fix merged reads being over-counted in some statistics

MikkelSchubert · Jul 6, 2024 · f389f81 · f389f81
1 parent 21d8546
commit f389f81
Show file tree

Hide file tree

Showing 12 changed files with 52 additions and 52 deletions.
diff --git a/src/reports_json.cpp b/src/reports_json.cpp
@@ -79,7 +79,7 @@ write_report_summary_stats(const json_dict_ptr& json,
   size_t n_q30 = 0;
 
   for (const auto& it : stats) {
-    n_reads += it->number_of_input_reads();
+    n_reads += it->number_of_output_reads();
     n_reads_s += it->number_of_sampled_reads();
     n_bases += it->length_dist().product();
     // The following stats are all (potentially) based on a subset of reads

diff --git a/src/statistics.cpp b/src/statistics.cpp
@@ -269,7 +269,7 @@ fastq_statistics::process(const fastq& read, size_t num_input_reads)
     m_nucleotide_pos.resize_up_to(m_max_sequence_len);
     m_quality_pos.resize_up_to(m_max_sequence_len);
 
-    m_number_of_sampled_reads += num_input_reads;
+    m_number_of_sampled_reads++;
 
     const std::string& sequence = read.sequence();
     const std::string& qualities = read.qualities();

diff --git a/tests/regression/demultiplexing/common/merge/your_output.json b/tests/regression/demultiplexing/common/merge/your_output.json
@@ -46,10 +46,10 @@
     },
     "output": {
       "passed": {
-        "reads": 12,
+        "reads": 8,
         "bases": 818,
-        "mean_length": 68.167,
-        "reads_sampled": 12,
+        "mean_length": 102.250,
+        "reads_sampled": 8,
         "q20_rate": 0.976,
         "q30_rate": 0.809,
         "uncalled_rate": 0.000,
@@ -66,10 +66,10 @@
         "gc_content": null
       },
       "discarded": {
-        "reads": 4,
+        "reads": 2,
         "bases": 0,
         "mean_length": 0.000,
-        "reads_sampled": 4,
+        "reads_sampled": 2,
         "q20_rate": null,
         "q30_rate": null,
         "uncalled_rate": null,
@@ -215,7 +215,7 @@
             "filenames": ["your_output.sample_1.merged.fastq"],
             "input_reads": 4,
             "output_reads": 2,
-            "reads_sampled": 4,
+            "reads_sampled": 2,
             "lengths": [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1],
             "quality_curves": {
               "a": [38.000, null, 38.000, 38.000, 38.000, null, 38.000, null, 38.000, null, 38.000, null, null, null, null, null, 37.000, null, null, null, null, null, 36.000, 36.000, null, null, 36.000, null, 36.000, null, null, null, 35.000, 35.000, 35.000, null, null, null, null, null, 34.500, 35.000, null, null, 35.000, null, null, 33.000, null, 34.000, null, 34.000, 36.000, null, 36.000, null, null, null, 31.000, null, 30.000, null, null, null, 33.500, null, 33.500, null, null, 33.000, null, null, 38.000, null, null, null, 27.000, 27.000, 27.000, 28.000, null, null, 28.000, 29.000, 29.000, 29.000, 30.000, null, null, null, null, null, null, 31.000, 31.000, 32.000, null, null, 32.000, null, null, 33.000, 33.000, 33.000, null, null, 33.000, null, null, 34.000, null, null, 34.000, null, null, 35.000, null, null, 35.000, null, null, null, null, 36.000, null, 36.000, 36.000, null, null, null, 37.000, null, null, null, null, null, null, null, null, null, 38.000, null, 38.000, 38.000, null, null, 38.000, null, 38.000, null],
@@ -238,7 +238,7 @@
             "filenames": ["your_output.sample_1.discarded.fastq"],
             "input_reads": 2,
             "output_reads": 1,
-            "reads_sampled": 2,
+            "reads_sampled": 1,
             "lengths": [1],
