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); }