/// <summary>
/// Create new instance of <see cref="TextureDescriptor"/> struct describing 2D texture.
/// </summary>
/// <param name="width">The width</param>
/// <param name="height">The height</param>
/// <param name="mipMap">Whether to compute mip levels from width and height, otherwise 1.</param>
/// <param name="arrayLayers">The array layers count.</param>
/// <param name="format">The <see cref="PixelFormat"/></param>
/// <param name="textureUsage">The texture usage.</param>
/// <param name="samples">The number of samples.</param>
/// <returns></returns>
public static TextureDescriptor Texture2D(
int width,
int height,
bool mipMap,
int arrayLayers = 1,
PixelFormat format = PixelFormat.RGBA8UNorm,
TextureUsage textureUsage = TextureUsage.ShaderRead,
SampleCount samples = SampleCount.Count1)
{
int mipLevels = 1;
if (mipMap)
{
while (height > 1 || width > 1)
{
++mipLevels;
if (height > 1)
{
height >>= 1;
}
if (width > 1)
{
width >>= 1;
}
}
}
width = Math.Max(width, 1);
height = Math.Max(height, 1);
arrayLayers = Math.Max(arrayLayers, 1);
return(new TextureDescriptor(TextureType.Texture2D, width, height, 1, mipLevels, arrayLayers, format, textureUsage, samples));
}
void CheckShaderStates(bool force)
{
if (!force)
{
if (__useNoise == (NoiseTexture != null) &&
__cutoffEnabled == CutoffEnabled &&
__lumContribution == LumContribution &&
__occlusionColor == OcclusionColor &&
__samples == Samples)
{
return;
}
}
Material.shaderKeywords = new string[]
{
(NoiseTexture != null) ? "NOISE_ON" : "NOISE_OFF",
(CutoffEnabled) ? "DISTANCE_CUTOFF_ON" : "DISTANCE_CUTOFF_OFF",
(LumContribution > 0.0001f) ? "LUM_CONTRIB_ON" : "LUM_CONTRIB_OFF",
(OcclusionColor == Color.black) ? "CUSTOM_COLOR_OFF" : "CUSTOM_COLOR_ON",
(Samples == SampleCount.Low) ? "SAMPLES_LOW"
: (Samples == SampleCount.Medium) ? "SAMPLES_MEDIUM"
: (Samples == SampleCount.High) ? "SAMPLES_HIGH"
: "SAMPLES_VERY_LOW"
};
__useNoise = (NoiseTexture != null);
__cutoffEnabled = CutoffEnabled;
__lumContribution = LumContribution;
__occlusionColor = OcclusionColor;
__samples = Samples;
}
/// <summary>
/// Configure the pass with the source and destination to execute on.
/// </summary>
/// <param name="source">Source Render Target</param>
/// <param name="destination">Destination Render Target</param>
public void Setup(RenderTextureDescriptor baseDescriptor, SampleCount sampleCount, RenderTargetHandle source, RenderTargetHandle intermediate, RenderTargetHandle destination)
{
this.source = source;
this.destination = destination;
this.intermediate = intermediate;
descriptor = baseDescriptor;
this.sampleCount = sampleCount;
}
/// <summary>
/// Configure the pass
/// </summary>
public void Setup(
RenderTextureDescriptor baseDescriptor,
RenderTargetHandle colorAttachmentHandle,
SampleCount samples)
{
this.colorAttachmentHandle = colorAttachmentHandle;
this.samples = samples;
descriptor = baseDescriptor;
}
/// <summary>
/// Configure the pass before execution
/// </summary>
/// <param name="baseDescriptor">Current target descriptor</param>
/// <param name="colorAttachmentHandle">Color attachment to render into</param>
/// <param name="depthAttachmentHandle">Depth attachment to render into</param>
/// <param name="configuration">Specific render configuration</param>
public void Setup(
RenderTextureDescriptor baseDescriptor,
RenderTargetHandle colorAttachmentHandle,
RenderTargetHandle depthAttachmentHandle,
RendererConfiguration configuration,
SampleCount samples)
{
this._ColorAttachmentHandle = colorAttachmentHandle;
this._DepthAttachmentHandle = depthAttachmentHandle;
_Descriptor = baseDescriptor;
