public void Histogram() { int[] tmp = new int[]{ 6,34,1,7,2,10,20,25,30,35,40,9,19,24,29,34,39,40,2,14,21,27,32,36,40 ,7,0,90,4,1,0,0,0,0,0,-70,22,4,0,-81,-49,1,0,-68,16,0,0,78,-86,42,0,0,0,0,0,0,0,0,0 ,7,0,90,4,2,0,0,0,0,0,75,-81,3,0,-96,-81,0,0,76,4,0,0,112,62,44,0,0,0,0,0,0,0,0,0 ,7,0,90,4,3,0,0,0,0,0,-80,60,3,0,-74,-46,0,0,-85,1,0,0,-106,-112,44,0,0,0,0,0,0,0,0,0 }; byte[] expected_binary_data = new byte[tmp.Length]; for(int i=0;i<expected_binary_data.Length;i++) expected_binary_data[i] = (byte)tmp[i]; run_metrics run = new run_metrics(); c_csharp_comm.read_interop_from_buffer(expected_binary_data, (uint)expected_binary_data.Length, run.q_metric_set()); filter_options options = new filter_options(tile_naming_method.FourDigit); read_info_vector reads = new read_info_vector(); reads.Add(new read_info(1, 1, 26)); reads.Add(new read_info(2, 27, 76)); run.run_info(new info( "", "", 1, new flowcell_layout(8, 2, 2, 36, 1, 1, new string_vector(), tile_naming_method.FourDigit), new string_vector(), new image_dimensions(), reads )); run.legacy_channel_update(instrument_type.HiSeq); run.finalize_after_load(); bar_plot_data data = new bar_plot_data(); c_csharp_plot.plot_qscore_histogram(run, options, data); Assert.AreEqual(data.size(), 1); }
public void TestBadMetricException() { int[] tmp = new int[] { 6, 34, 1, 7, 2, 10, 20, 25, 30, 35, 40, 9, 19, 24, 29, 34, 39, 40, 2, 14, 21, 27, 32, 36, 40 , 7, 0, 90, 4, 1, 0, 0, 0, 0, 0, -70, 22, 4, 0, -81, -49, 1, 0, -68, 16, 0, 0, 78, -86, 42, 0, 0, 0, 0, 0, 0, 0, 0, 0 , 7, 0, 90, 4, 2, 0, 0, 0, 0, 0, 75, -81, 3, 0, -96, -81, 0, 0, 76, 4, 0, 0, 112, 62, 44, 0, 0, 0, 0, 0, 0, 0, 0, 0 , 7, 0, 90, 4, 3, 0, 0, 0, 0, 0, -80, 60, 3, 0, -74, -46, 0, 0, -85, 1, 0, 0, -106, -112, 44, 0, 0, 0, 0, 0, 0, 0, 0, 0 }; byte[] expected_binary_data = new byte[tmp.Length]; for (int i = 0; i < expected_binary_data.Length; i++) { expected_binary_data[i] = (byte)tmp[i]; } run_metrics run = new run_metrics(); c_csharp_comm.read_interop_from_buffer(expected_binary_data, (uint)expected_binary_data.Length, run.q_metric_set()); uint ALL_IDS = (uint)filter_options.UseAll.ALL_IDS; filter_options options = new filter_options(tile_naming_method.FourDigit, ALL_IDS, 0, dna_bases.A, ALL_IDS, 1, 1); read_info_vector reads = new read_info_vector(); reads.Add(new read_info(1, 1, 26)); reads.Add(new read_info(2, 27, 76)); run.run_info(new info( new flowcell_layout(8, 2, 2, 36, 1, 1, new string_vector(), tile_naming_method.FourDigit), reads )); run.legacy_channel_update(instrument_type.HiSeq); run.finalize_after_load(); flowcell_data data = new flowcell_data(); c_csharp_plot.plot_flowcell_map(run, "NoMetric", options, data); }
public void TestListErrorMetricFilenames() { run_metrics run = new run_metrics(); read_info_vector reads = new read_info_vector(); reads.Add(new read_info(1, 1, 3)); run.run_info(new info( "", "", 1, new flowcell_layout(2, 2, 2, 16), new string_vector(), new image_dimensions(), reads )); run.set_naming_method(tile_naming_method.FourDigit); run.legacy_channel_update(instrument_type.HiSeq); string_vector filenames = new string_vector(); run.list_error_metric_filenames(filenames, "RunFolder"); Assert.AreEqual(filenames.Count, 1); Assert.AreEqual(filenames[0], Path.Combine("RunFolder", "InterOp", "ErrorMetricsOut.bin")); }
public void TestInvalidMetricName() { run_metrics metrics = new run_metrics(); filter_options options = new filter_options(tile_naming_method.FourDigit); candle_stick_plot_data data = new candle_stick_plot_data(); c_csharp_plot.plot_by_cycle(metrics, "NoMetric", options, data); }