             "quality_curves": null,
             "content_curves": null,
@@ -330,7 +330,7 @@
             "filenames": ["your_output.sample_2.merged.fastq"],
             "input_reads": 4,
             "output_reads": 2,
-            "reads_sampled": 4,
+            "reads_sampled": 2,
             "lengths": [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1],
             "quality_curves": {
               "a": [null, 38.000, null, 38.000, null, 38.000, 38.000, 38.000, 38.000, null, null, null, 37.000, 37.000, null, null, null, null, null, null, null, null, null, null, null, null, null, null, 36.000, null, null, null, 35.000, null, 35.000, 35.000, 34.000, 34.000, 34.000, null, 35.000, null, null, null, null, null, null, null, 33.000, 32.000, 34.000, null, null, 32.000, null, 37.000, 31.000, null, null, 37.000, 37.000, null, null, 30.000, null, 29.000, null, null, null, null, 28.000, 27.000, null, 38.000, null, null, 27.000, 27.000, 27.000, null, null, null, 28.000, null, null, null, null, null, null, null, null, 31.000, null, null, 31.000, null, 32.000, 32.000, null, null, 32.000, null, 33.000, null, 33.000, 33.000, null, 34.000, 34.000, null, 34.000, null, null, null, null, null, 35.000, null, null, null, null, null, 36.000, 36.000, null, 36.000, 36.000, null, null, null, null, null, null, 37.000, null, null, null, null, null, null, 38.000, 38.000, null, null, null, 38.000, null, 38.000, null, null],
@@ -353,7 +353,7 @@
             "filenames": ["your_output.sample_2.discarded.fastq"],
             "input_reads": 2,
             "output_reads": 1,
-            "reads_sampled": 2,
+            "reads_sampled": 1,
             "lengths": [1],
             "quality_curves": null,
             "content_curves": null,
@@ -415,7 +415,7 @@
       "filenames": ["your_output.sample_1.merged.fastq", "your_output.sample_2.merged.fastq"],
       "input_reads": 8,
       "output_reads": 4,
-      "reads_sampled": 8,
+      "reads_sampled": 4,
       "lengths": [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 2, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 2],
       "quality_curves": {
         "a": [38.000, 38.000, 38.000, 38.000, 38.000, 38.000, 38.000, 38.000, 38.000, null, 38.000, null, 37.000, 37.000, null, null, 37.000, null, null, null, null, null, 36.000, 36.000, null, null, 36.000, null, 36.000, null, null, null, 35.000, 35.000, 35.000, 35.000, 34.000, 34.000, 34.000, null, 34.667, 35.000, null, null, 35.000, null, null, 33.000, 33.000, 33.333, 34.000, 34.000, 36.000, 32.000, 36.000, 37.000, 31.000, null, 31.000, 37.000, 33.500, null, null, 30.000, 33.500, 29.000, 33.500, null, null, 33.000, 28.000, 27.000, 38.000, 38.000, null, null, 27.000, 27.000, 27.000, 28.000, null, null, 28.000, 29.000, 29.000, 29.000, 30.000, null, null, null, null, 31.000, null, 31.000, 31.000, 32.000, 32.000, 32.000, 32.000, null, 32.000, 33.000, 33.000, 33.000, 33.000, 33.000, 33.000, 34.000, 34.000, 34.000, 34.000, null, 34.000, null, null, 35.000, 35.000, null, 35.000, null, null, null, 36.000, 36.000, null, 36.000, 36.000, null, null, null, 37.000, null, null, 37.000, null, null, null, null, null, null, 38.000, 38.000, 38.000, 38.000, null, 38.000, 38.000, 38.000, 38.000, null],
@@ -471,7 +471,7 @@
       "filenames": ["your_output.sample_1.discarded.fastq", "your_output.sample_2.discarded.fastq"],
       "input_reads": 4,
       "output_reads": 2,
-      "reads_sampled": 4,
+      "reads_sampled": 2,
       "lengths": [2],
       "quality_curves": null,
       "content_curves": null,