_RendererConfiguration = configuration;
if ((int)samples > 1)
{
baseDescriptor.bindMS = false;
baseDescriptor.msaaSamples = (int)samples;
}
baseDescriptor.colorFormat = RenderTextureFormat.ARGBHalf;
baseDescriptor.depthBufferBits = 0;
_DescriptorAC = baseDescriptor;
baseDescriptor.colorFormat = SystemInfo.SupportsRenderTextureFormat(RenderTextureFormat.RHalf)
? RenderTextureFormat.RHalf
: RenderTextureFormat.ARGBHalf;
_DescriptorAA = baseDescriptor;
_AccumColorHandle.Init("_AccumColor");
_AccumGIHandle.Init("_AccumGI");
_AccumAlphaHandle.Init("_AccumAlpha");
_AccumBinding = new RenderTargetBinding(new RenderTargetIdentifier[]
{
_AccumColorHandle.Identifier(),
_AccumGIHandle.Identifier(),
_AccumAlphaHandle.Identifier(),
},
new RenderBufferLoadAction[]
{
RenderBufferLoadAction.DontCare,
RenderBufferLoadAction.DontCare,
RenderBufferLoadAction.DontCare,
},
new RenderBufferStoreAction[]
{
RenderBufferStoreAction.Store,
RenderBufferStoreAction.Store,
RenderBufferStoreAction.Store,
},
_DepthAttachmentHandle.Identifier(),
RenderBufferLoadAction.Load,
RenderBufferStoreAction.DontCare);
}
/// <summary>
/// Create new instance of <see cref="TextureDescriptor"/> struct describing 2D texture.
/// </summary>
/// <param name="width">The width</param>
/// <param name="height">The height</param>
/// <param name="mipLevels">The number of mip levels.</param>
/// <param name="arrayLayers">The array layers count.</param>
/// <param name="format">The <see cref="PixelFormat"/></param>
/// <param name="textureUsage">The texture usage</param>
/// <param name="samples">The number of samples.</param>
/// <returns></returns>
public static TextureDescriptor Texture2D(
int width,
int height,
int mipLevels = 1,
int arrayLayers = 1,
PixelFormat format = PixelFormat.RGBA8UNorm,
TextureUsage textureUsage = TextureUsage.ShaderRead,
SampleCount samples = SampleCount.Count1)
{
width = Math.Max(width, 1);
height = Math.Max(height, 1);
mipLevels = Math.Max(mipLevels, 1);
arrayLayers = Math.Max(arrayLayers, 1);
return(new TextureDescriptor(TextureType.Texture2D, width, height, 1, mipLevels, arrayLayers, format, textureUsage, samples));
}
/// <summary>
/// Initializes a new instance of the <see cref="TextureDescriptor"/> struct.
/// </summary>
/// <param name="textureType">The texture type</param>
/// <param name="width">The width</param>
/// <param name="height">The height</param>
/// <param name="depth">The depth</param>
/// <param name="mipLevels">The mipLevels</param>
/// <param name="arrayLayers">The array layers</param>
/// <param name="format">The <see cref="PixelFormat"/></param>
/// <param name="usage">The texture usage</param>
/// <param name="samples">The samples</param>
public TextureDescriptor(TextureType textureType,
int width, int height, int depth,
int mipLevels, int arrayLayers,
PixelFormat format,
TextureUsage usage,
SampleCount samples)
{
TextureType = textureType;
Width = width;
Height = height;
Depth = depth;
MipLevels = mipLevels;
ArrayLayers = arrayLayers;
Format = format;
Usage = usage;
Samples = samples;
}
/// <summary>
/// Configure the pass
/// </summary>
public void Setup(
RenderTextureDescriptor baseDescriptor,
RenderTargetHandle depthAttachmentHandle,
SampleCount samples)
{
this.depthAttachmentHandle = depthAttachmentHandle;
baseDescriptor.colorFormat = RenderTextureFormat.Depth;
baseDescriptor.depthBufferBits = kDepthBufferBits;
if ((int)samples > 1)
{
baseDescriptor.bindMS = (int)samples > 1;
baseDescriptor.msaaSamples = (int)samples;
}
descriptor = baseDescriptor;
}
/// <summary>
/// Create a new instance of <see cref="Texture"/> class.