public void Histogram() { int[] tmp = new int[] { 6, 34, 1, 7, 2, 10, 20, 25, 30, 35, 40, 9, 19, 24, 29, 34, 39, 40, 2, 14, 21, 27, 32, 36, 40 , 7, 0, 90, 4, 1, 0, 0, 0, 0, 0, -70, 22, 4, 0, -81, -49, 1, 0, -68, 16, 0, 0, 78, -86, 42, 0, 0, 0, 0, 0, 0, 0, 0, 0 , 7, 0, 90, 4, 2, 0, 0, 0, 0, 0, 75, -81, 3, 0, -96, -81, 0, 0, 76, 4, 0, 0, 112, 62, 44, 0, 0, 0, 0, 0, 0, 0, 0, 0 , 7, 0, 90, 4, 3, 0, 0, 0, 0, 0, -80, 60, 3, 0, -74, -46, 0, 0, -85, 1, 0, 0, -106, -112, 44, 0, 0, 0, 0, 0, 0, 0, 0, 0 }; byte[] expected_binary_data = new byte[tmp.Length]; for (int i = 0; i < expected_binary_data.Length; i++) { expected_binary_data[i] = (byte)tmp[i]; } run_metrics run = new run_metrics(); c_csharp_comm.read_interop_from_buffer(expected_binary_data, (uint)expected_binary_data.Length, run.q_metric_set()); filter_options options = new filter_options(tile_naming_method.FourDigit); read_info_vector reads = new read_info_vector(); reads.Add(new read_info(1, 1, 26)); reads.Add(new read_info(2, 27, 76)); run.run_info(new info( new flowcell_layout(8, 2, 2, 36, 1, 1, new string_vector(), tile_naming_method.FourDigit), reads )); run.legacy_channel_update(instrument_type.HiSeq); run.finalize_after_load(); bar_plot_data data = new bar_plot_data(); c_csharp_plot.plot_qscore_histogram(run, options, data); Assert.AreEqual(data.size(), 1); }
public void TestListErrorMetricFilenames() { run_metrics run = new run_metrics(); read_info_vector reads = new read_info_vector(); reads.Add(new read_info(1, 1, 3)); run.run_info(new info(new flowcell_layout(2, 2, 2, 16), reads )); run.set_naming_method(tile_naming_method.FourDigit); run.legacy_channel_update(instrument_type.HiSeq); string_vector filenames = new string_vector(); run.list_filenames(metric_group.Error, filenames, "RunFolder"); Assert.AreEqual(filenames.Count, 4); string interopFolder = Path.Combine("RunFolder", "InterOp"); string interopFolderCycle1 = Path.Combine(interopFolder, "C1.1"); string interopFolderCycle2 = Path.Combine(interopFolder, "C2.1"); string interopFolderCycle3 = Path.Combine(interopFolder, "C3.1"); Assert.AreEqual(filenames[0], Path.Combine(interopFolder, "ErrorMetricsOut.bin")); Assert.AreEqual(filenames[1], Path.Combine(interopFolderCycle1, "ErrorMetricsOut.bin")); Assert.AreEqual(filenames[2], Path.Combine(interopFolderCycle2, "ErrorMetricsOut.bin")); Assert.AreEqual(filenames[3], Path.Combine(interopFolderCycle3, "ErrorMetricsOut.bin")); }
static int Main(string[] args) { if (args.Length != 1) { if (args.Length < 1) { Console.WriteLine("No run folder"); } else { Console.WriteLine("Too many arguments"); } return(1); } run_metrics metrics = new run_metrics(); metrics.read(args[0]); run_summary summary = new run_summary(); c_csharp_summary.summarize_run_metrics(metrics, summary); Console.WriteLine("Yield: {0}", summary.total_summary().yield_g()); return(0); }
static int Main(string[] args) { if (args.Length != 1) { if (args.Length < 1) { Console.WriteLine("No run folder"); } else { Console.WriteLine("Too many arguments"); } return(1); } // @ [Reading only metrics required by the Imaging Tab] run_metrics metrics = new run_metrics(); uchar_vector interopsToLoad = new uchar_vector(); // Load only the metrics required by imaging table c_csharp_table.list_imaging_table_metrics_to_load(interopsToLoad); metrics.read(args[0], interopsToLoad); // @ [Reading only metrics required by the Imaging Tab] imaging_column_vector columnVector = new imaging_column_vector(); map_id_offset rowOffsets = new map_id_offset(); c_csharp_table.create_imaging_table_columns(metrics, columnVector); c_csharp_table.count_table_rows(metrics, rowOffsets); int