diff --git a/tests/regression/deprecated_features/merge_deterministic/your_output.json b/tests/regression/deprecated_features/merge_deterministic/your_output.json
@@ -37,10 +37,10 @@
     },
     "output": {
       "passed": {
-        "reads": 2,
+        "reads": 1,
         "bases": 50,
-        "mean_length": 25.000,
-        "reads_sampled": 2,
+        "mean_length": 50.000,
+        "reads_sampled": 1,
         "q20_rate": 0.980,
         "q30_rate": 0.980,
         "uncalled_rate": 0.000,
@@ -137,7 +137,7 @@
       "filenames": ["your_output.merged.fastq"],
       "input_reads": 2,
       "output_reads": 1,
-      "reads_sampled": 2,
+      "reads_sampled": 1,
       "lengths": [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1],
       "quality_curves": {
         "a": [41.000, null, 41.000, null, null, 41.000, null, null, 41.000, 41.000, null, 41.000, null, null, null, null, null, 41.000, 41.000, null, null, null, null, 41.000, null, null, null, 41.000, null, null, null, null, null, null, null, null, null, null, null, null, null, 41.000, null, null, 41.000, null, null, null, null, null],

diff --git a/tests/regression/misc/basename/alt/pe/alternative.json b/tests/regression/misc/basename/alt/pe/alternative.json
@@ -37,10 +37,10 @@
     },
     "output": {
       "passed": {
-        "reads": 2,
+        "reads": 1,
         "bases": 42,
-        "mean_length": 21.000,
-        "reads_sampled": 2,
+        "mean_length": 42.000,
+        "reads_sampled": 1,
         "q20_rate": 1.000,
         "q30_rate": 1.000,
         "uncalled_rate": 0.000,
@@ -137,7 +137,7 @@
       "filenames": ["alternative.merged.fastq"],
       "input_reads": 2,
       "output_reads": 1,
-      "reads_sampled": 2,
+      "reads_sampled": 1,
       "lengths": [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1],
       "quality_curves": {
         "a": [null, 41.000, null, null, 41.000, null, null, 40.000, 40.000, null, 41.000, null, null, null, null, null, 39.000, 40.000, null, null, null, null, 39.000, null, null, null, 38.000, null, null, null, null, null, null, null, null, null, null, null, null, null, 41.000, null],

diff --git a/tests/regression/misc/mate_separator/merged/your_output.json b/tests/regression/misc/mate_separator/merged/your_output.json
@@ -37,10 +37,10 @@
     },
     "output": {
       "passed": {
-        "reads": 2,
+        "reads": 1,
         "bases": 43,
-        "mean_length": 21.500,
-        "reads_sampled": 2,
+        "mean_length": 43.000,
+        "reads_sampled": 1,
         "q20_rate": 1.000,
         "q30_rate": 1.000,
         "uncalled_rate": 0.000,
@@ -137,7 +137,7 @@
       "filenames": ["your_output.merged.fastq"],
       "input_reads": 2,
       "output_reads": 1,
-      "reads_sampled": 2,
+      "reads_sampled": 1,
       "lengths": [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1],
       "quality_curves": {
         "a": [40.000, null, 41.000, null, null, 41.000, null, null, 40.000, 40.000, null, 41.000, null, null, null, null, null, 39.000, 40.000, null, null, null, null, 39.000, null, null, null, 38.000, null, null, null, null, null, null, null, null, null, null, null, null, null, 41.000, null],

