make output mode const

nanoporetech · Mar 20, 2024 · 9351670 · 9351670
1 parent 2f663ad
commit 9351670
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Showing 3 changed files with 6 additions and 2 deletions.
diff --git a/dorado/read_pipeline/HtsWriter.h b/dorado/read_pipeline/HtsWriter.h
@@ -24,6 +24,7 @@ class HtsWriter : public MessageSink {
     void terminate(const FlushOptions&) override;
     void restart() override { start_input_processing(&HtsWriter::input_thread_fn, this); }
 
+    int write(const bam1_t* record);
     size_t get_total() const { return m_total; }
     size_t get_primary() const { return m_primary; }
     size_t get_unmapped() const { return m_unmapped; }

diff --git a/dorado/utils/hts_file.h b/dorado/utils/hts_file.h
@@ -28,13 +28,14 @@ class HtsFile {
 
     bool finalise_is_noop() const { return m_finalise_is_noop; }
     void finalise(const ProgressCallback& progress_callback, int writer_threads);
+
 private:
     HtsFilePtr m_file;
     SamHdrPtr m_header;
     size_t m_num_records{0};
     bool m_finalised{false};
     bool m_finalise_is_noop;
-    OutputMode m_mode;
+    const OutputMode m_mode;
 };
 
 }  // namespace dorado::utils
diff --git a/tests/BamWriterTest.cpp b/tests/BamWriterTest.cpp
@@ -88,14 +88,16 @@ TEST_CASE("HtsWriterTest: Read and write FASTQ with tag", TEST_GROUP) {
     HtsReader reader(input_fastq.string(), std::nullopt);
     {
         // Write with tags into temporary folder.
-        HtsWriter writer(out_fastq.string(), HtsFile::OutputMode::FASTQ, 2);
+        utils::HtsFile hts_file(out_fastq.string(), HtsFile::OutputMode::FASTQ, 2);
+        HtsWriter writer(hts_file);
         reader.read();
         CHECK_THAT(bam_aux2Z(bam_aux_get(reader.record.get(), "RG")),
                    Equals("6a94c5e38fbe36232d63fd05555e41368b204cda_dna_r10.4.1_e8.2_400bps_hac@v4."
                           "3.0"));
         CHECK_THAT(bam_aux2Z(bam_aux_get(reader.record.get(), "st")),
                    Equals("2023-06-22T07:17:48.308+00:00"));
         writer.write(reader.record.get());
+        hts_file.finalise([](size_t) { /* noop */ }, 2);
     }
 
     // Read temporary file to make sure tags were correctly set.