public void Create_Filter_w_pass_tag_ignored()
{
var filterTags = new[] { "First", "Second", CanvasFilter.Pass };
var canvasFilter = CanvasFilter.Create(filterTags);
Assert.Equal("First;Second", canvasFilter.ToVcfString());
}
public void FormatCnvSizeWithSuffix_10kb_conversion()
{
const int size = 10000;
var cnvSizeFilter = CanvasFilter.GetCnvSizeFilter(size);
Assert.Equal("L10kb", cnvSizeFilter);
}
public void GetRecordLevelFilterFromSampleFiltersOnly_multi_sample_all_pass()
{
var sampleLevelFilters = new[] { CanvasFilter.PassFilter, CanvasFilter.PassFilter, CanvasFilter.PassFilter };
var recordLevelFilter = CanvasFilter.GetRecordLevelFilterFromSampleFiltersOnly(sampleLevelFilters);
Assert.Equal("PASS", recordLevelFilter.ToVcfString());
}
public void FormatCnvSizeWithSuffix_500bp_conversion()
{
const int size = 500;
var cnvSizeFilter = CanvasFilter.GetCnvSizeFilter(size);
Assert.Equal("L500bp", cnvSizeFilter);
}
NormalizedCoverageCalculator_OneSegmentPassOneSegmentFiltered_ReturnsBedGraphEntriesNormalizedByPassingSegmentCopyNumber()
{
var calculator = new NormalizedBinsCoverageCalculator();
var segments = new List <CanvasSegment>
{
new CanvasSegment("chr1", 0, 1, new List <SampleGenomicBin>
{
new SampleGenomicBin("chr1", 0, 1, 3f)
})
{
CopyNumber = 1,
Filter = CanvasFilter.PassFilter
},
new CanvasSegment("chr1", 1, 2, new List <SampleGenomicBin>
{
new SampleGenomicBin("chr1", 1, 2, 6f)
})
{
CopyNumber = 10,
Filter = CanvasFilter.Create(new[] { "Filtered" })
}
};
var results = calculator.Calculate(segments).ToList();
Assert.Equal(2, results.Count);
Assert.Equal(1, results[0].Value);
Assert.Equal(2, results[1].Value);
}
//static void Main(string[] args)
//{
// //GameOfLifeSource golSrc = new GameOfLifeSource(1680, 1050);
// GameOfLifeSource golSrc = new GameOfLifeSource(840, 525); // 1680 x 1050 / 2
// //GameOfLifeSource golSrc = new GameOfLifeSource(560, 350); // 1680 x 1050 / 3
// //GameOfLifeSource golSrc = new GameOfLifeSource(336, 210); // 1680 x 1050 / 5
// GenericDelay<Image> delayFilt = new GenericDelay<Image>(new TimeSpan(0, 0, 0, 0, 100));
// //WallpaperFilter wpFilt = new WallpaperFilter();
// DisplayFilter displayFilt = new DisplayFilter();
// golSrc.OutputPin.AttachTo(delayFilt.InputPin);
// delayFilt.OutputPin.AttachTo(displayFilt.InputPin);
// displayFilt.OutputPin.AttachTo(golSrc.InputPin);
// PinOut<Image> golSrcOut = new PinOut<Image>();
// golSrcOut.AttachTo(golSrc.InputPin);
// golSrcOut.Send(null);
// //golSrcOut.Send(null);
// //golSrcOut.Send(null);
// //golSrcOut.Send(null);
// Console.ReadLine();
//}
static void Main(string[] args)
{
RedditSource redditSource = new RedditSource("http://www.reddit.com/r/pics/.json");
GenericFilter <Image> sizeFilt = new GenericFilter <Image>(img => 100 < img.Width && img.Width < 1000 && 100 < img.Height && img.Height < 800);
BorderFilter brdInnerFilt = new BorderFilter(Color.Black, 1);
BorderFilter brdOuterFilt = new BorderFilter(Color.White, 9);
RotateFilter rotFilt = new RotateFilter(-30, 30);
CanvasFilter cvsFilt = new CanvasFilter();
GenericDelay <Image> delayFilt = new GenericDelay <Image>(new TimeSpan(0, 0, 30));
WallpaperFilter wpFilt = new WallpaperFilter();
redditSource.OutputPin.AttachTo(sizeFilt.InputPin);
sizeFilt.SuccessPin.AttachTo(brdInnerFilt.InputPin);
sizeFilt.FailurePin.AttachTo(redditSource.InputPin);
brdInnerFilt.OutputPin.AttachTo(brdOuterFilt.InputPin);
brdOuterFilt.OutputPin.AttachTo(rotFilt.InputPin);
rotFilt.OutputPin.AttachTo(cvsFilt.PictureInputPin);
cvsFilt.OutputPin.AttachTo(delayFilt.InputPin);
cvsFilt.OutputPin.AttachTo(cvsFilt.CanvasInputPin);
delayFilt.OutputPin.AttachTo(wpFilt.InputPin);
wpFilt.OutputPin.AttachTo(redditSource.InputPin);