rowCount = rowOffsets.Count; int columnCount = (int)c_csharp_table.count_table_columns(columnVector); float[] data = new float[rowCount * columnCount]; c_csharp_table.populate_imaging_table_data(metrics, columnVector, rowOffsets, data, (uint)data.Length); for (int rowIndex = 0; rowIndex < rowCount; ++rowIndex) { for (int groupIndex = 0; groupIndex < columnVector.Count; ++groupIndex) { if (columnVector[groupIndex].has_children()) { for (int subColumnIndex = 0; subColumnIndex < columnVector[groupIndex].subcolumns().Count; ++subColumnIndex) { int columnIndex = (int)(columnVector[groupIndex].offset() + subColumnIndex); Console.Write("{0},", data[rowIndex * columnCount + columnIndex]); } } else { int columnIndex = (int)(columnVector[groupIndex].offset()); Console.Write("{0},", data[rowIndex * columnCount + columnIndex]); } } Console.WriteLine(); } return(0); }
public static void plot_run_diagnostics_flowcell_map(run_metrics metrics, string metric_name, filter_options options, flowcell_data data) { c_csharp_plotPINVOKE.plot_run_diagnostics_flowcell_map__SWIG_5(run_metrics.getCPtr(metrics), metric_name, filter_options.getCPtr(options), flowcell_data.getCPtr(data)); if (c_csharp_plotPINVOKE.SWIGPendingException.Pending) { throw c_csharp_plotPINVOKE.SWIGPendingException.Retrieve(); } }
public static void plot_run_diagnostics_by_cycle(run_metrics metrics, filter_options options, candle_stick_plot_data data) { c_csharp_plotPINVOKE.plot_run_diagnostics_by_cycle(run_metrics.getCPtr(metrics), filter_options.getCPtr(options), candle_stick_plot_data.getCPtr(data)); if (c_csharp_plotPINVOKE.SWIGPendingException.Pending) { throw c_csharp_plotPINVOKE.SWIGPendingException.Retrieve(); } }
public static void plot_event_by_event_type(run_metrics metrics, filter_options options, candle_stick_plot_data data, bool save_outliers) { c_csharp_plotPINVOKE.plot_event_by_event_type__SWIG_0(run_metrics.getCPtr(metrics), filter_options.getCPtr(options), candle_stick_plot_data.getCPtr(data), save_outliers); if (c_csharp_plotPINVOKE.SWIGPendingException.Pending) { throw c_csharp_plotPINVOKE.SWIGPendingException.Retrieve(); } }
public static void plot_distortion(run_metrics metrics, filter_options options, uint distortion_curve_index, candle_stick_plot_data data) { c_csharp_plotPINVOKE.plot_distortion(run_metrics.getCPtr(metrics), filter_options.getCPtr(options), distortion_curve_index, candle_stick_plot_data.getCPtr(data)); if (c_csharp_plotPINVOKE.SWIGPendingException.Pending) { throw c_csharp_plotPINVOKE.SWIGPendingException.Retrieve(); } }
public static void summarize_compass_run_metrics(run_metrics metrics, run_summary summary, bool skip_median, bool clear) { c_csharp_summaryPINVOKE.summarize_compass_run_metrics__SWIG_0(run_metrics.getCPtr(metrics), run_summary.getCPtr(summary), skip_median, clear); if (c_csharp_summaryPINVOKE.SWIGPendingException.Pending) { throw c_csharp_summaryPINVOKE.SWIGPendingException.Retrieve(); } }
public static void plot_sample_qc(run_metrics metrics, uint lane, bar_plot_data data) { c_csharp_plotPINVOKE.plot_sample_qc(run_metrics.getCPtr(metrics), lane, bar_plot_data.getCPtr(data)); if (c_csharp_plotPINVOKE.SWIGPendingException.Pending) { throw c_csharp_plotPINVOKE.SWIGPendingException.Retrieve(); } }
public static void plot_by_cycle(run_metrics metrics, string metric_name, filter_options options, candle_stick_plot_data data, bool skip_empty) { c_csharp_plotPINVOKE.plot_by_cycle__SWIG_2(run_metrics.getCPtr(metrics), metric_name, filter_options.getCPtr(options), candle_stick_plot_data.getCPtr(data), skip_empty); if (c_csharp_plotPINVOKE.SWIGPendingException.Pending) { throw c_csharp_plotPINVOKE.SWIGPendingException.Retrieve(); } }
