Issue-250: Improve cluster count precision (#251)

* Issue-250: Improve cluster count precision * Fix version history
Illumina · Jan 29, 2021 · 58b4e77 · 58b4e77
1 parent 610da20
commit 58b4e77
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Showing 6 changed files with 24 additions and 25 deletions.
diff --git a/docs/src/changes.md b/docs/src/changes.md
@@ -1,14 +1,13 @@
 # Changes                                               {#changes}
 
 
-
 ## v1.1.20
 
 Date       | Description
 ---------- | -----------
+2021-01-27 | Issue-250: Improve cluster count precision
 2021-01-05 | Fix documentation deployment
 
-
 ## v1.1.19
 
 Date       | Description

diff --git a/interop/logic/summary/tile_summary.h b/interop/logic/summary/tile_summary.h
@@ -89,14 +89,14 @@ namespace illumina { namespace interop { namespace logic { namespace summary
                   util::op::const_member_function_less(&model::metrics::tile_metric::percent_pf),
                   skip_median);
         stat_summary.percent_pf(stat);
-        stat_summary.reads(nan_accumulate(tile_data.begin(),
+        stat_summary.reads(std::accumulate(tile_data.begin(),
                                            tile_data.end(),
-                                          float(0),
+                                           uint64_t(0),
                                            util::op::const_member_function(
                                                    &model::metrics::tile_metric::cluster_count)));
-        stat_summary.reads_pf(nan_accumulate(tile_data.begin(),
+        stat_summary.reads_pf(std::accumulate(tile_data.begin(),
                                              tile_data.end(),
-                                             float(0),
+                                              uint64_t(0),
                                              util::op::const_member_function(
                                                      &model::metrics::tile_metric::cluster_count_pf)));
     }

diff --git a/interop/model/summary/stat_summary.h b/interop/model/summary/stat_summary.h
@@ -35,8 +35,8 @@ namespace illumina { namespace interop { namespace model { namespace summary
                 m_percent_gt_q30(std::numeric_limits<float>::quiet_NaN()),
                 m_yield_g(std::numeric_limits<float>::quiet_NaN()),
                 m_projected_yield_g(0),
-                m_reads(std::numeric_limits<float>::quiet_NaN()),
-                m_reads_pf(std::numeric_limits<float>::quiet_NaN()),
+                m_reads(0),
+                m_reads_pf(0),
                 m_percent_occupied(std::numeric_limits<float>::quiet_NaN())
 
         {
@@ -89,7 +89,7 @@ namespace illumina { namespace interop { namespace model { namespace summary
          *
          * @return total number of clusters in the lane
          */
-        float reads() const
+        uint64_t reads() const
         {
             return m_reads;
         }
@@ -98,7 +98,7 @@ namespace illumina { namespace interop { namespace model { namespace summary
          *
          * @return total number of clusters passing filter in the lane
          */
-        float reads_pf() const
+        uint64_t reads_pf() const
         {
             return m_reads_pf;
         }
@@ -311,15 +311,15 @@ namespace illumina { namespace interop { namespace model { namespace summary
          *
          * @param val total number of clusters in the lane
          */
-        void reads(const float val)
+        void reads(const uint64_t val)
         {
             m_reads = val;
         }
         /** Set the total number of clusters passing filter in the lane
          *
          * @param val total number of clusters passing filter in the lane
          */
-        void reads_pf(const float val)
+        void reads_pf(const uint64_t val)
         {
             m_reads_pf = val;
         }
@@ -487,8 +487,8 @@ namespace illumina { namespace interop { namespace model { namespace summary
         float m_percent_gt_q30;
         float m_yield_g;
         float m_projected_yield_g;
-        float m_reads;
-        float m_reads_pf;
+        uint64_t m_reads;
+        uint64_t m_reads_pf;
 
     private:
         metric_stat_t m_density;

diff --git a/src/apps/summary.cpp b/src/apps/summary.cpp
@@ -272,8 +272,8 @@ void summarize(const surface_summary& summary, std::vector<std::string>& values,
     values[i++] = util::format(summary.prephasing_slope().mean(), 3, 3) + " / "
                   + util::format(summary.prephasing_offset().mean(), 3, 3);
 