/* prime canvas */
PinOut <Image> canvasOut = new PinOut <Image>();
canvasOut.AttachTo(cvsFilt.CanvasInputPin);
Image canvas;
try
{
int bytesRead;
byte[] buf = new byte[1024];
FileStream fs = new FileStream(Path.Combine(Environment.CurrentDirectory, "wall.bmp"), FileMode.Open);
MemoryStream ms = new MemoryStream();
while ((bytesRead = fs.Read(buf, 0, 1024)) > 0)
{
ms.Write(buf, 0, bytesRead);
}
ms.Seek(0, SeekOrigin.Begin);
fs.Close();
canvas = Image.FromStream(ms);
}
catch (FileNotFoundException)
{
Size monitorSize = SystemInformation.PrimaryMonitorSize;
canvas = new Bitmap(monitorSize.Width, monitorSize.Height);
}
canvasOut.Send(canvas);
PinOut <Image> ljSrcOut = new PinOut <Image>();
ljSrcOut.AttachTo(redditSource.InputPin);
ljSrcOut.Send(null); /* only need a signal to kick off the source */
ljSrcOut.Send(null); /* put two images in the loop to test multithreading */
//ljSrcOut.Send(null); /* hell, why not three? */
//ljSrcOut.Send(null); /* we are approaching levels of insanity heretofore untold */
Console.ReadLine();
}
public void GetRecordLevelFilter_multi_sample_failed_common_filter()
{
var sampleLevelFilters = new[]
{
CanvasFilter.Create(new [] { "Failed1" }),
CanvasFilter.Create(new [] { "Failed1", "Failed2" }),
CanvasFilter.Create(new [] { "Failed1", "Failed3" })
};
var recordLevelFilter = CanvasFilter.GetRecordLevelFilterFromSampleFiltersOnly(sampleLevelFilters);
Assert.Equal("FailedFT", recordLevelFilter.ToVcfString());
}
public void GetRecordLevelFilterFromSampleFiltersOnly_multi_sample_one_pass()
{
var sampleLevelFilters = new[]
{
CanvasFilter.PassFilter,
CanvasFilter.Create(new [] { "Failed1" }),
CanvasFilter.Create(new [] { "Failed2" }),
};
var recordLevelFilter = CanvasFilter.GetRecordLevelFilterFromSampleFiltersOnly(sampleLevelFilters);
Assert.Equal("PASS", recordLevelFilter.ToVcfString());
}
//static void Main(string[] args)
//{
// //GameOfLifeSource golSrc = new GameOfLifeSource(1680, 1050);
// GameOfLifeSource golSrc = new GameOfLifeSource(840, 525); // 1680 x 1050 / 2
// //GameOfLifeSource golSrc = new GameOfLifeSource(560, 350); // 1680 x 1050 / 3
// //GameOfLifeSource golSrc = new GameOfLifeSource(336, 210); // 1680 x 1050 / 5
// GenericDelay<Image> delayFilt = new GenericDelay<Image>(new TimeSpan(0, 0, 0, 0, 100));
// //WallpaperFilter wpFilt = new WallpaperFilter();
// DisplayFilter displayFilt = new DisplayFilter();
// golSrc.OutputPin.AttachTo(delayFilt.InputPin);
// delayFilt.OutputPin.AttachTo(displayFilt.InputPin);
// displayFilt.OutputPin.AttachTo(golSrc.InputPin);
// PinOut<Image> golSrcOut = new PinOut<Image>();
// golSrcOut.AttachTo(golSrc.InputPin);
// golSrcOut.Send(null);
// //golSrcOut.Send(null);
// //golSrcOut.Send(null);
// //golSrcOut.Send(null);
// Console.ReadLine();
//}
static void Main(string[] args)
{
RedditSource redditSource = new RedditSource("http://www.reddit.com/r/pics/.json");
GenericFilter<Image> sizeFilt = new GenericFilter<Image>(img => 100 < img.Width && img.Width < 1000 && 100 < img.Height && img.Height < 800);
BorderFilter brdInnerFilt = new BorderFilter(Color.Black, 1);
BorderFilter brdOuterFilt = new BorderFilter(Color.White, 9);
RotateFilter rotFilt = new RotateFilter(-30, 30);
CanvasFilter cvsFilt = new CanvasFilter();
GenericDelay<Image> delayFilt = new GenericDelay<Image>(new TimeSpan(0, 0, 30));
WallpaperFilter wpFilt = new WallpaperFilter();
redditSource.OutputPin.AttachTo(sizeFilt.InputPin);
sizeFilt.SuccessPin.AttachTo(brdInnerFilt.InputPin);
sizeFilt.FailurePin.AttachTo(redditSource.InputPin);
brdInnerFilt.OutputPin.AttachTo(brdOuterFilt.InputPin);
brdOuterFilt.OutputPin.AttachTo(rotFilt.InputPin);
rotFilt.OutputPin.AttachTo(cvsFilt.PictureInputPin);