public static void plot_qscore_heatmap(run_metrics metrics, filter_options options, heatmap_data data) { c_csharp_plotPINVOKE.plot_qscore_heatmap__SWIG_2(run_metrics.getCPtr(metrics), filter_options.getCPtr(options), heatmap_data.getCPtr(data)); if (c_csharp_plotPINVOKE.SWIGPendingException.Pending) { throw c_csharp_plotPINVOKE.SWIGPendingException.Retrieve(); } }
public static void plot_qscore_histogram(run_metrics metrics, filter_options options, bar_plot_data data, uint boundary) { c_csharp_plotPINVOKE.plot_qscore_histogram__SWIG_0(run_metrics.getCPtr(metrics), filter_options.getCPtr(options), bar_plot_data.getCPtr(data), boundary); if (c_csharp_plotPINVOKE.SWIGPendingException.Pending) { throw c_csharp_plotPINVOKE.SWIGPendingException.Retrieve(); } }
public void TestInvalidMetricName() { run_metrics metrics = new run_metrics(); filter_options options = new filter_options(tile_naming_method.FourDigit); candle_stick_plot_data data = new candle_stick_plot_data(); c_csharp_plot.plot_by_cycle(metrics, "NoMetric", options, data); }
public static void plot_subtile_map(run_metrics metrics, metric_type type, filter_options options, subtile_data data) { c_csharp_plotPINVOKE.plot_subtile_map__SWIG_2(run_metrics.getCPtr(metrics), (int)type, filter_options.getCPtr(options), subtile_data.getCPtr(data)); if (c_csharp_plotPINVOKE.SWIGPendingException.Pending) { throw c_csharp_plotPINVOKE.SWIGPendingException.Retrieve(); } }
public void TestInvalidFilterOption() { run_metrics metrics = new run_metrics(); filter_options options = new filter_options(tile_naming_method.FourDigit); candle_stick_plot_data data = new candle_stick_plot_data(); options.cycle(1); c_csharp_plot.plot_by_cycle(metrics, metric_type.Intensity, options, data); }
public static void summarize_compass_cycle_metrics(run_metrics metrics, compass_cycle_table table) { c_csharp_summaryPINVOKE.summarize_compass_cycle_metrics(run_metrics.getCPtr(metrics), compass_cycle_table.getCPtr(table)); if (c_csharp_summaryPINVOKE.SWIGPendingException.Pending) { throw c_csharp_summaryPINVOKE.SWIGPendingException.Retrieve(); } }
public static void list_subtile_metrics(run_metrics metrics, metric_type_description_vector types) { c_csharp_plotPINVOKE.list_subtile_metrics__SWIG_1(run_metrics.getCPtr(metrics), metric_type_description_vector.getCPtr(types)); if (c_csharp_plotPINVOKE.SWIGPendingException.Pending) { throw c_csharp_plotPINVOKE.SWIGPendingException.Retrieve(); } }
public static void summarize_compass_run_metrics(run_metrics metrics, run_summary summary) { c_csharp_summaryPINVOKE.summarize_compass_run_metrics__SWIG_2(run_metrics.getCPtr(metrics), run_summary.getCPtr(summary)); if (c_csharp_summaryPINVOKE.SWIGPendingException.Pending) { throw c_csharp_summaryPINVOKE.SWIGPendingException.Retrieve(); } }
public static void plot_subtile_aggregate(run_metrics metrics, string metric_name, filter_options options, candle_stick_plot_data data_x, candle_stick_plot_data data_y) { c_csharp_plotPINVOKE.plot_subtile_aggregate__SWIG_1(run_metrics.getCPtr(metrics), metric_name, filter_options.getCPtr(options), candle_stick_plot_data.getCPtr(data_x), candle_stick_plot_data.getCPtr(data_y)); if (c_csharp_plotPINVOKE.SWIGPendingException.Pending) { throw c_csharp_plotPINVOKE.SWIGPendingException.Retrieve(); } }