-    values[i++] = format(summary.reads(), 0, 2, 1e6);
-    values[i++] = format(summary.reads_pf(), 0, 2, 1e6);
+    values[i++] = format(static_cast<float>(summary.reads()), 0, 2, 1e6);
+    values[i++] = format(static_cast<float>(summary.reads_pf()), 0, 2, 1e6);
     values[i++] = format(summary.percent_gt_q30(), 0, 2);
     values[i++] = format(summary.yield_g(), 0, 2);
     values[i++] = "-";
@@ -303,8 +303,8 @@ void summarize(const lane_summary& summary, std::vector<std::string>& values)
                 + util::format(summary.phasing_offset().mean(), 3, 3);
     values[i++] = util::format(summary.prephasing_slope().mean(), 3, 3) + " / "
                 + util::format(summary.prephasing_offset().mean(), 3, 3);
-    values[i++] = format(summary.reads(), 0, 2, 1e6);
-    values[i++] = format(summary.reads_pf(), 0, 2, 1e6);
+    values[i++] = format(static_cast<float>(summary.reads()), 0, 2, 1e6);
+    values[i++] = format(static_cast<float>(summary.reads_pf()), 0, 2, 1e6);
     values[i++] = format(summary.percent_gt_q30(), 0, 2);
     values[i++] = format(summary.yield_g(), 0, 2);
     values[i++] = format(summary.cycle_state().error_cycle_range());

diff --git a/src/tests/interop/logic/summary_metrics_test.cpp b/src/tests/interop/logic/summary_metrics_test.cpp
@@ -214,10 +214,10 @@ TEST_P(run_summary_tests, lane_summary)
                         expected_lane_summary.yield_g(), tol);
             INTEROP_EXPECT_NEAR(actual_lane_summary.projected_yield_g(),
                         expected_lane_summary.projected_yield_g(), tol);
-            INTEROP_EXPECT_NEAR(actual_lane_summary.reads_pf(),
-                        expected_lane_summary.reads_pf(), tol);
-            INTEROP_EXPECT_NEAR(actual_lane_summary.reads(),
-                        expected_lane_summary.reads(), tol);
+            EXPECT_EQ(actual_lane_summary.reads_pf(),
+                        expected_lane_summary.reads_pf());
+            EXPECT_EQ(actual_lane_summary.reads(),
+                        expected_lane_summary.reads());
             INTEROP_EXPECT_STAT_NEAR(actual_lane_summary.density(), expected_lane_summary.density(), density_tol);
             INTEROP_EXPECT_STAT_NEAR(actual_lane_summary.density_pf(),
                                      expected_lane_summary.density_pf(),
@@ -310,8 +310,8 @@ TEST_P(run_summary_tests, surface_summary)
                 INTEROP_EXPECT_NEAR(actual_surface_summary.yield_g(), expected_surface_summary.yield_g(), tol);
                 INTEROP_EXPECT_NEAR(actual_surface_summary.projected_yield_g(), expected_surface_summary.projected_yield_g(),
                             tol);
-                INTEROP_EXPECT_NEAR(actual_surface_summary.reads_pf(), expected_surface_summary.reads_pf(), tol);
-                INTEROP_EXPECT_NEAR(actual_surface_summary.reads(), expected_surface_summary.reads(), tol);
+                EXPECT_EQ(actual_surface_summary.reads_pf(), expected_surface_summary.reads_pf());
+                EXPECT_EQ(actual_surface_summary.reads(), expected_surface_summary.reads());
                 INTEROP_EXPECT_STAT_NEAR(actual_surface_summary.density(),
                                          expected_surface_summary.density(),
                                          density_tol);

diff --git a/src/tests/interop/metrics/inc/tile_metrics_test.h b/src/tests/interop/metrics/inc/tile_metrics_test.h
@@ -126,7 +126,7 @@ namespace illumina{ namespace interop { namespace unittest
                 //
                 summary[read][0].tile_count(3);
                 summary[read][0].reads_pf(9738715);
-                summary[read][0].reads(19412848);
+                summary[read][0].reads(19412847);
                 summary[read][0].density(model::summary::metric_stat(2355119.25f, 0, 2355119.25f));
                 summary[read][0].density_pf(model::summary::metric_stat(1181477.125f, 27380.955078125f, 1174757.75f));
                 summary[read][0].cluster_count(model::summary::metric_stat(6470949.5f, 0, 6470949));