cvsFilt.OutputPin.AttachTo(delayFilt.InputPin);
cvsFilt.OutputPin.AttachTo(cvsFilt.CanvasInputPin);
delayFilt.OutputPin.AttachTo(wpFilt.InputPin);
wpFilt.OutputPin.AttachTo(redditSource.InputPin);
/* prime canvas */
PinOut<Image> canvasOut = new PinOut<Image>();
canvasOut.AttachTo(cvsFilt.CanvasInputPin);
Image canvas;
try
{
int bytesRead;
byte[] buf = new byte[1024];
FileStream fs = new FileStream(Path.Combine(Environment.CurrentDirectory, "wall.bmp"), FileMode.Open);
MemoryStream ms = new MemoryStream();
while ((bytesRead = fs.Read(buf, 0, 1024)) > 0)
ms.Write(buf, 0, bytesRead);
ms.Seek(0, SeekOrigin.Begin);
fs.Close();
canvas = Image.FromStream(ms);
}
catch (FileNotFoundException)
{
Size monitorSize = SystemInformation.PrimaryMonitorSize;
canvas = new Bitmap(monitorSize.Width, monitorSize.Height);
}
canvasOut.Send(canvas);
PinOut<Image> ljSrcOut = new PinOut<Image>();
ljSrcOut.AttachTo(redditSource.InputPin);
ljSrcOut.Send(null); /* only need a signal to kick off the source */
ljSrcOut.Send(null); /* put two images in the loop to test multithreading */
//ljSrcOut.Send(null); /* hell, why not three? */
//ljSrcOut.Send(null); /* we are approaching levels of insanity heretofore untold */
Console.ReadLine();
}
public void UpdateRecordLevelFilter_w_MinQual()
{
var sampleLevelFilters = new[]
{
CanvasFilter.Create(new [] { "Failed1" }),
CanvasFilter.Create(new [] { "Failed1", "Failed2" }),
CanvasFilter.Create(new [] { "Failed1", "Failed3" })
};
var recordLevelFitler = CanvasFilter.Create(new[] { "MinQual" });
var updatedrecordLevelFilter = CanvasFilter.UpdateRecordLevelFilter(recordLevelFitler, sampleLevelFilters);
Assert.Equal("MinQual;FailedFT", updatedrecordLevelFilter.ToVcfString());
}
/// <summary>
/// For each segment shorter than 10kb, flag it as filtered.
/// </summary>
private void FilterExcessivelyShortSegments(ISampleMap <List <CanvasSegment> > segments)
{
string sizeFilter = CanvasFilter.GetCnvSizeFilter(CanvasFilter.SegmentSizeCutoff);
foreach (var segmentList in segments.Values)
{
foreach (var segment in segmentList)
{
if (segment.Length >= CanvasFilter.SegmentSizeCutoff)
{
continue;
}
segment.Filter = segment.Filter.AddFilter(sizeFilter);
}
}
}
private void EstimateQScores(ISampleMap <CanvasSegment> canvasSegments, ISampleMap <SampleMetrics> pedigreeMembersInfo,
PedigreeInfo pedigreeInfo, ISampleMap <Dictionary <Genotype, double> > singleSampleLikelihoods, JointLikelihoods copyNumberLikelihoods, ISampleMap <Genotype> copyNumbers)
{
foreach (var sampleId in canvasSegments.SampleIds)
{
canvasSegments[sampleId].QScore = GetSingleSampleQualityScore(singleSampleLikelihoods[sampleId], copyNumbers[sampleId]);
canvasSegments[sampleId].CopyNumber = copyNumbers[sampleId].TotalCopyNumber;
if (canvasSegments[sampleId].QScore < _qualityFilterThreshold)
{
canvasSegments[sampleId].Filter = CanvasFilter.Create(new[] { $"q{_qualityFilterThreshold}" });
}
}
if (pedigreeInfo.HasFullPedigree())
{
SetDenovoQualityScores(canvasSegments, pedigreeMembersInfo, pedigreeInfo.ParentsIds, pedigreeInfo.OffspringIds, copyNumberLikelihoods);
}
}
public void FiltersNonPassSegments()
{
var calculator = new CopyNumberBedGraphCalculator();
var segments = new List <CanvasSegment>
{
new CanvasSegment("chr1", 0, 1, new List <SampleGenomicBin>
{
new SampleGenomicBin("chr1", 0, 1, 3f)
})
{
CopyNumber = 0,
Filter = CanvasFilter.Create("NonPass".Yield())
}
};
var ploidyInfo = new PloidyInfo();
var results = calculator.Calculate(segments, ploidyInfo);
Assert.Empty(results);
}
public void ToVcfString_test()
{
var canvasFilter = CanvasFilter.Create(new[] { "First", "Second", "Third" });
Assert.Equal("First;Second;Third", canvasFilter.ToVcfString());
}
