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 info(flowcell_layout flowcell, read_info_vector reads) : this(c_csharp_runPINVOKE.new_info__SWIG_11(flowcell_layout.getCPtr(flowcell), read_info_vector.getCPtr(reads)), true)
{
if (c_csharp_runPINVOKE.SWIGPendingException.Pending)
{
throw c_csharp_runPINVOKE.SWIGPendingException.Retrieve();
}
}
public read_info_vector(read_info_vector other) : this(c_csharp_runPINVOKE.new_read_info_vector__SWIG_1(read_info_vector.getCPtr(other)), true)
{
if (c_csharp_runPINVOKE.SWIGPendingException.Pending)
{
throw c_csharp_runPINVOKE.SWIGPendingException.Retrieve();
}
}
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"));
}
public run_summary(read_info_vector reads, uint lane_count, uint surface_count, uint channel_count) : this(c_csharp_summaryPINVOKE.new_run_summary__SWIG_2(read_info_vector.getCPtr(reads), lane_count, surface_count, channel_count), true)
{
if (c_csharp_summaryPINVOKE.SWIGPendingException.Pending)
{
throw c_csharp_summaryPINVOKE.SWIGPendingException.Retrieve();
}
}
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 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(
"",
"",
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 read_info_vectorEnumerator(read_info_vector collection)
{
collectionRef = collection;
currentIndex = -1;
currentObject = null;
currentSize = collectionRef.Count;
}
public void SetRange(int index, read_info_vector values)
{
c_csharp_runPINVOKE.read_info_vector_SetRange(swigCPtr, index, read_info_vector.getCPtr(values));
if (c_csharp_runPINVOKE.SWIGPendingException.Pending)
{
throw c_csharp_runPINVOKE.SWIGPendingException.Retrieve();
}
}
public void reads(read_info_vector read_vec)
{
c_csharp_runPINVOKE.info_reads__SWIG_1(swigCPtr, read_info_vector.getCPtr(read_vec));
if (c_csharp_runPINVOKE.SWIGPendingException.Pending)
{
throw c_csharp_runPINVOKE.SWIGPendingException.Retrieve();
}
}
public void initialize(read_info_vector reads, uint lane_count, uint surface_count, uint channel_count)
{
c_csharp_summaryPINVOKE.run_summary_initialize__SWIG_1(swigCPtr, read_info_vector.getCPtr(reads), lane_count, surface_count, channel_count);
if (c_csharp_summaryPINVOKE.SWIGPendingException.Pending)
{
throw c_csharp_summaryPINVOKE.SWIGPendingException.Retrieve();
}
}
public void copy_reads(read_info_vector dst)
{
c_csharp_summaryPINVOKE.run_summary_copy_reads(swigCPtr, read_info_vector.getCPtr(dst));
if (c_csharp_summaryPINVOKE.SWIGPendingException.Pending)
{
throw c_csharp_summaryPINVOKE.SWIGPendingException.Retrieve();
}
}
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 read_info_vector GetRange(int index, int count)
{
global::System.IntPtr cPtr = c_csharp_runPINVOKE.read_info_vector_GetRange(swigCPtr, index, count);
read_info_vector ret = (cPtr == global::System.IntPtr.Zero) ? null : new read_info_vector(cPtr, true);
if (c_csharp_runPINVOKE.SWIGPendingException.Pending)
{
throw c_csharp_runPINVOKE.SWIGPendingException.Retrieve();
}
return(ret);
}
public static read_info_vector Repeat(read_info value, int count)
{
global::System.IntPtr cPtr = c_csharp_runPINVOKE.read_info_vector_Repeat(read_info.getCPtr(value), count);
read_info_vector ret = (cPtr == global::System.IntPtr.Zero) ? null : new read_info_vector(cPtr, true);
if (c_csharp_runPINVOKE.SWIGPendingException.Pending)
{
throw c_csharp_runPINVOKE.SWIGPendingException.Retrieve();
}
return(ret);
}
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 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 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().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(
"",
"",
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_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);
var 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 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 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 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().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(