diff --git a/tests/regression/misc/merging/your_output.json b/tests/regression/misc/merging/your_output.json
@@ -37,21 +37,21 @@
     },
     "output": {
       "passed": {
-        "reads": 10,
+        "reads": 6,
         "bases": 577,
-        "mean_length": 57.700,
-        "reads_sampled": 10,
+        "mean_length": 96.167,
+        "reads_sampled": 6,
         "q20_rate": 0.981,
         "q30_rate": 0.898,
         "uncalled_rate": 0.005,
         "gc_content": 0.487
       },
       "unidentified": null,
       "discarded": {
-        "reads": 2,
+        "reads": 1,
         "bases": 0,
         "mean_length": 0.000,
-        "reads_sampled": 2,
+        "reads_sampled": 1,
         "q20_rate": null,
         "q30_rate": null,
         "uncalled_rate": null,
@@ -161,7 +161,7 @@
       "filenames": ["your_output.merged.fastq"],
       "input_reads": 8,
       "output_reads": 4,
-      "reads_sampled": 8,
+      "reads_sampled": 4,
       "lengths": [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 2],
       "quality_curves": {
         "a": [40.000, 41.000, 41.000, null, 41.000, 40.333, null, 40.000, 40.000, 40.000, 41.000, 41.000, null, 41.000, null, null, 38.333, 39.250, 40.000, null, null, null, 39.000, 39.000, null, null, 38.000, 38.667, null, null, null, null, 38.000, null, null, 37.000, 37.000, null, null, 37.000, 41.000, 41.000, null, null, null, 35.000, null, null, null, null, null, 36.000, null, null, null, 32.000, null, null, null, null, null, null, null, null, 32.000, null, null, null, null, null, null, null, null, null, null, 31.000, null, 30.000, null, null, null, null, 31.000, 33.000, null, null, null, 31.000, null, 33.000, null, null, null, null, 32.000, null, 35.000, null, null, 34.000, null, null, 34.000, null, 35.000, 36.000, 34.000, 35.000, null, 36.000, 36.000, 37.000, 37.000, 37.000, null, null, null, null, null, null, null, 37.000, null, null, null, null, null, null, null, null, 39.000, null, null, null, 38.000, null, null, null, 41.000, null, 40.000, 39.000, null, null, null, 40.000, null, 41.000, null, null],
@@ -197,7 +197,7 @@
       "filenames": ["your_output.discarded.fastq"],
       "input_reads": 2,
       "output_reads": 1,
-      "reads_sampled": 2,
+      "reads_sampled": 1,
       "lengths": [1],
       "quality_curves": null,
       "content_curves": null,

diff --git a/tests/regression/misc/out_options/pe/out.json b/tests/regression/misc/out_options/pe/out.json
@@ -37,10 +37,10 @@
     },
     "output": {
       "passed": {
-        "reads": 2,
+        "reads": 1,
         "bases": 42,
-        "mean_length": 21.000,
-        "reads_sampled": 2,
+        "mean_length": 42.000,
+        "reads_sampled": 1,
         "q20_rate": 1.000,
         "q30_rate": 1.000,
         "uncalled_rate": 0.000,
@@ -137,7 +137,7 @@
       "filenames": ["oc"],
       "input_reads": 2,
       "output_reads": 1,
-      "reads_sampled": 2,
+      "reads_sampled": 1,
       "lengths": [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1],
       "quality_curves": {
         "a": [null, 41.000, null, null, 41.000, null, null, 40.000, 40.000, null, 41.000, null, null, null, null, null, 39.000, 40.000, null, null, null, null, 39.000, null, null, null, 38.000, null, null, null, null, null, null, null, null, null, null, null, null, null, 41.000, null],

diff --git a/tests/regression/misc/preserve5p/pe/collapsed/your_output.json b/tests/regression/misc/preserve5p/pe/collapsed/your_output.json
@@ -37,10 +37,10 @@
     },
     "output": {
       "passed": {
-        "reads": 12,
+        "reads": 11,
         "bases": 535,
-        "mean_length": 44.583,
-        "reads_sampled": 12,
+        "mean_length": 48.636,
+        "reads_sampled": 11,
         "q20_rate": 0.944,
         "q30_rate": 0.944,
         "uncalled_rate": 0.056,
@@ -161,7 +161,7 @@
       "filenames": ["your_output.merged.fastq"],
       "input_reads": 2,
       "output_reads": 1,
-      "reads_sampled": 2,
+      "reads_sampled": 1,
       "lengths": [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1],
       "quality_curves": {
         "a": [null, null, null, null, null, null, null, null, 41.000, null, null, null, null, null, null, null, null, null, null, null, 41.000, 41.000, null, null, 41.000, null, 41.000, null, null, null, null, 41.000, null, null, null, null, 41.000, null, 41.000, null, 41.000, null, null, null, null, null, 41.000, null, null, null, null, null, 41.000, null, null, 41.000, null, 41.000, null, null, null, null, null, null, null, 41.000, null, null, null, null, null, null, null, null, null],

diff --git a/tests/regression/quality_trimming/trimfixed/pe/collapse_5p/your_output.json b/tests/regression/quality_trimming/trimfixed/pe/collapse_5p/your_output.json
@@ -38,10 +38,10 @@
     },
     "output": {
       "passed": {
-        "reads": 2,
+        "reads": 1,
         "bases": 37,
-        "mean_length": 18.500,
-        "reads_sampled": 2,
+        "mean_length": 37.000,
+        "reads_sampled": 1,
         "q20_rate": 1.000,
         "q30_rate": 1.000,
         "uncalled_rate": 0.000,
@@ -138,7 +138,7 @@
       "filenames": ["your_output.merged.fastq"],
       "input_reads": 2,
       "output_reads": 1,
-      "reads_sampled": 2,
+      "reads_sampled": 1,
       "lengths": [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1],
       "quality_curves": {
         "a": [null, null, 40.000, 40.000, null, 41.000, null, null, null, null, null, 39.000, 40.000, null, null, null, null, 39.000, null, null, null, 38.000, null, null, null, null, null, null, null, null, null, null, null, null, null, 41.000, null],

diff --git a/tests/regression/quality_trimming/trimfixed/pe/collapse_5p_and_3p/your_output.json b/tests/regression/quality_trimming/trimfixed/pe/collapse_5p_and_3p/your_output.json
@@ -38,10 +38,10 @@
     },
     "output": {
       "passed": {
-        "reads": 2,
+        "reads": 1,
         "bases": 37,
-        "mean_length": 18.500,
-        "reads_sampled": 2,
+        "mean_length": 37.000,
+        "reads_sampled": 1,
         "q20_rate": 1.000,
         "q30_rate": 1.000,
         "uncalled_rate": 0.000,
@@ -138,7 +138,7 @@
       "filenames": ["your_output.merged.fastq"],
       "input_reads": 2,
       "output_reads": 1,
-      "reads_sampled": 2,
+      "reads_sampled": 1,
       "lengths": [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1],
       "quality_curves": {
         "a": [null, null, 40.000, 40.000, null, 41.000, null, null, null, null, null, 39.000, 40.000, null, null, null, null, 39.000, null, null, null, 38.000, null, null, null, null, null, null, null, null, null, null, null, null, null, 41.000, null],

diff --git a/tests/regression/quality_trimming/trimfixed/pe/collapse_5p_both_set/your_output.json b/tests/regression/quality_trimming/trimfixed/pe/collapse_5p_both_set/your_output.json
@@ -38,10 +38,10 @@
     },
     "output": {
       "passed": {
-        "reads": 2,
+        "reads": 1,
         "bases": 36,
-        "mean_length": 18.000,
-        "reads_sampled": 2,
+        "mean_length": 36.000,
+        "reads_sampled": 1,
         "q20_rate": 1.000,
         "q30_rate": 1.000,
         "uncalled_rate": 0.000,
@@ -138,7 +138,7 @@
       "filenames": ["your_output.merged.fastq"],
       "input_reads": 2,
       "output_reads": 1,
-      "reads_sampled": 2,
+      "reads_sampled": 1,
       "lengths": [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1],
       "quality_curves": {
         "a": [null, null, 40.000, 40.000, null, 41.000, null, null, null, null, null, 39.000, 40.000, null, null, null, null, 39.000, null, null, null, 38.000, null, null, null, null, null, null, null, null, null, null, null, null, null, 41.000],