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 info(flowcell_layout flowcell, read_info_vector reads, string_vector channels) : this(c_csharp_runPINVOKE.new_info__SWIG_10(flowcell_layout.getCPtr(flowcell), read_info_vector.getCPtr(reads), string_vector.getCPtr(channels)), true)
{
if (c_csharp_runPINVOKE.SWIGPendingException.Pending)
{
throw c_csharp_runPINVOKE.SWIGPendingException.Retrieve();
}
}
public string_vectorEnumerator(string_vector collection)
{
collectionRef = collection;
currentIndex = -1;
currentObject = null;
currentSize = collectionRef.Count;
}
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_diagnostics_column(uint index, uint offset, string_vector sub_columns) : this(c_csharp_tablePINVOKE.new_run_diagnostics_column__SWIG_3(index, offset, string_vector.getCPtr(sub_columns)), true)
{
if (c_csharp_tablePINVOKE.SWIGPendingException.Pending)
{
throw c_csharp_tablePINVOKE.SWIGPendingException.Retrieve();
}
}
public string_vector(string_vector other) : this(c_csharp_runPINVOKE.new_string_vector__SWIG_1(string_vector.getCPtr(other)), true)
{
if (c_csharp_runPINVOKE.SWIGPendingException.Pending)
{
throw c_csharp_runPINVOKE.SWIGPendingException.Retrieve();
}
}
public void list_filenames(string_vector files, string run_folder)
{
c_csharp_run_metricsPINVOKE.run_metrics_list_filenames__SWIG_4(swigCPtr, string_vector.getCPtr(files), run_folder);
if (c_csharp_run_metricsPINVOKE.SWIGPendingException.Pending)
{
throw c_csharp_run_metricsPINVOKE.SWIGPendingException.Retrieve();
}
}
public void list_filenames(metric_group group, string_vector files, string run_folder, bool use_out)
{
c_csharp_run_metricsPINVOKE.run_metrics_list_filenames__SWIG_0(swigCPtr, (int)group, string_vector.getCPtr(files), run_folder, use_out);
if (c_csharp_run_metricsPINVOKE.SWIGPendingException.Pending)
{
throw c_csharp_run_metricsPINVOKE.SWIGPendingException.Retrieve();
}
}
public void index_order(string_vector order)
{
c_csharp_metricsPINVOKE.index_metric_header_index_order__SWIG_1(swigCPtr, string_vector.getCPtr(order));
if (c_csharp_metricsPINVOKE.SWIGPendingException.Pending)
{
throw c_csharp_metricsPINVOKE.SWIGPendingException.Retrieve();
}
}
public static void list_metric_group(string_vector vec)
{
c_csharp_runPINVOKE.list_metric_group__SWIG_1(string_vector.getCPtr(vec));
if (c_csharp_runPINVOKE.SWIGPendingException.Pending)
{
throw c_csharp_runPINVOKE.SWIGPendingException.Retrieve();
}
}
public static void list_distortion_curve_type(string_vector vec)
{
c_csharp_runPINVOKE.list_distortion_curve_type__SWIG_1(string_vector.getCPtr(vec));
if (c_csharp_runPINVOKE.SWIGPendingException.Pending)
{
throw c_csharp_runPINVOKE.SWIGPendingException.Retrieve();
}
}
public static void list_event_type(string_vector vec, uint skip)
{
c_csharp_runPINVOKE.list_event_type__SWIG_0(string_vector.getCPtr(vec), skip);
if (c_csharp_runPINVOKE.SWIGPendingException.Pending)
{
throw c_csharp_runPINVOKE.SWIGPendingException.Retrieve();
}
}
public static void list_sub_tile_region_name(string_vector vec)
{
c_csharp_runPINVOKE.list_sub_tile_region_name__SWIG_1(string_vector.getCPtr(vec));
if (c_csharp_runPINVOKE.SWIGPendingException.Pending)
{
throw c_csharp_runPINVOKE.SWIGPendingException.Retrieve();
}
}
public void channels(string_vector channels)
{
c_csharp_runPINVOKE.info_channels__SWIG_1(swigCPtr, string_vector.getCPtr(channels));
if (c_csharp_runPINVOKE.SWIGPendingException.Pending)
{
throw c_csharp_runPINVOKE.SWIGPendingException.Retrieve();
}
}
public static void list_run_diagnostics_metrics(string_vector types)
{
c_csharp_tablePINVOKE.list_run_diagnostics_metrics(string_vector.getCPtr(types));
if (c_csharp_tablePINVOKE.SWIGPendingException.Pending)
{
throw c_csharp_tablePINVOKE.SWIGPendingException.Retrieve();
}
}
public static void create_imaging_table_columns(string_vector channels, bool_vector filled, imaging_column_vector columns, uint registration_sub_region_count, layout_type fiducial_layout)
{