/// </summary>
/// <param name="device">The creation device.</param>
/// <param name="descriptor">The texture descriptor.</param>
protected Texture(GraphicsDevice device, ref TextureDescriptor descriptor)
: base(device, GraphicsResourceType.Texture, GraphicsResourceUsage.Default)
{
Guard.IsTrue(descriptor.TextureType != TextureType.Unknown, nameof(descriptor), $"TextureType cannot be {nameof(TextureType.Unknown)}");
Guard.MustBeGreaterThanOrEqualTo(descriptor.Width, 1, nameof(descriptor.Width));
Guard.MustBeGreaterThanOrEqualTo(descriptor.Height, 1, nameof(descriptor.Height));
Guard.MustBeGreaterThanOrEqualTo(descriptor.Depth, 1, nameof(descriptor.Depth));
TextureType = descriptor.TextureType;
Width = descriptor.Width;
Height = descriptor.Height;
Depth = descriptor.Depth;
MipLevels = descriptor.MipLevels;
ArrayLayers = descriptor.ArrayLayers;
Format = descriptor.Format;
Usage = descriptor.Usage;
Samples = descriptor.Samples;
}
protected override void Window(int windowId)
{
EditorGUILayout.BeginHorizontal();
m_sampleCount = (SampleCount)SynthGraphEditorFactory.EnumFieldWithLabel( m_sampleCount, "Sample Count" );
m_fftWindow = (FFTWindow)SynthGraphEditorFactory.EnumFieldWithLabel( m_fftWindow, "Window Type" );
EditorGUILayout.EndHorizontal();
if ( ( m_windowRect.width >= MIN_GRAPH_WIDTH) && ( m_windowRect.height >= MIN_GRAPH_HEIGHT ) )
{
DrawGrid();
if ( m_playbackObject == null )
{
SetRequiresContiniousUpdates( false );
}
else
{
DrawPlaybackSpectrum();
}
}
}
void CheckShaderStates(bool force)
{
if (!HighPrecision)
{
m_Camera.depthTextureMode |= DepthTextureMode.Depth;
}
if (!force &&
__aoMode == Mode &&
__useNoise == (NoiseTexture != null) &&
__highPrecision == HighPrecision &&
__lumContribution == LumContribution &&
__occlusionColor == OcclusionColor &&
__samples == Samples)
{
return;
}
Material.shaderKeywords = new string[]
{
(NoiseTexture != null) ? "NOISE_ON" : "NOISE_OFF",
(HighPrecision) ? "HIGH_PRECISION_ON" : "HIGH_PRECISION_OFF",
(LumContribution > 0.0001f) ? "LUM_CONTRIB_ON" : "LUM_CONTRIB_OFF",
(OcclusionColor == Color.black) ? "CUSTOM_COLOR_OFF" : "CUSTOM_COLOR_ON",
(Samples == SampleCount.Low) ? "SAMPLES_LOW"
: (Samples == SampleCount.Medium) ? "SAMPLES_MEDIUM"
: (Samples == SampleCount.High) ? "SAMPLES_HIGH"
: "SAMPLES_VERY_LOW"
};
__useNoise = (NoiseTexture != null);
__highPrecision = HighPrecision;
__lumContribution = LumContribution;
__occlusionColor = OcclusionColor;
__samples = Samples;
__aoMode = Mode;
}
// Sort largest count first
int scomp(SampleCount a, SampleCount b)
{
return b.Count - a.Count;
}
private void cmdSampInfo_Click(object sender, EventArgs e)
{
int Hour, Minute, Second;
int Month, Day, Year;
int SampleInterval, SampleCount;
int StartDate, StartTime;
int Postfix;
string PostfixStr, StartDateStr;
string StartTimeStr;
PostfixStr = "";
SampleInterval = 0;
SampleCount = 0;
StartDate = 0;
StartTime = 0;
// Get the sample information
// Parameters:
