Merge pull request #529 from Bioinformatics/ipa-6039-fix-q-by-lane-pu…

…blic IPA-6036: Explicit exception for writing binned q-metric as unbinned
Illumina · Jan 24, 2017 · 8abfede · 8abfede
2 parents bc8610b + b0edf2f
commit 8abfede
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Showing 3 changed files with 49 additions and 1 deletion.
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -3,7 +3,7 @@ project(InterOp)
 set(CMAKE_MODULE_PATH ${PROJECT_SOURCE_DIR}/cmake/Modules)
 enable_testing()
 include(${PROJECT_SOURCE_DIR}/cmake/Modules/UseGitVersion.cmake)
-set(ARCHIVE_VERSION "v1.0.13-src")
+set(ARCHIVE_VERSION "v1.0.16-src")
 
 
 if (NOT CMAKE_BUILD_TYPE)

diff --git a/src/interop/model/metrics/q_metric.cpp b/src/interop/model/metrics/q_metric.cpp
@@ -82,6 +82,8 @@ namespace illumina { namespace interop { namespace io
         template<class Stream, class Metric, class Header>
         static std::streamsize map_stream(Stream &stream, Metric &metric, Header &, const bool)
         {
+            if(metric.size() < q_metric::MAX_Q_BINS)
+                INTEROP_THROW(bad_format_exception, "Cannot write out binned q-score histogram in an unbinned format");
             const std::streamsize count = stream_map<count_t>(stream, metric.m_qscore_hist, q_metric::MAX_Q_BINS);
             resize_accumulated(stream, metric);
             return count;

diff --git a/src/tests/interop/metrics/q_by_lane_metric_test.cpp b/src/tests/interop/metrics/q_by_lane_metric_test.cpp
@@ -80,3 +80,49 @@ TEST(run_metrics_q_by_lane_test, test_is_group_empty)
     logic::metric::create_q_metrics_by_lane(metrics.get<q_metric>(), metrics.get<q_by_lane_metric>());
     EXPECT_FALSE(metrics.is_group_empty(constants::QByLane));
 }
+
+// Test that unsupported feature throws an exception
+TEST(run_metrics_q_by_lane_test, try_write_binned_as_unbinned)
+{
+    typedef model::run::flowcell_layout::uint_t  uint_t;
+    run_metrics metrics;
+
+
+    const uint_t swath_count = 4;
+    const uint_t tile_count = 99;
+    const uint_t sections_per_lane = 1;
+    const uint_t lanes_per_section = 1;
+    const uint_t lane_count = 8;//expected.max_lane();
+    const uint_t surface_count = 2;
+    const model::run::read_info read_array[]={
+            model::run::read_info(1, 1, 4, false)
+    };
+    std::vector<std::string> channels;
+    model::run::info run_info("XX",
+                              "",
+                              1,
+                              model::run::flowcell_layout(lane_count,
+                                                          surface_count,
+                                                          swath_count,
+                                                          tile_count,
+                                                          sections_per_lane,
+                                                          lanes_per_section),
+                              channels,
+                              model::run::image_dimensions(),
+                              util::to_vector(read_array));
+
+    q_metric_v6::create_expected(metrics.get<q_metric>());
+    metrics.run_info(run_info);
+    metrics.legacy_channel_update(constants::HiSeq);
+    metrics.finalize_after_load();
+
+    ASSERT_GT(metrics.get<q_by_lane_metric>().size(), 0u);
+
+    const size_t buffer_size = io::compute_buffer_size(metrics.get<q_by_lane_metric>());
+    ASSERT_GT(buffer_size, 0u);
+    std::vector< ::uint8_t > buffer(buffer_size);
+    metrics.get<q_by_lane_metric>().set_version(4);
+    EXPECT_THROW(io::write_interop_to_buffer(metrics.get<q_by_lane_metric>(), &buffer.front(), buffer.size()),
+                 io::bad_format_exception);
+
+}