diff --git a/src/reports_json.cpp b/src/reports_json.cpp index e58b87b1..ce3fa9f2 100644 --- 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 index e2e2f0a0..b1b8a9ea 100644 --- 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 index 3cbec8bc..09e63f16 100644 --- 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 index 467d6ffc..0b82ab73 100644 --- 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 index a79d6d48..3375d05a 100644 --- 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 index 7a42e1bb..c634132b 100644 --- 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 index 73a4165a..40001c63 100644 --- a/tests/regression/misc/merging/your_output.json +++ b/tests/regression/misc/merging/your_output.json @@ -37,10 +37,10 @@ }, "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, @@ -48,10 +48,10 @@ }, "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 index df64c3fe..a363b800 100644 --- 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 index cee6ed6d..5c9199fe 100644 --- 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 index 67a9dcee..6cf3ae6c 100644 --- 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 index 67a9dcee..6cf3ae6c 100644 --- 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 index 4c7dc3d5..fa133122 100644 --- 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],