// Filename :name of file to get information from
// SampleInterval :time between samples
// SampleCount :number of samples in the file
// StartDate :date of first sample
// StartTime :time of first sample
ULStat = logger.GetSampleInfo(ref SampleInterval, ref SampleCount, ref StartDate, ref StartTime);
if (ULStat.Value != MccDaq.ErrorInfo.ErrorCode.NoErrors)
{
lblComment.Text = ULStat.Message + ".";
}
else
{
//Parse the date from the StartDate parameter
Month = (StartDate >> 8) & 0xff;
Day = StartDate & 0xff;
Year = (StartDate >> 16) & 0xffff;
StartDateStr = Month.ToString("00") + "/" +
Day.ToString("00") + "/" + Year.ToString("0000");
//Parse the time from the StartTime parameter
Hour = (StartTime >> 16) & 0xffff;
Minute = (StartTime >> 8) & 0xff;
Second = StartTime & 0xff;
Postfix = (StartTime >> 24) & 0xff;
if (Postfix == 0)
{
PostfixStr = " AM";
}
if (Postfix == 1)
{
PostfixStr = " PM";
}
StartTimeStr = Hour.ToString("00") + ":" +
Minute.ToString("00") + ":" + Second.ToString("00")
+ PostfixStr;
txtResults.Text =
"The sample properties of '" + logger.FileName + "' are:" +
"\r\n" + "\r\n" + "\t" + "SampleInterval: " + "\t" +
SampleInterval.ToString("0") + "\r\n" + "\t" + "SampleCount: " +
"\t" + SampleCount.ToString("0") + "\r\n" + "\t" +
"Start Date: " + "\t" + StartDateStr + "\r\n" + "\t" +
"Start Time: " + "\t" + StartTimeStr;
}
}
public Device(IntPtr instance, IntPtr phy, IntPtr dev, uint qFamIdx, SampleCount samples = SampleCount.Sample_1, uint qIndex = 0)
{
handle = NativeMethods.vkvg_device_create_multisample(instance, phy, dev, qFamIdx, qIndex, samples, false);
}
internal static extern IntPtr vkvg_device_create_multisample(IntPtr inst, IntPtr phy, IntPtr vkdev, uint qFamIdx, uint qIndex, SampleCount samples, bool deferredResolve);
/// <summary>
/// Configure the pass
/// </summary>
public void Setup(
RenderTextureDescriptor baseDescriptor, RenderTargetHandle depthNormalsHandle, RenderTargetHandle depthAttachmentHandle, bool depthPrepass, SampleCount samples)
{
this.depthNormalsHandle = depthNormalsHandle;
this.depthAttachmentHandle = depthAttachmentHandle;
baseDescriptor.depthBufferBits = depthPrepass ? 0 : kDepthBufferBits;
baseDescriptor.colorFormat = RenderTextureFormat.ARGB32;
if ((int)samples > 1 && depthPrepass)
{
baseDescriptor.bindMS = false;
baseDescriptor.msaaSamples = (int)samples;
}
descriptor = baseDescriptor;
this.isDepthPrepassEnabled = depthPrepass;
}
void CheckShaderStates(bool force)
{
if (!force)
{
if (__useNoise == (NoiseTexture != null) &&
__cutoffEnabled == CutoffEnabled &&
__lumContribution == LumContribution &&
__occlusionColor == OcclusionColor &&
__samples == Samples)
{
return;
}
}
Material.shaderKeywords = new string[]
{
(NoiseTexture != null) ? "NOISE_ON" : "NOISE_OFF",
(CutoffEnabled) ? "DISTANCE_CUTOFF_ON" : "DISTANCE_CUTOFF_OFF",
(LumContribution > 0.0001f) ? "LUM_CONTRIB_ON" : "LUM_CONTRIB_OFF",
(OcclusionColor == Color.black) ? "CUSTOM_COLOR_OFF" : "CUSTOM_COLOR_ON",
