Merge branch 'mvella/fastq-tags-alt-format' into 'master'

Alternative format for FASTQ readgroup and sam tags See merge request machine-learning/dorado!858
nanoporetech · Mar 20, 2024 · a0f9462 · a0f9462
2 parents ff330f6 + 9351670
commit a0f9462
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Showing 6 changed files with 55 additions and 9 deletions.
diff --git a/dorado/read_pipeline/HtsReader.cpp b/dorado/read_pipeline/HtsReader.cpp
@@ -22,6 +22,8 @@ HtsReader::HtsReader(const std::string& filename,
     if (!m_file) {
         throw std::runtime_error("Could not open file: " + filename);
     }
+    // If input format is FASTX, read tags from the query name line.
+    hts_set_opt(m_file, FASTQ_OPT_AUX, "1");
     format = hts_format_description(hts_get_format(m_file));
     header = sam_hdr_read(m_file);
     if (!header) {

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; }
@@ -40,7 +41,6 @@ class HtsWriter : public MessageSink {
     utils::HtsFile& m_file;
 
     void input_thread_fn();
-    int write(const bam1_t* record);
     std::atomic<int> m_duplex_reads_written{0};
     std::atomic<int> m_split_reads_written{0};
 

diff --git a/dorado/utils/hts_file.cpp b/dorado/utils/hts_file.cpp
@@ -22,10 +22,12 @@ uint64_t calculate_sorting_key(bam1_t* const record) {
 
 namespace dorado::utils {
 
-HtsFile::HtsFile(const std::string& filename, OutputMode mode, size_t threads) {
+HtsFile::HtsFile(const std::string& filename, OutputMode mode, size_t threads) : m_mode(mode) {
     switch (mode) {
     case OutputMode::FASTQ:
         m_file.reset(hts_open(filename.c_str(), "wf"));
+        hts_set_opt(m_file.get(), FASTQ_OPT_AUX, "RG");
+        hts_set_opt(m_file.get(), FASTQ_OPT_AUX, "st");
         break;
     case OutputMode::BAM: {
         auto file = filename;
@@ -191,7 +193,9 @@ int HtsFile::write(const bam1_t* const record) {
     // FIXME -- HtsFile is constructed in a state where attempting to write
     // will segfault, since set_and_write_header has to have been called
     // in order to set m_header.
-    assert(m_header);
+    if (m_mode != OutputMode::FASTQ) {
+        assert(m_header);
+    }
     ++m_num_records;
     return sam_write1(m_file.get(), m_header.get(), record);
 }

diff --git a/dorado/utils/hts_file.h b/dorado/utils/hts_file.h
@@ -8,12 +8,6 @@
 namespace dorado::utils {
 
 class HtsFile {
-    HtsFilePtr m_file;
-    SamHdrPtr m_header;
-    size_t m_num_records{0};
-    bool m_finalised{false};
-    bool m_finalise_is_noop;
-
 public:
     enum class OutputMode {
         UBAM,
@@ -34,6 +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;
+    const OutputMode m_mode;
 };
 
 }  // namespace dorado::utils
diff --git a/tests/BamWriterTest.cpp b/tests/BamWriterTest.cpp
@@ -14,6 +14,7 @@
 
 namespace fs = std::filesystem;
 using namespace dorado;
+using Catch::Matchers::Equals;
 using utils::HtsFile;
 
