Merge branch 'DOR-707_fix_trimmed_summary' into 'master'

DOR-707 Fix summary output when data is trimmed with no move table Closes DOR-707 See merge request machine-learning/dorado!1003
nanoporetech · May 16, 2024 · 70ff95d · 70ff95d
2 parents bd2f026 + 67090cb
commit 70ff95d
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Showing 2 changed files with 28 additions and 12 deletions.
diff --git a/dorado/demux/Trimmer.cpp b/dorado/demux/Trimmer.cpp
@@ -142,17 +142,24 @@ BamPtr Trimmer::trim_sequence(bam1_t* input_record, std::pair<int, int> trim_int
     auto trimmed_seq = utils::trim_sequence(seq, trim_interval);
     auto trimmed_qual = utils::trim_quality(qual, trim_interval);
     auto [positions_trimmed, trimmed_moves] = utils::trim_move_table(move_vals, trim_interval);
-    if (ts >= 0) {
-        ts += positions_trimmed * stride;
-    }
-    if (ns >= 0) {
-        // After sequence trimming, the number of samples corresponding to the sequence is the size of
-        // the new move table * stride. However, the ns tag includes the number of samples trimmed from the
-        // front of the read as well.
-        // |---------------------- ns ------------------|
-        // |----ts----|--------moves signal-------------|
-        ns = int(trimmed_moves.size() * stride) + ts;
+
+    if (move_vals.empty()) {
+        ns = -1;
+        ts = -1;
+    } else {
+        if (ts >= 0) {
+            ts += positions_trimmed * stride;
+        }
+        if (ns >= 0) {
+            // After sequence trimming, the number of samples corresponding to the sequence is the size of
+            // the new move table * stride. However, the ns tag includes the number of samples trimmed from
+            // the front of the read as well. If ts is negative, the tag is not present, so treat it as 0.
+            // |---------------------- ns ------------------|
+            // |----ts----|--------moves signal-------------|
+            ns = int(trimmed_moves.size() * stride) + std::max(0, ts);
+        }
     }
+
     auto [trimmed_modbase_str, trimmed_modbase_probs] = utils::trim_modbase_info(
             is_seq_reversed ? utils::reverse_complement(seq) : seq, modbase_str, modbase_probs,
             is_seq_reversed ? reverse_complement_interval(trim_interval, int(seq.length()))
@@ -183,9 +190,13 @@ BamPtr Trimmer::trim_sequence(bam1_t* input_record, std::pair<int, int> trim_int
 
     if (ts >= 0) {
         bam_aux_update_int(out_record, "ts", ts);
+    } else if (bam_aux_get(out_record, "ts")) {
+        bam_aux_del(out_record, bam_aux_get(out_record, "ts"));
     }
     if (ns >= 0) {
         bam_aux_update_int(out_record, "ns", ns);
+    } else if (bam_aux_get(out_record, "ns")) {
+        bam_aux_del(out_record, bam_aux_get(out_record, "ns"));
     }
 
     return output;

diff --git a/dorado/summary/summary.cpp b/dorado/summary/summary.cpp
@@ -178,8 +178,13 @@ bool SummaryData::write_rows_from_reader(
             barcode = "unclassified";
         }
 
-        float sample_rate = num_samples / duration;
-        float template_duration = (num_samples - trim_samples) / sample_rate;
+        float template_duration = duration;
+        if (num_samples > 0 && duration > 0) {
+            // If either num_samples or duration are 0 (due to missing tags), then
+            // we can't properly compute template_duration.
+            float sample_rate = num_samples / duration;
+            template_duration = (num_samples - trim_samples) / sample_rate;
+        }
         auto start_time = 0.0;
         auto exp_start_time_iter = read_group_exp_start_time.find(rg_value);
         if (exp_start_time_iter != read_group_exp_start_time.end()) {