Merge branch 'feature/format_read_as_string' into 'master'

Format a read id as a string See merge request minknow/mkr-file-format!15
nanoporetech · May 10, 2022 · 1d947e7 · 1d947e7
2 parents 7a024bd + fc8e909
commit 1d947e7
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diff --git a/c++/mkr_format/c_api.cpp b/c++/mkr_format/c_api.cpp
@@ -12,6 +12,7 @@
 #include <arrow/array/array_primitive.h>
 #include <arrow/memory_pool.h>
 #include <arrow/type.h>
+#include <boost/uuid/uuid_io.hpp>
 
 #include <chrono>
 #include <iostream>
@@ -962,6 +963,26 @@ mkr_error_t mkr_vbz_decompress_signal(char const* compressed_signal,
 
     return MKR_OK;
 }
+
+mkr_error_t mkr_format_read_id(uint8_t* read_id, char* read_id_string) {
+    mkr_reset_error();
+
+    if (!check_not_null(read_id) || !check_output_pointer_not_null(read_id_string)) {
+        return g_mkr_error_no;
+    }
+
+    boost::uuids::uuid* uuid_data = reinterpret_cast<boost::uuids::uuid*>(read_id);
+    std::string string_data = boost::uuids::to_string(*uuid_data);
+    if (string_data.size() != 36) {
+        mkr_set_error(mkr::Status::Invalid("Unexpected length of UUID"));
+        return g_mkr_error_no;
+    }
+
+    std::copy(string_data.begin(), string_data.end(), read_id_string);
+    read_id_string[string_data.size()] = '\0';
+
+    return MKR_OK;
+}
 }
 
 //---------------------------------------------------------------------------------------------------------------------

diff --git a/c++/mkr_format/c_api.h b/c++/mkr_format/c_api.h
@@ -541,6 +541,15 @@ MKR_FORMAT_EXPORT mkr_error_t mkr_vbz_decompress_signal(char const* compressed_s
                                                         size_t sample_count,
                                                         short* signal_out);
 
+//---------------------------------------------------------------------------------------------------------------------
+// Global state
+//---------------------------------------------------------------------------------------------------------------------
+
+/// \brief Format a packed binary read id as a readable read id string:
+/// \param          read_id           A 16 byte binary formatted UUID.
+/// \param[out]     read_id_string    Output string containing the string formatted UUID (expects a string of at least 37 bytes, one null byte is written.)
+MKR_FORMAT_EXPORT mkr_error_t mkr_format_read_id(uint8_t* read_id, char* read_id_string);
+
 #ifdef __cplusplus
 }
 #endif

diff --git a/c++/test/c_api_tests.cpp b/c++/test/c_api_tests.cpp
@@ -2,6 +2,7 @@
 
 #include <boost/filesystem.hpp>
 #include <boost/uuid/random_generator.hpp>
+#include <boost/uuid/uuid_io.hpp>
 #include <catch2/catch.hpp>
 #include <gsl/gsl-lite.hpp>
 
@@ -136,6 +137,11 @@ SCENARIO("C API") {
                                               &median_before, &end_reason, &run_info,
                                               &signal_row_count) == MKR_OK);
 
+            std::string formatted_uuid(36, '\0');
+            CHECK(mkr_format_read_id((uint8_t*)read_id.begin(), &formatted_uuid[0]) == MKR_OK);
+            CHECK(formatted_uuid.size() == boost::uuids::to_string(read_id).size());
+            CHECK(formatted_uuid == boost::uuids::to_string(read_id));
+
             CHECK(read_number == 12);
             CHECK(start_sample == 10245);
             CHECK(median_before == 200.0f);