(Samples == SampleCount.Low) ? "SAMPLES_LOW"
: (Samples == SampleCount.Medium) ? "SAMPLES_MEDIUM"
: (Samples == SampleCount.High) ? "SAMPLES_HIGH"
: "SAMPLES_VERY_LOW"
};
__useNoise = (NoiseTexture != null);
__cutoffEnabled = CutoffEnabled;
__lumContribution = LumContribution;
__occlusionColor = OcclusionColor;
__samples = Samples;
}
public override IEnumerable<string> Process()
{
var sampleInfos = new List<SampleCount>();
using (var sw = new StreamWriter(options.OutputFile))
using (var swUnfiltered = new StreamWriter(Path.ChangeExtension(options.OutputFile, ".unfiltered.tsv")))
{
var header = "File\tCategory\tName\tUniqueRead\tUniqueT2CRead\tUniqueT2CRate\tAvergeT2CIn10BasesOfUniqueRead\tAvergeT2COfUniqueRead\tTotalRead\tTotalT2CRead\tTotalT2CRate\tT2C_pvalue\tAverageT2CIn10BasesOfTotalRead\tAverageT2COfTotalRead";
swUnfiltered.WriteLine(header);
sw.WriteLine(header);
var inputFiles = options.GetCountXmlFiles();
foreach (var file in inputFiles)
{
var sc = new SampleCount();
sc.Name = file.Name;
sampleInfos.Add(sc);
var subjects = new FeatureItemGroupXmlFormat().ReadFromFile(file.File);
var group = subjects.GroupBy(m => m[0].Name.StringBefore(":")).ToList();
foreach (var g in group)
{
var items = g.ToList();
foreach (var item in items)
{
var queries = new HashSet<string>(item.GetAlignedLocations().ConvertAll(l => l.Parent.Qname));
List<FeatureSamLocation> locs = new List<FeatureSamLocation>();
foreach (var l in item)
{
foreach (var loc in l.Locations)
{
foreach (var sl in loc.SamLocations)
{
if (queries.Contains(sl.SamLocation.Parent.Qname))
{
locs.Add(sl);
queries.Remove(sl.SamLocation.Parent.Qname);
}
}
}
}
var t2c = locs.Where(m => m.NumberOfNoPenaltyMutation > 0).ToList();
var ave_t2c_uniquereads = (t2c.Count > 0) ? t2c.ConvertAll(m => m.NumberOfNoPenaltyMutation * 10.0 / m.SamLocation.Parent.Sequence.Length).Average() : 0.0;
var ave_t2c_perread_uniquereads = (t2c.Count > 0) ? t2c.ConvertAll(m => m.NumberOfNoPenaltyMutation).Average() : 0.0;
double ave_t2c_allreads = 0.0;
double ave_t2c_perread_allreads = 0.0;
if (t2c.Count > 0)
{
List<double> values = new List<double>();
List<double> perread_values = new List<double>();
foreach (var t2citem in t2c)
{
var v = t2citem.NumberOfNoPenaltyMutation * 10.0 / t2citem.SamLocation.Parent.Sequence.Length;
for (int i = 0; i < t2citem.SamLocation.Parent.QueryCount; i++)
{
values.Add(v);
perread_values.Add(t2citem.NumberOfNoPenaltyMutation);
}
}
ave_t2c_allreads = values.Average();
ave_t2c_perread_allreads = perread_values.Average();
}
var totalCount = locs.Sum(l => l.SamLocation.Parent.QueryCount);
var totalT2CCount = t2c.Sum(l => l.SamLocation.Parent.QueryCount);
var pvalue = SmallRNAT2CMutationBuilder.CalculateT2CPvalue(totalCount, totalT2CCount, options.ExpectRate);
var t2crate = totalT2CCount == 0 ? 0 : totalT2CCount * 1.0 / totalCount;
var value = string.Format("{0}\t{1}\t{2}\t{3:0.###}\t{4:0.###}\t{5:0.###}\t{6:0.###}\t{7:0.###}\t{8:0.###}\t{9:0.###}\t{10:0.###}\t{11:0.###E+0}\t{12:0.###}\t{13:0.###}",