public static void plot_by_lane(run_metrics metrics, metric_type type, filter_options options, candle_stick_plot_data data) { c_csharp_plotPINVOKE.plot_by_lane__SWIG_1(run_metrics.getCPtr(metrics), (int)type, filter_options.getCPtr(options), candle_stick_plot_data.getCPtr(data)); if (c_csharp_plotPINVOKE.SWIGPendingException.Pending) { throw c_csharp_plotPINVOKE.SWIGPendingException.Retrieve(); } }
public static void count_table_rows(run_metrics metrics, map_id_offset row_offset) { c_csharp_tablePINVOKE.count_table_rows(run_metrics.getCPtr(metrics), map_id_offset.getCPtr(row_offset)); if (c_csharp_tablePINVOKE.SWIGPendingException.Pending) { throw c_csharp_tablePINVOKE.SWIGPendingException.Retrieve(); } }
public static void create_imaging_table(run_metrics metrics, imaging_table table) { c_csharp_tablePINVOKE.create_imaging_table(run_metrics.getCPtr(metrics), imaging_table.getCPtr(table)); if (c_csharp_tablePINVOKE.SWIGPendingException.Pending) { throw c_csharp_tablePINVOKE.SWIGPendingException.Retrieve(); } }
public static void summarize_index_metrics(run_metrics metrics, uint lane, index_lane_summary summary) { c_csharp_summaryPINVOKE.summarize_index_metrics__SWIG_0(run_metrics.getCPtr(metrics), lane, index_lane_summary.getCPtr(summary)); if (c_csharp_summaryPINVOKE.SWIGPendingException.Pending) { throw c_csharp_summaryPINVOKE.SWIGPendingException.Retrieve(); } }
public static void create_run_diagnostics_table_columns(run_metrics metrics, run_diagnostics_column_vector columns) { c_csharp_tablePINVOKE.create_run_diagnostics_table_columns__SWIG_1(run_metrics.getCPtr(metrics), run_diagnostics_column_vector.getCPtr(columns)); if (c_csharp_tablePINVOKE.SWIGPendingException.Pending) { throw c_csharp_tablePINVOKE.SWIGPendingException.Retrieve(); } }
public void ListAvailablePlotMetrics() { run_metrics run = new run_metrics(); metric_type_description_vector metricTypeList = new metric_type_description_vector(); c_csharp_plot.list_available_plot_metrics(run, metricTypeList); Assert.AreEqual(0, metricTypeList.Count); }
public void Test_invalid_channel_exception() { run_metrics metrics = new run_metrics(); try{ metrics.finalize_after_load(); Assert.Fail("No exception thrown!"); }catch (Illumina.InterOp.RunMetrics.invalid_channel_exception) {} }
public void TestFileNotFoundException() { run_metrics metrics = new run_metrics(); try{ metrics.read("/NO/FILE/EXISTS"); } catch (Exception) {} }
public static uint calculate_run_diagnostics_flowcell_buffer_size(run_metrics metrics, filter_options options) { uint ret = c_csharp_plotPINVOKE.calculate_run_diagnostics_flowcell_buffer_size(run_metrics.getCPtr(metrics), filter_options.getCPtr(options)); if (c_csharp_plotPINVOKE.SWIGPendingException.Pending) { throw c_csharp_plotPINVOKE.SWIGPendingException.Retrieve(); } return(ret); }
public void IntensityTest() { int[] tmp = new int[]{2,10 ,7,0,90,4,100,0,-67,-66,15,74 ,7,0,90,4,102,0,74,122,-59,74 ,7,0,90,4,101,0,12,94,-115,73 ,7,0,90,4,103,0,16,54,66,74 ,7,0,90,4,-56,0,82,-11,80,58 ,7,0,90,4,-55,0,-62,42,-99,58 ,7,0,90,4,44,1,-102,113,39,64 ,7,0,-66,4,100,0,-67,-66,15,74 ,7,0,-66,4,102,0,74,122,-59,74 ,7,0,-66,4,101,0,46,103,-113,73 ,7,0,-66,4,103,0,0,2,69,74 ,7,0,-66,4,-56,0,21,111,-87,58 ,7,0,-66,4,-55,0,-86,29,-79,58 ,7,0,-66,4,44,1,6,-42,39,64 ,7,0,66,8,100,0,-67,-66,15,74 ,7,0,66,8,102,0,74,122,-59,74 ,7,0,66,8,101,0,67,-26,-109,73 ,7,0,66,8,103,0,92,47,75,74 ,7,0,66,8,-56,0,123,22,-100,58 ,7,0,66,8,-55,0,85,6,115,58 ,7,0,66,8,44,1,57,97,31,64 }; byte[] expected_binary_data = new byte[tmp.Length]; for(int i=0;i<expected_binary_data.Length;i++) expected_binary_data[i] = (byte)tmp[i]; run_metrics run = new