 class HtsWriterTestsFixture {
@@ -75,3 +76,36 @@ TEST_CASE_METHOD(HtsWriterTestsFixture, "HtsWriter: Count reads written", TEST_G
     CHECK(stats.at("unique_simplex_reads_written") == 6);
     CHECK(stats.at("split_reads_written") == 2);
 }
+
+TEST_CASE("HtsWriterTest: Read and write FASTQ with tag", TEST_GROUP) {
+    fs::path bam_test_dir = fs::path(get_data_dir("bam_reader"));
+    auto input_fastq = bam_test_dir / "fastq_with_tags.fq";
+    auto tmp_dir = TempDir(fs::temp_directory_path() / "writer_test");
+    std::filesystem::create_directories(tmp_dir.m_path);
+    auto out_fastq = tmp_dir.m_path / "output.fq";
+
+    // Read input file to check all tags are reads.
+    HtsReader reader(input_fastq.string(), std::nullopt);
+    {
+        // Write with tags into temporary folder.
+        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.
+    HtsReader new_fastq_reader(out_fastq.string(), std::nullopt);
+    new_fastq_reader.read();
+    CHECK_THAT(
+            bam_aux2Z(bam_aux_get(new_fastq_reader.record.get(), "RG")),
+            Equals("6a94c5e38fbe36232d63fd05555e41368b204cda_dna_r10.4.1_e8.2_400bps_hac@v4.3.0"));
+    CHECK_THAT(bam_aux2Z(bam_aux_get(new_fastq_reader.record.get(), "st")),
+               Equals("2023-06-22T07:17:48.308+00:00"));
+}
diff --git a/tests/data/bam_reader/fastq_with_tags.fq b/tests/data/bam_reader/fastq_with_tags.fq
@@ -0,0 +1,4 @@
+@8623ac42-0956-4692-9a93-bdd99bf1a94e	st:Z:2023-06-22T07:17:48.308+00:00	RG:Z:6a94c5e38fbe36232d63fd05555e41368b204cda_dna_r10.4.1_e8.2_400bps_hac@v4.3.0
+GTTATGTTAGTCTACCTTGGTTGCAAGTTGTGGTGCTTGCTGGTTTTTGGCTTGAAGTCTGTGTTTGAAAGCCCTGGCCTTCACAACCCAAACTGAAACTCCAGATTGGAACCAAGAAAAGCACAGTGGATATGGACAGTGGTACAAGTAAGCCTCAGGCTGGAGTCACTGGCTTTGGGTATCTGATGGTGACACCACATGTTCCAGAATGGTTGTCTGTTAAATGTTTACTAGAGTTGGGTCTGGAGCATAGAGTGAAGGGAAGGAATATAATGGAAGGTTGTAGAGTATGACAGCTAAGACTTGGAATCAGGCCGGGTGCGGTGGTTCACACCTGTAATCCCAGCACTTTGGGAGACCGAGGTGGGTGAATCATGAGGTCAGAAGTTTGAGACCAGCCTGGCTAACACAGTGAAACCCTGTCTGTACTAAAAATACAAAAATTTAGCTGGGTGTAGTGGCAGGTGCCTGTAATCCCAGCTACTTGGGAGGCTGAGTCAGGAGAATTGCTTGAACCCAGGAGGCAGAGGTTACAGTGAGCCGAGATTGCGCCACTGCACTCCAGCCCAGGTGACAGAGTGAGACTCCATCTCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGTTTGGACTGTGTTCATATCAAAACTCAGAGCTACTAGCTAGCGTGTGGAACCTGGAAGGTTACTTAGCTTCTCTAAGTTTTTTTTTTTTAATCTGTAAAAGAGGAATAAAAGTTTGGAGTTAGGTGGAAGTTATAAAAAAAAAAAAACAAGGCTCAAATTATGTATAGAATTGAAAAGTCCAGGAGCAGTCTGGGTTTCAGATACGACTTGATCCGGGGCAGACCCTTTCCTCCCTGTGGCAAGATGGCGTCTTGGTGCTCTAGGCCTGCAAATCTTACCCTTTCAGTAACCCTAATAAAGCATGAAAGTATTTCTTCCTTGCCAGTACCAGCGAAAAAAAAAAAAAGTCCTGAGGTTGACTCTTGGCTTATTAGTTGATTATAAACACTTGAGTCAATTGCTAAGAACTGGGTCACTGCCCAGCCCTGGAGCCAGGAAAGGGGTCAGCCCCACCCGAGCTACAAGAACAGACAATAGCAAAGGGATGATTTTTTTCCAAATGAAAATAAATCATGGTGCTAGTACCAGAGGAAGGGGGGATGGATGCTGGGCAGGCCAAAACAATAGATGCCCACTGAAGAAGCACTCCGTTCCAGGTCATCCTTGTTAATAAGGAAGTGGGACAAGTACAGGAACCAAAAACACTTATTTATGAGGATCCGGGCCAGGGTCAGGCATGGCATCAGCAACTCCCTACCCTGCCTTTCTACACAGTAGCACAGTCTTTATATGATAGAAATTTGGTTGCAGCTTCAATGTGACATACACATGCTTTCAACTCTCAAGGCATCAAACCTTGTTTAATTACTATTATTCTTTTCTAAGGTTTTGGTATTTTCCCTCTGTATTTCTGATGTGCCCTTCTGGCTACAGATAATCCAGATAGTGGTTGTTGTTGTGGGACTGTGAGGCAGGGAAGTCCAAAAAGTGAGGCTAACGGCCACTACTGACAGATGAAGGGGCTTCCTCAGGGGCAGAGGCACAGTGTCCGGTGATACAGGCTGGCACCTCGAGAATCAGGGATGGGATTTTCCTGGGAGCCACAGGGTTCATACTTGAGGGAGGCTTGGGAGTTTTTCACTCTCTGCATAATGGGTCTGTTCCCCTGGGGATAACCCACGACAAGATATGCCTTGTGAATGTGGGTGGCAGAGGGACACACAGGTGCAGGGGCATCTTCCAGCCCTGGACGGTGCCACATGAGGGATGGATGTAAGACTGGCCATATAGGTGAAGTGTCCGAGGCTCAGAGAGATGGCAGGGTTCACCTCTGGACAGAGCAGGACAGAACTAGAATCAATGTATAACACCGGGGAAAAGATTGTTACATGTAGAAATGCTCCACACAAACACATTCCAAGAACATGAGTGAGAGAAAGAGATGGACTGTGCTTGGTGGTGGTGGTTCGGTGCACTTCCCTCTGGGTTGGGCTGGGCTGTGGTGACAGAGGAGATGGGTACAAGGGAATTATGAGAATTTTAGATGCATTGCTCAAAATTTAGGGGCTTGGTGTGTCCAGACTTTGATGTGGGATAAGAGAAAAGGAGAGCCCTCACGGCGGGACATAAATGGGTTAATCAGGTTGGGAGAAGTGGTATCCAGTGGTTGGGCCAAACCGCCAAGTGGGGAGCCTGGGTCCAAGCAGAAAAGACAGTTTCCTCCTTTAGCAATCAAAGGAGTCCAGAGGGGGTGCCCAGCCTTGGGCCAGAGGGAGAAAGGAAGAGGGAAAGCTTTGCTCTGAGGATGAGGTTTAGAGCAGAAGGAAACAGAGACCACCCAGAAAAGGGAGACTTTTCCTGTGCCAAGGCGGAGACCCAGGGGACTGTGCACAGTTATCTCGGCCCTTTGAGCGCCTCCGTTTTCCCTTGTCTGTGGTCAAGCCTAGCTCTGTATTCCAGCCAGCTGTGGGAGGATGGGGTGACAGAGTGATGCTCAAAGAGAATGTGGGGCCAGCAGGGGCAGCCCAGGACTCTGGACTGAGGCCTTCAACAGAGAAGTCTCCCCTCCCCTCCCTTCCCCTCCCCCTCTCCCTCCCCCTCCCCTCCCCTTCCCCTCCCCCTCCTCCTTCTCCTGCTGGGAGTTAGCTGGAGAACCAACAGGCAGCATTACAGAAAGCTATAAGGCCCCTTCAGCTGGTTGAGGGGGCTCAGCTGGCCCCATGGCTAGGGCATTTGTGTCCTGTTTCCTGCCGTGCAGGAAGAGGGGCACTGTGAGGTCCTCCCGCGTCTCACCCCAACCACATACACACCTGTGAACGATGGAGCAGTCCAGATTGTCCCAGCCCTACCTAGAGGAGCGATTTGTTCTCTGATTTCCATAACACAGAAAAAATAAGAAAAAAAGAAAAAAAAATCCAAAACGAAAAGTAAAACCACTTTAAACAATTAGGAGTTTTGTTCGGTTATTTGGCGAAGGCTGTGTGCTGGGGGAGTGGGTAGTGAGGGAGTTCTTTATCCCTGGAGAATCTAAATGAAGGAAAAGTCAGTTTGAAACCGGCTCCCAAGATGACGCAGGGTCTGAACCCAGAATAAACTCTGAAAGCTATATTTTCAGCACAGAAAAGAGGGGCTTCCTAATGGAAGCTTTGGCAGCCCTTGTGCTGTGGCCCTGGCCCTGGGCAGTGCTGCGCTGCTGTTTATTTGAGAGGAAGTGGTGGAGAGTGGTCCCTCTTTTGTGGCGTGTGGTTTTGGCAGTGCCTGGGCTCTCCGTCTTCTGTTTGGGAGTCTGGCCCACCATGGAGCCCTTGCTCTTGGTTCCATTGTTAAAGGATTCCTGCTGCAGTGCATCCGGGGTGCCCACCATGAGATTCCTTTGTCGTGGAAGAAGGTGCCACCCTTTCCACCTGCCTCTTTTCTGGGGGGATTTTCTGCCTGCTTGCATGGGAGGCATGTGGCTGTAGGTGGGGAGGGCAAGGGGCTGACTAGAAGTGGAGGTGAAGGGTGAAGCCACGGAGGTGCCGTGGCACTTGTCTTCTTGGCCCTCCTGCCTCTGAACCCCAGTGACGGTCTCTTGCGGGCTGGTGGCTCCACCTTTTGGTCTGTGCTGGGACCTGGCAGGAAAACCATGCTTGGCTGTGTGAGAATGGCAGAGTATGGTGGGCCTGGGGCAGAGTGGTGGTGGTGGCAGAGGAACGAAAAGGATGGTGTTGGGGTAGCCATGGGAACGCCAGCTTTGTAACAAGACAGATACGGGTTTGAATCTTGGCCCCAGCACTGATTGCTGATGACTTTGGGTAAATAGCTTGACCTTTCTGAGGGCCAGTTTCTTGATCTTTAATACGGCCATAATCATACCTACCCCAGATAAAGGCTCAGGACCTCTTGTGTCACACAAAATATCGTGTGATTTTGAAAGCAATGCCTCGGACTCAGACCTATAGGCCATAGTTTAGGGAAACCCAAATCCTTCTCCAGAAATAGGGCTTATGCTCATGTGGAGTCCTCTGTCCCAGCTACCAATTGGTGCTGTAGCCTGTTTTGCCTCCATCAGCCCACACTCAAAACTCAGCTCCTGCCCCGATTTTCCACAAAACCCACTCATAGCAAGCACTTTGCAAGCTTAATATACCTTACAGACAATCTGGGGATACTGAACAAGCAGCTTATTATCTCATTCACTGTTCTTTTTCCTCATCTTTCTTTACTCCTGTCCTCCTAGATTTCTCAGACTGCCAAATTATCCCCCTCTATGCACAGGGCAATTCAGCTCTCCCCATGTCCTACTCCCAATATTGCACACCAACACTTCTAGAATTGCTTAACAGATTTCACCAGATCTAAATGTCTCTAAAAACAGTGGAATAGAAAATAACAAATCTACTACTGATAGTGCCTACTTCATAGCATTTTTATGAGTAATACTATCACCACAGTGACTAGCACATGGTAATACTATCACCACAGTGACTAGCGCATAGTGATCAATAGCTATAACCATTTGAAGAAACCAGGGGTGAGTGTATCTGAGAATCCAAGAAAAGATATTGGCACGTTGGTGGATCAAAAAGCAGATATTGGGGTCAGCATATTTTGCCTTTAATCTGACCAGCATTTCTACATCTTGTTGACACTTTGTGAAGTGGGCAGGACAGCCTCCACCACACCCTTTATACAGGAAGACAAAGCGAGAACTGCCCAGATTCACCAACTGGGAAGTGGCGAGTGTTTATTATGGATCAACATGTGTAAACTGTAGGGGGAGGGATTCATGGGACAGAGGGAGAAGTTGATCAGCAAACCCTATTGGGAGCTGTGGAGCATACGCAGCCCTCAGAGGTGTCCTGTCATGGGTCTTTGTACCCCTGCCACTGTTAGCTGTTGCATTTGGGCTACCCGGAAAGGAAAGAGATGCCCTTGGGCAAAGCAGCTGTCTATGGCAAGCACACTCTGAAGGAGCTGACAGCTGGAGGCAAGTCCTTCCCTCCAGAAAGGGCATTTGGGCAGTGCATCTCCTGTCCTACCACTTTCTTCCATCTGCAAAATGGGGATCATGATAGTACCAGCTTGCAGGGTTAAAGTAAGGTAGTGGGTGCAGGTGTCTTCCATAAACAACAGTTGTCTTTAAGGGCACTGTGGGTACTCTGTCTACCAGGCAGCTCTGGCTGTGGGAGCCCCTCCCAATAGAGCTGCCACCAGCCCTTTCTGATAGGACTAACTCCCCAGGAATGTCAGGGTGGTGACTCCGGAGCACTTACAATTGGACACTGTGAAGATGATCATTGTGTTGCATCACCACTGCCCTTCATTCAGTTGTTTCAGATTAAATTCATCATAACAAGAGGTCTCTAATCAGAAACACAGCTGAACTTAAATACAGGGGGGAACTCTGGAAAAAAAGGAATGCTGAAAGAAGCTGAGTTTCCTTCATTCTGAGGACTCTGAATACATTTGAGACTTGCATCTTACTCTTCTAAAGCCATGCAGCCCAAGCTTTCTATTCCATGTTAGTCAGATGTGGAGTCATTTCAGACCAAGATAGAGTAGGGGTAGATAAGATTCAATGATGCTTGTAGAGATTATCACAATAATAGCCAATAAATCATATCTGATACCATGCCCTTGTGTAGTGTTCTTCCACACTGACTCTGGGCCTCACCCATGTGTCCTGTTTTGGTCAGTGTGGCATCAGCTAACATTGACCCAACAGAGACTGGTAAGTGCTTGCTCACCAAAATACTGAAGCTCCAACTGGCCTCTTGAGATCAAAACCAGGTAAAAAGAAGGACCTGCCTCCAGCCAAT
++
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