c_csharp_tablePINVOKE.create_imaging_table_columns__SWIG_0(string_vector.getCPtr(channels), bool_vector.getCPtr(filled), imaging_column_vector.getCPtr(columns), registration_sub_region_count, (int)fiducial_layout);
if (c_csharp_tablePINVOKE.SWIGPendingException.Pending)
{
throw c_csharp_tablePINVOKE.SWIGPendingException.Retrieve();
}
}
public void SetRange(int index, string_vector values)
{
c_csharp_runPINVOKE.string_vector_SetRange(swigCPtr, index, string_vector.getCPtr(values));
if (c_csharp_runPINVOKE.SWIGPendingException.Pending)
{
throw c_csharp_runPINVOKE.SWIGPendingException.Retrieve();
}
}
public string channel_description(string_vector channels)
{
string ret = c_csharp_plotPINVOKE.filter_options_channel_description(swigCPtr, string_vector.getCPtr(channels));
if (c_csharp_plotPINVOKE.SWIGPendingException.Pending)
{
throw c_csharp_plotPINVOKE.SWIGPendingException.Retrieve();
}
return(ret);
}
public void Test_invalid_column_type()
{
string_vector channels = new string_vector();
bool_vector filled = new bool_vector();
imaging_column_vector columns = new imaging_column_vector();
try{
c_csharp_table.create_imaging_table_columns(channels, filled, columns);
Assert.Fail("No exception thrown!");
}catch (Illumina.InterOp.Table.invalid_column_type) {}
}
public static string_vector Repeat(string value, int count)
{
global::System.IntPtr cPtr = c_csharp_runPINVOKE.string_vector_Repeat(value, count);
string_vector ret = (cPtr == global::System.IntPtr.Zero) ? null : new string_vector(cPtr, true);
if (c_csharp_runPINVOKE.SWIGPendingException.Pending)
{
throw c_csharp_runPINVOKE.SWIGPendingException.Retrieve();
}
return(ret);
}
public string_vector GetRange(int index, int count)
{
global::System.IntPtr cPtr = c_csharp_runPINVOKE.string_vector_GetRange(swigCPtr, index, count);
string_vector ret = (cPtr == global::System.IntPtr.Zero) ? null : new string_vector(cPtr, true);
if (c_csharp_runPINVOKE.SWIGPendingException.Pending)
{
throw c_csharp_runPINVOKE.SWIGPendingException.Retrieve();
}
return(ret);
}
internal static global::System.Runtime.InteropServices.HandleRef getCPtr(string_vector obj)
{
return((obj == null) ? new global::System.Runtime.InteropServices.HandleRef(null, global::System.IntPtr.Zero) : obj.swigCPtr);
}
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 flowcell_layout(uint lane_count, uint surface_count, uint swath_count, uint tile_count, uint sections_per_lane, uint lanes_per_section, string_vector tiles) : this(c_csharp_runPINVOKE.new_flowcell_layout__SWIG_2(lane_count, surface_count, swath_count, tile_count, sections_per_lane, lanes_per_section, string_vector.getCPtr(tiles)), true)
{
if (c_csharp_runPINVOKE.SWIGPendingException.Pending)
{
throw c_csharp_runPINVOKE.SWIGPendingException.Retrieve();
}
}
public string_vector tiles()
{
string_vector ret = new string_vector(c_csharp_runPINVOKE.flowcell_layout_tiles(swigCPtr), false);
return(ret);
}
public string_vector index_order()
{
string_vector ret = new string_vector(c_csharp_metricsPINVOKE.index_metric_header_index_order__SWIG_0(swigCPtr), false);
return(ret);
}
public string_vector subcolumns()
{
string_vector ret = new string_vector(c_csharp_tablePINVOKE.run_diagnostics_column_subcolumns(swigCPtr), false);
return(ret);
}
public info(string name, string date, string instrument_name, uint run_number, uint version, flowcell_layout flowcell, string_vector channels) : this(c_csharp_runPINVOKE.new_info__SWIG_2(name, date, instrument_name, run_number, version, flowcell_layout.getCPtr(flowcell), string_vector.getCPtr(channels)), true)
{
if (c_csharp_runPINVOKE.SWIGPendingException.Pending)
{
throw c_csharp_runPINVOKE.SWIGPendingException.Retrieve();
}
}
public string_vector channels()
{
string_vector ret = new string_vector(c_csharp_runPINVOKE.info_channels__SWIG_0(swigCPtr), false);
return(ret);
}
public string_vector options()
{
string_vector ret = new string_vector(c_csharp_plotPINVOKE.bar_series_options(swigCPtr), false);
return(ret);
}