run_metrics(); c_csharp_comm.read_interop_from_buffer(expected_binary_data, (uint)expected_binary_data.Length, run.tile_metric_set()); filter_options options = new filter_options(tile_naming_method.FourDigit); read_info_vector reads = new read_info_vector(); reads.Add(new read_info(1, 1, 26)); reads.Add(new read_info(2, 27, 76)); run.run_info(new info( "", "", 1, new flowcell_layout(2, 2, 2, 16), new string_vector(), new image_dimensions(), reads )); run.set_naming_method(tile_naming_method.FourDigit); run.legacy_channel_update(instrument_type.HiSeq); candle_stick_plot_data data = new candle_stick_plot_data(); c_csharp_plot.plot_by_lane(run, metric_type.ClusterCountPF, options, data); Assert.AreEqual(data.size(), 1); }
public void Heatmap() { int[] tmp = new int[]{ 6,34,1,7,2,10,20,25,30,35,40,9,19,24,29,34,39,40,2,14,21,27,32,36,40 ,7,0,90,4,1,0,0,0,0,0,-70,22,4,0,-81,-49,1,0,-68,16,0,0,78,-86,42,0,0,0,0,0,0,0,0,0 ,7,0,90,4,2,0,0,0,0,0,75,-81,3,0,-96,-81,0,0,76,4,0,0,112,62,44,0,0,0,0,0,0,0,0,0 ,7,0,90,4,3,0,0,0,0,0,-80,60,3,0,-74,-46,0,0,-85,1,0,0,-106,-112,44,0,0,0,0,0,0,0,0,0 }; byte[] expected_binary_data = new byte[tmp.Length]; for(int i=0;i<expected_binary_data.Length;i++) expected_binary_data[i] = (byte)tmp[i]; run_metrics run = new run_metrics(); c_csharp_comm.read_interop_from_buffer(expected_binary_data, (uint)expected_binary_data.Length, run.q_metric_set()); filter_options options = new filter_options(tile_naming_method.FourDigit); read_info_vector reads = new read_info_vector(); reads.Add(new read_info(1, 1, 26)); reads.Add(new read_info(2, 27, 76)); run.run_info(new info( "", "", 1, new flowcell_layout(8, 2, 2, 36, 1, 1, new string_vector(), tile_naming_method.FourDigit), new string_vector(), new image_dimensions(), reads )); run.legacy_channel_update(instrument_type.HiSeq); run.finalize_after_load(); uint row_count = c_csharp_plot.count_rows_for_heatmap(run); uint col_count = c_csharp_plot.count_columns_for_heatmap(run); var buffer = new float[row_count*col_count]; heatmap_data data = new heatmap_data(); c_csharp_plot.plot_qscore_heatmap(run, options, data, buffer); Assert.AreEqual(data.row_count(), 3); Assert.AreEqual(data.column_count(), 40); heatmap_data data2 = new heatmap_data(); c_csharp_plot.plot_qscore_heatmap(run, options, data2); for(uint row=0;row<data.row_count();row++) { for(uint col=0;col<data.column_count();col++) { Assert.AreEqual(buffer[row*data.column_count()+col], data2.at(row,col)); } } }
public void PopulateFloatBackedTableTest() { int[] tmp = new int[]{ 2,38 ,7,0,90,4,1,0,-12,-56,15,64,-98,35,12,64,0,0,0,0,0,0,0,0,46,1,17,1,0,0,0,0,96,-41,-104,36,122,-86,-46,-120 ,7,0,-66,4,1,0,96,-43,14,64,-63,49,13,64,0,0,0,0,0,0,0,0,56,1,17,1,0,0,0,0,112,125,77,38,122,-86,-46,-120 ,7,0,66,8,1,0,74,-68,6,64,-118,-7,8,64,0,0,0,0,0,0,0,0,93,1,46,1,0,0,0,0,-47,-104,2,40,122,-86,-46,-120 }; byte[] expected_binary_data = new byte[tmp.Length]; for(int i=0;i<expected_binary_data.Length;i++) expected_binary_data[i] = (byte)tmp[i]; run_metrics run = new run_metrics(); c_csharp_comm.read_interop_from_buffer(expected_binary_data, (uint)expected_binary_data.Length, run.extraction_metric_set()); var run_param = new parameters(); Assert.AreEqual(run_param.version(), 0); Assert.AreEqual(run.extraction_metric_set().MaxCycle, 1); read_info_vector reads = new read_info_vector(); reads.Add(new read_info(1, 1, 26)); reads.Add(new read_info(2, 27, 76)); run.run_info(new info( "", "", 1, new flowcell_layout(2, 2, 2, 16), new string_vector(), new image_dimensions(), reads )); run.legacy_channel_update(instrument_type.HiSeq); imaging_column_vector columnVector = new imaging_column_vector(); c_csharp_imaging.create_imaging_table_columns(run, columnVector); map_id_offset rowOffsets = new map_id_offset(); c_csharp_imaging.count_table_rows(run, rowOffsets); uint columnCount = c_csharp_imaging.count_table_columns(columnVector); var data = new float[rowOffsets.Count*columnCount]; c_csharp_imaging.populate_imaging_table_data(run, columnVector, rowOffsets, data, (uint)data.Length); Assert.AreEqual(rowOffsets.Count, 3); Assert.AreEqual(data[0], 7); }
