public SampleSet <CanvasOutput> Run(SampleSet <CanvasTumorNormalWgsInput> inputs, IDirectoryLocation sandbox)
{
var outputs = new SampleSet <CanvasOutput>();
foreach (var input in inputs)
{
IDirectoryLocation sampleSandbox = sandbox.CreateSubdirectory(input.Key.Id);
outputs.Add(input.Key, RunSingleSample(input.Key.Id, input.Value, sampleSandbox));
}
return(outputs);
}
public SampleSet <T> Load(SampleSet <TIn> input)
{
var set = new SampleSet <T>();
foreach (var sample in input)
{
IFileLocation stub = _convention(sample.Key);
ILoadingConvention <TIn, T> namingConvention = _loadingConventionGenerator(stub);
T output = namingConvention.Load(sample.Value);
set.Add(sample.Key, output);
}
return(set);
}
public SampleSet <CanvasEnrichmentOutput> Run(SampleSet <CanvasEnrichmentInput> inputs, IDirectoryLocation sandbox)
{
var targetedDbSnpVcfs = _enrichmentInputCreator.CreateDbSnpVcfForManifests(inputs, sandbox, _annotationFileProvider);
var manifests = _enrichmentInputCreator.WriteManifests(inputs, sandbox);
var outputs = new SampleSet <CanvasEnrichmentOutput>();
foreach (var input in inputs)
{
IDirectoryLocation sampleSandbox = sandbox.CreateSubdirectory(input.Key.Id);
var dbSnpVcf = targetedDbSnpVcfs[input.Value.NexteraManifest];
var manifest = manifests[input.Value.NexteraManifest];
outputs.Add(input.Key, RunSingleSample(input.Key.Id, input.Value, dbSnpVcf, manifest, sampleSandbox));
}
return(outputs);
}
public SampleSet <CanvasOutput> Run(SampleSet <CanvasTumorNormalEnrichmentInput> inputs, IDirectoryLocation sandbox)
{
var bAlleleVcfs = GetBAlleleVcfs(inputs, sandbox);
var manifests = _enrichmentInputCreator.WriteManifests(inputs, sandbox);
var outputs = new SampleSet <CanvasOutput>();
foreach (var input in inputs)
{
IDirectoryLocation sampleSandbox = sandbox.CreateSubdirectory(input.Key.Id);
var bAlleleVcf = bAlleleVcfs[input.Key].Item1;
var isDbSnpVcf = bAlleleVcfs[input.Key].Item2;
var manifest = manifests[input.Value.NexteraManifest];
outputs.Add(input.Key, RunSingleSample(input.Key.Id, input.Value, bAlleleVcf, isDbSnpVcf, manifest, sampleSandbox));
}
return(outputs);
}
private void ProcessSample(SampleSet sample)
{
#if UseAverage
if (!isSumInitialized)
{
isSumInitialized = true;
// init running averaging store
indexSamples = 0;
samplesSum = sample * samples.Length;
for (int indexSample = 0; indexSample < samples.Length; indexSample++)
{
samples[indexSample] = sample;
}
}
else
{
samplesSum.Subtract(samples[indexSamples]);
samplesSum.Add(sample);
samples[indexSamples] = sample;
}
SampleSet averageSample = samplesSum / samples.Length;
#endif
this.Dispatcher.BeginInvoke(DispatcherPriority.Normal,
new UpdateTbsDelegate(
delegate()
{
for (int indexChannel = 0; indexChannel < sample.Channels.Length; indexChannel++)
{
switch (sample.Channels[indexChannel].Channel)
{
case 0:
UpdateGraphBar(sample.Channels[indexChannel],
sample.Channels[indexChannel],
tbs1Label,
tbs1DeltaLabel,
tbs1RpmLabel,
tbs1,
tbs1Average,
tbs1Reading,
tbs1MinMax);
break;
case 1:
UpdateGraphBar(sample.Channels[indexChannel],
sample.Channels[indexChannel],
tbs2Label,
tbs2DeltaLabel,
tbs2RpmLabel,
tbs2,
tbs2Average,
tbs2Reading,
tbs2MinMax);
break;
case 2:
UpdateGraphBar(sample.Channels[indexChannel],
sample.Channels[indexChannel],
tbs3Label,
tbs3DeltaLabel,
tbs3RpmLabel,
tbs3,
tbs3Average,
tbs3Reading,
tbs3MinMax);
break;
case 3:
UpdateGraphBar(sample.Channels[indexChannel],
sample.Channels[indexChannel],
tbs4Label,
tbs4DeltaLabel,
tbs4RpmLabel,
tbs4,
tbs4Average,
tbs4Reading,
tbs4MinMax);
break;
}
}
}));
}