"",
"",
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());
var 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(
"",
"",
1,
new flowcell_layout(2, 2, 2, 16),
new string_vector(),
new image_dimensions(),
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, 0u), 7);
}
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 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 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);
}
protected override void SetUp()
{
string xml_file = "<?xml version=\"1.0\"?>\n" +
"<RunInfo xmlns:xsd=\"http://www.w3.org/2001/XMLSchema\" xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\" Version=\"2\">\n" +
" <Run Id=\"120705_M00903_0009_A000000000-A12V4\" Number=\"8\">\n" +
" <Flowcell>000000000-A12V4</Flowcell>\n" +
" <Instrument>M00903</Instrument>\n" +
" <Date>120705</Date>\n" +
" <Reads>\n" +
" <Read NumCycles=\"251\" Number=\"1\" IsIndexedRead=\"N\" />\n" +
" <Read NumCycles=\"12\" Number=\"2\" IsIndexedRead=\"Y\" />\n" +
" <Read NumCycles=\"251\" Number=\"3\" IsIndexedRead=\"N\" />\n" +
" </Reads>\n" +
" <FlowcellLayout LaneCount=\"1\" SurfaceCount=\"2\" SwathCount=\"1\" TileCount=\"14\" />\n" +
" </Run>\n" +
"</RunInfo>";
string_vector Tiles = new string_vector();
string_vector ImageChannels = new string_vector();
read_info[] ReadsArr = new read_info[] {
/*Number, IsIndexedRead, CycleStart, CycleEnd*/
new read_info(1, 1, 251, false),
new read_info(2, 252, 263, true),
new read_info(3, 264, 514, false)
};
read_info_vector Reads = new read_info_vector();
for (int i = 0; i < ReadsArr.Length; i++)
{
Reads.Add(ReadsArr[i]);
}
tile_naming_method TileNamingConvention = tile_naming_method.UnknownTileNamingMethod;
uint LaneCount = 1;
uint SurfaceCount = 2;
uint SwathCount = 1;
uint TileCount = 14;
uint SectionPerLane = 1;
uint LanePerSection = 1;
flowcell_layout FlowcellLayout = new flowcell_layout(
LaneCount,
SurfaceCount,
SwathCount,
TileCount,
SectionPerLane,
LanePerSection,
Tiles,
TileNamingConvention);
string Run_Id = "120705_M00903_0009_A000000000-A12V4";
string Date = "120705";
string InstrumentName = "M00903";
uint RunNumber = 8;
uint version = 2;
image_dimensions ImageDimensions = new image_dimensions(/*Width*/ 0, /*Height*/ 0);
expected_run_info = new info(Run_Id,
Date,
InstrumentName,
RunNumber,
version,
FlowcellLayout,
ImageChannels,
ImageDimensions,
Reads);
run_info.parse(xml_file);
}
public void TestLogic()
{
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);
index_flowcell_summary summary = new index_flowcell_summary();
c_csharp_summary.summarize_index_metrics(run, summary);
Assert.AreEqual(summary.size(), 2);
//Assert.AreEqual(summary.at(0).at(0).total_reads(), 2);
}
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(
new flowcell_layout(2, 2, 2, 16),
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);
}
internal static global::System.Runtime.InteropServices.HandleRef getCPtr(read_info_vector obj)
{
return((obj == null) ? new global::System.Runtime.InteropServices.HandleRef(null, global::System.IntPtr.Zero) : obj.swigCPtr);
}
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);
}
public read_info_vector reads()
{
read_info_vector ret = new read_info_vector(c_csharp_runPINVOKE.info_reads__SWIG_0(swigCPtr), false);
return(ret);
}
public info(string name, string date, string instrument_name, uint run_number, uint version, flowcell_layout flowcell, string_vector channels, image_dimensions image_dim, read_info_vector reads) : this(c_csharp_runPINVOKE.new_info__SWIG_0(name, date, instrument_name, run_number, version, flowcell_layout.getCPtr(flowcell), string_vector.getCPtr(channels), image_dimensions.getCPtr(image_dim), read_info_vector.getCPtr(reads)), true)
{
if (c_csharp_runPINVOKE.SWIGPendingException.Pending)
{
throw c_csharp_runPINVOKE.SWIGPendingException.Retrieve();
}
}