file.Name,
g.Key,
item.Name,
locs.Count,
t2c.Count,
t2c.Count * 1.0 / locs.Count,
ave_t2c_uniquereads,
ave_t2c_perread_uniquereads,
totalCount,
totalT2CCount,
t2crate,
pvalue,
ave_t2c_allreads,
ave_t2c_perread_allreads);
swUnfiltered.WriteLine(value);
if(!ParclipSmallRNAT2CBuilder.Accept(pvalue, totalCount, totalT2CCount, options.Pvalue, options.MinimumCount, options.ExpectRate))
{
continue;
}
sw.WriteLine(value);
sc.GoodReadCount += totalCount;
sc.GoodT2CReadCount += totalT2CCount;
if (g.Key.Equals(SmallRNAConsts.miRNA))
{
sc.MiRNACount++;
}
else if (g.Key.Equals(SmallRNAConsts.tRNA))
{
sc.TRNACount++;
}
else
{
sc.OtherSmallRNACount++;
}
}
}
}
}
using (var sw = new StreamWriter(options.OutputFile + ".summary"))
{
sw.WriteLine("File\tTotalRead\tT2CRead\tT2CRate\tSmallRNA\tMicroRNA\ttRNA\tOtherSmallRNA");
foreach (var si in sampleInfos)
{
sw.WriteLine("{0}\t{1}\t{2}\t{3}\t{4}\t{5}\t{6}\t{7}",
si.Name,
si.GoodReadCount,
si.GoodT2CReadCount,
si.GoodT2CRate,
si.SmallRNACount,
si.MiRNACount,
si.TRNACount,
si.OtherSmallRNACount);
}
}
return new[] { Path.GetFullPath(options.OutputFile), Path.GetFullPath(options.OutputFile + ".summary") };
}
/// <summary>
/// Configure the pass before execution
/// </summary>
/// <param name="baseDescriptor">Current target descriptor</param>
/// <param name="colorAttachmentHandle">Color attachment to render into</param>
/// <param name="depthAttachmentHandle">Depth attachment to render into</param>
/// <param name="configuration">Specific render configuration</param>
public bool Setup(
RenderTextureDescriptor baseDescriptor,
RenderTargetHandle colorAttachmentHandle,
RenderTargetHandle depthAttachmentHandle,
RendererConfiguration configuration,
SampleCount samples,
RenderingData renderingData)
{
if (!GetViewDepthMinMaxWithRenderQueue(renderingData.cameraData.camera, RenderQueueUtils.oit, out _ViewDepthMinMax))
{
return(false);
}
this._ColorAttachmentHandle = colorAttachmentHandle;
this._DepthAttachmentHandle = depthAttachmentHandle;
_RendererConfiguration = configuration;
if ((int)samples > 1)
{
baseDescriptor.bindMS = false;
baseDescriptor.msaaSamples = (int)samples;
}
baseDescriptor.depthBufferBits = 0;
_Descriptor = baseDescriptor;
_MomentsPrecision = renderingData.cameraData.momentsPrecision;
if (_MomentsPrecision == FloatPrecision._Single)
{
baseDescriptor.colorFormat = RenderTextureFormat.ARGBFloat;
_DescriptorFloat4 = baseDescriptor;
baseDescriptor.colorFormat = SystemInfo.SupportsRenderTextureFormat(RenderTextureFormat.RGFloat)
? RenderTextureFormat.RGFloat
: RenderTextureFormat.ARGBFloat;
_DescriptorFloat2 = baseDescriptor;
baseDescriptor.colorFormat = SystemInfo.SupportsRenderTextureFormat(RenderTextureFormat.RFloat)
? RenderTextureFormat.RFloat
: RenderTextureFormat.ARGBFloat;
_DescriptorFloat = baseDescriptor;
}
else
{
baseDescriptor.colorFormat = RenderTextureFormat.ARGBHalf;
_DescriptorFloat4 = baseDescriptor;