public void ClearTest() { int[] tmp = new int[]{ 2,38 ,7,0,90,4,1,0,-12,-56,15,64,-98,35,12,64,0,0,0,0,0,0,0,0,46,1,17,1,0,0,0,0,96,-41,-104,36,122,-86,-46,-120 ,7,0,-66,4,1,0,96,-43,14,64,-63,49,13,64,0,0,0,0,0,0,0,0,56,1,17,1,0,0,0,0,112,125,77,38,122,-86,-46,-120 ,7,0,66,8,1,0,74,-68,6,64,-118,-7,8,64,0,0,0,0,0,0,0,0,93,1,46,1,0,0,0,0,-47,-104,2,40,122,-86,-46,-120 }; byte[] expected_binary_data = new byte[tmp.Length]; for(int i=0;i<expected_binary_data.Length;i++) expected_binary_data[i] = (byte)tmp[i]; run_metrics run = new run_metrics(); c_csharp_comm.read_interop_from_buffer(expected_binary_data, (uint)expected_binary_data.Length, run.extraction_metric_set()); run.set_naming_method(tile_naming_method.FourDigit); run.legacy_channel_update(instrument_type.HiSeq); run.clear(); Assert.IsTrue(run.empty()); }
public void PlotFlowcellMap() { int[] tmp = new int[]{ 6,34,1,7,2,10,20,25,30,35,40,9,19,24,29,34,39,40,2,14,21,27,32,36,40 ,7,0,90,4,1,0,0,0,0,0,-70,22,4,0,-81,-49,1,0,-68,16,0,0,78,-86,42,0,0,0,0,0,0,0,0,0 ,7,0,90,4,2,0,0,0,0,0,75,-81,3,0,-96,-81,0,0,76,4,0,0,112,62,44,0,0,0,0,0,0,0,0,0 ,7,0,90,4,3,0,0,0,0,0,-80,60,3,0,-74,-46,0,0,-85,1,0,0,-106,-112,44,0,0,0,0,0,0,0,0,0 }; byte[] expected_binary_data = new byte[tmp.Length]; for(int i=0;i<expected_binary_data.Length;i++) expected_binary_data[i] = (byte)tmp[i]; run_metrics run = new run_metrics(); c_csharp_comm.read_interop_from_buffer(expected_binary_data, (uint)expected_binary_data.Length, run.q_metric_set()); uint ALL_IDS = (uint)filter_options.UseAll.ALL_IDS; filter_options options = new filter_options(tile_naming_method.FourDigit, ALL_IDS, 0, dna_bases.A, ALL_IDS, 1, 1); read_info_vector reads = new read_info_vector(); reads.Add(new read_info(1, 1, 26)); reads.Add(new read_info(2, 27, 76)); run.run_info(new info( "", "", 1, new flowcell_layout(8, 2, 2, 36, 1, 1, new string_vector(), tile_naming_method.FourDigit), new string_vector(), new image_dimensions(), reads )); run.legacy_channel_update(instrument_type.HiSeq); run.finalize_after_load(); var layout = run.run_info().flowcell(); uint lane_count = layout.lane_count(); uint swath_count = layout.total_swaths(layout.surface_count() > 1 && !options.is_specific_surface()); uint tile_count = layout.tiles_per_lane(); float[] data_buffer = new float[lane_count*swath_count*tile_count]; uint[] tile_buffer = new uint[lane_count*swath_count*tile_count]; flowcell_data data = new flowcell_data(); c_csharp_plot.plot_flowcell_map(run, metric_type.QScore, options, data, data_buffer, tile_buffer); Assert.AreEqual(data.row_count(), 8); }
static int Main(string[] args) { if (args.Length != 1) { if (args.Length < 1) Console.WriteLine ("No run folder"); else Console.WriteLine ("Too many arguments"); return 1; } run_metrics metrics = new run_metrics(); metrics.read(args[0]); run_summary summary = new run_summary(); c_csharp_summary.summarize_run_metrics(metrics, summary); Console.WriteLine("Yield: {0}", summary.total_summary().yield_g()); return 0; }
