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 Test_invalid_metric_type_for_plot_flowcell_map()
{
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);
run_metrics run = new run_metrics();
flowcell_data data = new flowcell_data();
try{
c_csharp_plot.plot_flowcell_map(run, "NoMetric", options, data);
Assert.Fail("No exception thrown!");
}catch (Illumina.InterOp.RunMetrics.invalid_metric_type) {}
}
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);
}
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);
}
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(
"",
"",
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();
flowcell_data data = new flowcell_data();
c_csharp_plot.plot_flowcell_map(run, "NoMetric", options, data);
}
