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());
run.extraction_metric_set().rebuild_index();
parameters run_param = new parameters();
Assert.AreEqual(run_param.version(), 0);
Assert.AreEqual(run.extraction_metric_set().max_cycle(), 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(2, 2, 2, 16),
reads
));
run.legacy_channel_update(instrument_type.HiSeq);
imaging_column_vector columnVector = new imaging_column_vector();
c_csharp_table.create_imaging_table_columns(run, columnVector);
map_id_offset rowOffsets = new map_id_offset();
c_csharp_table.count_table_rows(run, rowOffsets);
uint columnCount = c_csharp_table.count_table_columns(columnVector);
float[] data = new float[rowOffsets.Count * columnCount];
c_csharp_table.populate_imaging_table_data(run, columnVector, rowOffsets, data, (uint)data.Length);
Assert.AreEqual(rowOffsets.Count, 3);
Assert.AreEqual(data[0], 7);
}
public void TestDispose()
{
run_metrics tmp = new run_metrics();
using (var set = tmp.extraction_metric_set())
{
ushort_vector tmp1 = new ushort_vector();
float_vector tmp2 = new float_vector();
set.insert(new extraction_metric(1, 1, 1, tmp1, tmp2));
}
using (var set = tmp.extraction_metric_set())
{
Assert.AreEqual((int)set.size(), 1);
}
using (var set = tmp.extraction_metric_set())
{
Assert.AreEqual((int)set.at(0).lane(), 1);
}
}
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 TestInvalidFilterOption()
{
run_metrics metrics = new run_metrics();
filter_options options = new filter_options(tile_naming_method.FourDigit);
metrics.extraction_metric_set().insert(new extraction_metric(1, 1101, 1, new ushort_vector(), new float_vector()));
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 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());
run.extraction_metric_set().rebuild_index();
parameters run_param = new parameters();
Assert.AreEqual(run_param.version(), 0);
Assert.AreEqual(run.extraction_metric_set().max_cycle(), 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(new flowcell_layout(2, 2, 2, 16),
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 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 PopulateTableTest()
{
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.extraction_metric_set().rebuild_index();
parameters run_param = new parameters();
Assert.AreEqual(run_param.version(), 0);
Assert.AreEqual(run.extraction_metric_set().max_cycle(), 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(2, 2, 2, 16),
reads
));
run.legacy_channel_update(instrument_type.HiSeq);
imaging_table table = new imaging_table();
c_csharp_table.create_imaging_table(run, table);
Assert.AreEqual(table.row_count(), 3);
Assert.AreEqual(table.at(0u, (column_id)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 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());
}