public void IntensityTest() { int[] tmp = new int[]{ 2,38 ,7,0,90,4,1,0,-12,-56,15,64,-98,35,12,64,0,0,0,0,0,0,0,0,46,1,17,1,0,0,0,0,96,-41,-104,36,122,-86,-46,-120 ,7,0,-66,4,1,0,96,-43,14,64,-63,49,13,64,0,0,0,0,0,0,0,0,56,1,17,1,0,0,0,0,112,125,77,38,122,-86,-46,-120 ,7,0,66,8,1,0,74,-68,6,64,-118,-7,8,64,0,0,0,0,0,0,0,0,93,1,46,1,0,0,0,0,-47,-104,2,40,122,-86,-46,-120 }; byte[] expected_binary_data = new byte[tmp.Length]; for(int i=0;i<expected_binary_data.Length;i++) expected_binary_data[i] = (byte)tmp[i]; run_metrics run = new run_metrics(); c_csharp_comm.read_interop_from_buffer(expected_binary_data, (uint)expected_binary_data.Length, run.extraction_metric_set()); var run_param = new parameters(); Assert.AreEqual(run_param.version(), 0); Assert.AreEqual(run.extraction_metric_set().MaxCycle, 1); filter_options options = new filter_options(tile_naming_method.FourDigit); read_info_vector reads = new read_info_vector(); reads.Add(new read_info(1, 1, 26)); reads.Add(new read_info(2, 27, 76)); run.run_info(new info( "", "", 1, new flowcell_layout(2, 2, 2, 16), new string_vector(), new image_dimensions(), reads )); run.set_naming_method(tile_naming_method.FourDigit); run.legacy_channel_update(instrument_type.HiSeq); candle_stick_plot_data data = new candle_stick_plot_data(); c_csharp_plot.plot_by_cycle(run, metric_type.Intensity, options, data); Assert.AreEqual(data.size(), 4); }
public void TestXMLFileNotFoundException() { run_metrics metrics = new run_metrics(); metrics.read("/nofilecanexist/test/seef"); }
public void ReadsIdentified() { int[] tmp1 = new int[]{1 ,1,0,74,47,3,0 ,17,0,65,84,67,65,67,71,65,67,45,65,65,71,71,84,84,67,65,218,17,0,0,1,0,49,11,0,84,83,67,65,73,110 ,100,101,120,101,115 ,2,0,74,47,3,0 // changed to lane 2 ,17,0,65,67,65,71,84,71,71,84,45,65,65,71,71,84,84,67,65,125,17,0,0,1,0,50,11,0,84,83,67,65,73,110 ,100,101,120,101,115 ,3,0,74,47,3,0 // changed to lane 3 ,17,0,67,65,71,65,84,67,67,65,45,65,65,71,71,84,84,67,65,226,17,0,0,1,0,51,11,0,84,83,67,65,73,110 ,100,101,120,101,115 }; int[] tmp2 = new int[]{2,10 ,7,0,90,4,100,0,-67,-66,15,74 ,7,0,90,4,102,0,74,122,-59,74 ,7,0,90,4,101,0,12,94,-115,73 ,7,0,90,4,103,0,16,54,66,74 ,7,0,90,4,-56,0,82,-11,80,58 ,7,0,90,4,-55,0,-62,42,-99,58 ,7,0,90,4,44,1,-102,113,39,64 ,7,0,-66,4,100,0,-67,-66,15,74 ,7,0,-66,4,102,0,74,122,-59,74 ,7,0,-66,4,101,0,46,103,-113,73 ,7,0,-66,4,103,0,0,2,69,74 ,7,0,-66,4,-56,0,21,111,-87,58 ,7,0,-66,4,-55,0,-86,29,-79,58 ,7,0,-66,4,44,1,6,-42,39,64 ,7,0,66,8,100,0,-67,-66,15,74 ,7,0,66,8,102,0,74,122,-59,74 ,7,0,66,8,101,0,67,-26,-109,73 ,7,0,66,8,103,0,92,47,75,74 ,7,0,66,8,-56,0,123,22,-100,58 ,7,0,66,8,-55,0,85,6,115,58 ,7,0,66,8,44,1,57,97,31,64 }; byte[] expected_binary_data1 = new byte[tmp1.Length]; for(int i=0;i<expected_binary_data1.Length;i++) expected_binary_data1[i] = (byte)tmp1[i]; byte[] expected_binary_data2 = new byte[tmp2.Length]; for(int i=0;i<expected_binary_data2.Length;i++) expected_binary_data2[i] = (byte)tmp2[i]; run_metrics run = new run_metrics(); c_csharp_comm.read_interop_from_buffer(expected_binary_data1, (uint)expected_binary_data1.Length, run.index_metric_set()); c_csharp_comm.read_interop_from_buffer(expected_binary_data2, (uint)expected_binary_data2.Length, run.tile_metric_set()); read_info_vector reads = new read_info_vector(); reads.Add(new read_info(1, 1, 26)); reads.Add(new read_info(2, 27, 76)); run.run_info(new info( "", "", 1, new flowcell_layout(2, 2, 2, 16), new string_vector(), new image_dimensions(), reads )); run.legacy_channel_update(instrument_type.HiSeq); bar_plot_data data = new bar_plot_data(); c_csharp_plot.plot_sample_qc(run, 1, data); Assert.AreEqual(data.size(), 1); }