Merge branch 'mvella/fix-incorrect-dx-tag' into 'master'

Fix incorrect dx tag See merge request machine-learning/dorado!639
nanoporetech · Oct 10, 2023 · 7fefd5d · 7fefd5d
2 parents c3e22c6 + 6c54109
commit 7fefd5d
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Showing 3 changed files with 11 additions and 2 deletions.
diff --git a/dorado/read_pipeline/ReadPipeline.cpp b/dorado/read_pipeline/ReadPipeline.cpp
@@ -252,7 +252,7 @@ std::vector<BamPtr> ReadCommon::extract_sam_lines(bool emit_moves,
     if (is_duplex) {
         generate_duplex_read_tags(aln);
     } else {
-        generate_read_tags(aln, emit_moves);
+        generate_read_tags(aln, emit_moves, is_duplex_parent);
     }
     generate_modbase_tags(aln, modbase_threshold);
     alns.push_back(BamPtr(aln));

diff --git a/dorado/read_pipeline/ReadPipeline.h b/dorado/read_pipeline/ReadPipeline.h
@@ -91,7 +91,7 @@ class ReadCommon {
 
 private:
     void generate_duplex_read_tags(bam1_t*) const;
-    void generate_read_tags(bam1_t* aln, bool emit_moves, bool is_duplex_parent = false) const;
+    void generate_read_tags(bam1_t* aln, bool emit_moves, bool is_duplex_parent) const;
     void generate_modbase_tags(bam1_t* aln, uint8_t threshold = 0) const;
     std::string generate_read_group() const;
 };

diff --git a/tests/ReadTest.cpp b/tests/ReadTest.cpp
@@ -72,6 +72,15 @@ TEST_CASE(TEST_GROUP ": Test tag generation", TEST_GROUP) {
         read_common.is_duplex = was_duplex;
     }
 
+    SECTION("Duplex Parent") {
+        // Update read to be duplex parent
+        auto alignments = read_common.extract_sam_lines(false, 0, true);
+        REQUIRE(alignments.size() == 1);
+        auto* aln = alignments[0].get();
+
+        CHECK(bam_aux2i(bam_aux_get(aln, "dx")) == -1);
+    }
+
     SECTION("No model") {
         auto old_model = std::exchange(read_common.model_name, "");