baseDescriptor.colorFormat = SystemInfo.SupportsRenderTextureFormat(RenderTextureFormat.RGHalf)
? RenderTextureFormat.RGHalf
: RenderTextureFormat.ARGBHalf;
_DescriptorFloat2 = baseDescriptor;
baseDescriptor.colorFormat = SystemInfo.SupportsRenderTextureFormat(RenderTextureFormat.RHalf)
? RenderTextureFormat.RHalf
: RenderTextureFormat.ARGBHalf;
_DescriptorFloat = baseDescriptor;
}
_B0Handle.Init("_B0");
_B1Handle.Init("_B1");
_B2Handle.Init("_B2");
_MomentsCount = (MomentsCount)renderingData.cameraData.momentsCount;
if (MomentsCount._4 != _MomentsCount)
{
_GMBinding = new RenderTargetBinding(
new RenderTargetIdentifier[]
{
_B0Handle.Identifier(),
_B1Handle.Identifier(),
_B2Handle.Identifier(),
},
new RenderBufferLoadAction[]
{
RenderBufferLoadAction.DontCare,
RenderBufferLoadAction.DontCare,
RenderBufferLoadAction.DontCare,
},
new RenderBufferStoreAction[]
{
RenderBufferStoreAction.Store,
RenderBufferStoreAction.Store,
RenderBufferStoreAction.Store,
},
_DepthAttachmentHandle.Identifier(),
RenderBufferLoadAction.Load,
RenderBufferStoreAction.DontCare);
}
else
{
_GMBinding = new RenderTargetBinding(
new RenderTargetIdentifier[]
{
_B0Handle.Identifier(),
_B1Handle.Identifier(),
},
new RenderBufferLoadAction[]
{
RenderBufferLoadAction.DontCare,
RenderBufferLoadAction.DontCare,
},
new RenderBufferStoreAction[]
{
RenderBufferStoreAction.Store,
RenderBufferStoreAction.Store,
},
_DepthAttachmentHandle.Identifier(),
RenderBufferLoadAction.Load,
RenderBufferStoreAction.DontCare);
}
_MOITHandle.Init("_MOIT");
_GIALHandle.Init("_GIAL");
_RMBinding = new RenderTargetBinding(
new RenderTargetIdentifier[]
{
_MOITHandle.Identifier(),
_GIALHandle.Identifier(),
},
new RenderBufferLoadAction[]
{
RenderBufferLoadAction.DontCare,
RenderBufferLoadAction.DontCare,
},
new RenderBufferStoreAction[]
{
RenderBufferStoreAction.Store,
RenderBufferStoreAction.Store,
},
_DepthAttachmentHandle.Identifier(),
RenderBufferLoadAction.Load,
RenderBufferStoreAction.DontCare
);
return(true);
}
// Sort largest count first
int scomp(SampleCount a, SampleCount b)
{
return(b.Count - a.Count);
}
public override IEnumerable <string> Process()
{
var sampleInfos = new List <SampleCount>();
using (var sw = new StreamWriter(options.OutputFile))
using (var swUnfiltered = new StreamWriter(Path.ChangeExtension(options.OutputFile, ".unfiltered.tsv")))
{
var header = "File\tCategory\tName\tUniqueRead\tUniqueT2CRead\tUniqueT2CRate\tAvergeT2CIn10BasesOfUniqueRead\tAvergeT2COfUniqueRead\tTotalRead\tTotalT2CRead\tTotalT2CRate\tT2C_pvalue\tAverageT2CIn10BasesOfTotalRead\tAverageT2COfTotalRead";
swUnfiltered.WriteLine(header);
sw.WriteLine(header);
var inputFiles = options.GetCountXmlFiles();
foreach (var file in inputFiles)
{
var sc = new SampleCount();
sc.Name = file.Name;
sampleInfos.Add(sc);
var subjects = new FeatureItemGroupXmlFormat().ReadFromFile(file.File);
var group = subjects.GroupBy(m => m[0].Name.StringBefore(":")).ToList();
foreach (var g in group)
{
