.str());
   return make_cigar_element(element_length, static_cast<CigarOperator>(encoded_op));

diff --git a/gamgee/cigar.h b/gamgee/cigar.h
@@ -56,7 +56,6 @@ class Cigar {
    *        out of a length and a CigarOperator
    */
   inline static CigarElement make_cigar_element(const uint32_t oplen, const CigarOperator op) {
-    printf("making -- len: %d, op: %d\n", oplen, op);
     return (oplen << BAM_CIGAR_SHIFT) | static_cast<uint8_t>(op);
   }
 
@@ -80,7 +79,7 @@ class Cigar {
    * }
    * ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    *
-   * @return a pair with the element length and operator respectively. Both values can be converted using the Cigar API to actual elements.
+   * @return a CigarElement with the length and operator. Both values can be converted using the Cigar API (Cigar::cigar_op and Cigar::cigar_oplen) to actual elements.
    */
   static CigarElement parse_next_cigar_element (std::stringstream& cigar_stream);
 

diff --git a/gamgee/sam.cpp b/gamgee/sam.cpp
@@ -84,7 +84,6 @@ uint32_t Sam::mate_alignment_stop() const {
   stringstream cigar_stream {mate_cigar.value()};
   while (cigar_stream.peek() != std::char_traits<char>::eof()) {
     const auto element = Cigar::parse_next_cigar_element(cigar_stream);
-    printf("element length: %d, op: %d\n", Cigar::cigar_oplen(element), static_cast<int>(Cigar::cigar_op(element)));
     result += Cigar::consumes_reference_bases(Cigar::cigar_op(element)) ? Cigar::cigar_oplen(element) : 0;
   }
   return result-1; // we want the last base to be 1-based and **inclusive**

diff --git a/test/sam_test.cpp b/test/sam_test.cpp
@@ -441,11 +441,18 @@ BOOST_AUTO_TEST_CASE( sam_mate_alignment_stop ) {
   auto i = 0u;
   for (const auto& record : SingleSamReader{"testdata/test_simple.sam"}) {
     if (!missing(record.string_tag("MC"))) {
-      printf("read: %d, mate cigar: %s, astart: %d, astop: %d, mate_start: %d, mate_stop: %d\n", i, record.string_tag("MC").value().c_str(), record.alignment_start(), record.alignment_stop(), record.mate_alignment_start(), record.mate_alignment_stop());
       BOOST_CHECK_EQUAL(record.mate_alignment_stop(), truth_mate_alignment_stop[i++]);
     }
     else {
       BOOST_CHECK_THROW(record.mate_alignment_stop(), invalid_argument);
     }
   }
 }
+
+BOOST_AUTO_TEST_CASE( sam_off_by_one_uber_test ) {
+  const auto header = SingleSamReader{"testdata/test_simple.bam"}.header();
+  auto builder = SamBuilder{header};
+  const auto record = builder.set_name("TEST").set_bases("A").set_cigar("1M").set_base_quals({20}).set_alignment_start(1).build();
+  BOOST_CHECK_EQUAL(record.alignment_start(), 1);
+  BOOST_CHECK_EQUAL(record.alignment_stop(), 1);
+}