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);
}