var items = g.ToList();
foreach (var item in items)
{
var queries = new HashSet <string>(item.GetAlignedLocations().ConvertAll(l => l.Parent.Qname));
List <FeatureSamLocation> locs = new List <FeatureSamLocation>();
foreach (var l in item)
{
foreach (var loc in l.Locations)
{
foreach (var sl in loc.SamLocations)
{
if (queries.Contains(sl.SamLocation.Parent.Qname))
{
locs.Add(sl);
queries.Remove(sl.SamLocation.Parent.Qname);
}
}
}
}
var t2c = locs.Where(m => m.NumberOfNoPenaltyMutation > 0).ToList();
var ave_t2c_uniquereads = (t2c.Count > 0) ? t2c.ConvertAll(m => m.NumberOfNoPenaltyMutation * 10.0 / m.SamLocation.Parent.Sequence.Length).Average() : 0.0;
var ave_t2c_perread_uniquereads = (t2c.Count > 0) ? t2c.ConvertAll(m => m.NumberOfNoPenaltyMutation).Average() : 0.0;
double ave_t2c_allreads = 0.0;
double ave_t2c_perread_allreads = 0.0;
if (t2c.Count > 0)
{
List <double> values = new List <double>();
List <double> perread_values = new List <double>();
foreach (var t2citem in t2c)
{
var v = t2citem.NumberOfNoPenaltyMutation * 10.0 / t2citem.SamLocation.Parent.Sequence.Length;
for (int i = 0; i < t2citem.SamLocation.Parent.QueryCount; i++)
{
values.Add(v);
perread_values.Add(t2citem.NumberOfNoPenaltyMutation);
}
}
ave_t2c_allreads = values.Average();
ave_t2c_perread_allreads = perread_values.Average();
}
var totalCount = locs.Sum(l => l.SamLocation.Parent.QueryCount);
var totalT2CCount = t2c.Sum(l => l.SamLocation.Parent.QueryCount);
var pvalue = SmallRNAT2CMutationBuilder.CalculateT2CPvalue(totalCount, totalT2CCount, options.ExpectRate);
var t2crate = totalT2CCount == 0 ? 0 : totalT2CCount * 1.0 / totalCount;
var value = string.Format("{0}\t{1}\t{2}\t{3:0.###}\t{4:0.###}\t{5:0.###}\t{6:0.###}\t{7:0.###}\t{8:0.###}\t{9:0.###}\t{10:0.###}\t{11:0.###E+0}\t{12:0.###}\t{13:0.###}",
file.Name,
g.Key,
item.Name,
locs.Count,
t2c.Count,
t2c.Count * 1.0 / locs.Count,
ave_t2c_uniquereads,
ave_t2c_perread_uniquereads,
totalCount,
totalT2CCount,
t2crate,
pvalue,
ave_t2c_allreads,
ave_t2c_perread_allreads);
swUnfiltered.WriteLine(value);
if (!ParclipSmallRNAT2CBuilder.Accept(pvalue, totalCount, totalT2CCount, options.Pvalue, options.MinimumCount, options.ExpectRate))
{
continue;
}
sw.WriteLine(value);
sc.GoodReadCount += totalCount;
sc.GoodT2CReadCount += totalT2CCount;
if (g.Key.Equals(SmallRNAConsts.miRNA))
{
sc.MiRNACount++;
}
else if (g.Key.Equals(SmallRNAConsts.tRNA))
{
sc.TRNACount++;
}
else
{
sc.OtherSmallRNACount++;
}
}
}
}
}
using (var sw = new StreamWriter(options.OutputFile + ".summary"))
{
sw.WriteLine("File\tTotalRead\tT2CRead\tT2CRate\tSmallRNA\tMicroRNA\ttRNA\tOtherSmallRNA");
foreach (var si in sampleInfos)
{
sw.WriteLine("{0}\t{1}\t{2}\t{3}\t{4}\t{5}\t{6}\t{7}",
si.Name,
si.GoodReadCount,
si.GoodT2CReadCount,
si.GoodT2CRate,
si.SmallRNACount,
si.MiRNACount,
si.TRNACount,
si.OtherSmallRNACount);
}
}
return(new[] { Path.GetFullPath(options.OutputFile), Path.GetFullPath(options.OutputFile + ".summary") });
}
