[chainerutils] Rename create_simple_overlap to create_overlap

Author: edawson

cudamapper/src/chainer_utils.cu

@@ -38,7 +38,7 @@ struct OverlapToNumResiduesOp
     }
 };
 
-__host__ __device__ Overlap create_simple_overlap(const Anchor& start, const Anchor& end, const int32_t num_anchors)
+__host__ __device__ Overlap create_overlap(const Anchor& start, const Anchor& end, const int32_t num_anchors)
 {
     Overlap overlap;
     overlap.num_residues_ = num_anchors;
@@ -96,7 +96,7 @@ __global__ void backtrace_anchors_to_overlaps(const Anchor* const anchors,
                 index = predecessors[index];
             }
             Anchor first_anchor = anchors[first_index];
-            overlaps[i]         = create_simple_overlap(first_anchor, final_anchor, num_anchors_in_chain);
+            overlaps[i]         = create_overlap(first_anchor, final_anchor, num_anchors_in_chain);
         }
         else
         {

cudamapper/src/chainer_utils.cuh

@@ -36,7 +36,7 @@ namespace chainerutils
 /// \param start The first anchor in the chain.
 /// \param end The last anchor in the chain.
 /// \param num_anchors The total number of anchors in the chain.
-__host__ __device__ Overlap create_simple_overlap(const Anchor& start,
+__host__ __device__ Overlap create_overlap(const Anchor& start,
                                                   const Anchor& end,
                                                   const int32_t num_anchors);
 

cudamapper/tests/Test_CudamapperChainerUtils.cu

@@ -32,7 +32,7 @@ namespace genomeworks
 namespace cudamapper
 {
 
-TEST(TestChainerUtils, Create_Simple_Overlap_Tests)
+TEST(TestChainerUtils, Create_Overlap_Tests)
 {
     Anchor a;
     a.query_read_id_           = 12;
@@ -46,7 +46,7 @@ TEST(TestChainerUtils, Create_Simple_Overlap_Tests)
     b.target_read_id_          = 46;
     b.target_position_in_read_ = 20400;
 
-    Overlap p_ab = chainerutils::create_simple_overlap(a, b, 12);
+    Overlap p_ab = chainerutils::create_overlap(a, b, 12);
     ASSERT_EQ(p_ab.query_read_id_, static_cast<uint32_t>(12));
     ASSERT_EQ(p_ab.target_read_id_, 46);
     ASSERT_EQ(p_ab.query_start_position_in_read_, 130);
@@ -61,7 +61,7 @@ TEST(TestChainerUtils, Create_Simple_Overlap_Tests)
     c.target_read_id_          = 46;
     c.target_position_in_read_ = 16000;
 
-    Overlap p_bc = chainerutils::create_simple_overlap(b, c, 22);
+    Overlap p_bc = chainerutils::create_overlap(b, c, 22);
     ASSERT_EQ(p_bc.target_start_position_in_read_, 16000);
     ASSERT_EQ(p_bc.target_end_position_in_read_, 20400);
     ASSERT_EQ(static_cast<char>(p_bc.relative_strand), static_cast<char>(RelativeStrand::Reverse));
@@ -86,15 +86,15 @@ TEST(TestChainerUtils, Anchor_Chain_Extraction_Tests)
     b.target_read_id_          = 46;
     b.target_position_in_read_ = 20400;
 
-    Overlap p_ab = chainerutils::create_simple_overlap(a, b, 2);
+    Overlap p_ab = chainerutils::create_overlap(a, b, 2);
 
     Anchor c;
     c.query_read_id_           = 12;
     c.query_position_in_read_  = 15000;
     c.target_read_id_          = 46;
     c.target_position_in_read_ = 16000;
 
-    Overlap p_bc = chainerutils::create_simple_overlap(b, c, 2);
+    Overlap p_bc = chainerutils::create_overlap(b, c, 2);
 
     std::vector<Anchor> anchors;
     anchors.push_back(a);