public static CanvasEnrichmentOutput GetFromStub(IFileLocation stub)
{
var canvasOutput = CanvasOutput.GetFromStub(stub);
IFileLocation binSize = stub.AppendName(".binsize");
IFileLocation normalBinned = stub.AppendName(".binned");
IFileLocation unsmoothedCnd = stub.AppendName(".unsmoothed.cnd");
return(new CanvasEnrichmentOutput(canvasOutput, binSize, normalBinned, unsmoothedCnd));
}
public static CanvasOutput GetFromStub(IFileLocation stub)
{
Vcf cnvVcf = Vcf.GetVcfFromStub(stub);
IFileLocation coverageAndVariantFrequencies = stub.AppendName(".CoverageAndVariantFrequency.txt");
IFileLocation variantFrequencies = stub.AppendName(".VFResults.txt.gz");
IFileLocation variantFrequenciesBaf = stub.AppendName(".VFResults.baf");
IFileLocation partitioned = stub.AppendName(".partitioned");
return(new CanvasOutput(cnvVcf, coverageAndVariantFrequencies, variantFrequencies,
variantFrequenciesBaf, partitioned));
}
public static CanvasEnrichmentOutput GetFromStub(IFileLocation stub, bool includeIntermediateResults)
{
var canvasOutput = CanvasOutput.GetFromStub(stub, includeIntermediateResults);
if (!includeIntermediateResults)
{
return(new CanvasEnrichmentOutput(canvasOutput));
}
IFileLocation binSize = stub.AppendName(".binsize");
IFileLocation normalBinned = stub.AppendName(".binned");
IFileLocation unsmoothedCnd = stub.AppendName(".unsmoothed.cnd");
return(new CanvasEnrichmentOutput(canvasOutput, binSize, normalBinned, unsmoothedCnd));
}
private CanvasEnrichmentOutput GetCanvasOutput(string sampleId, IDirectoryLocation sampleSandbox)
{
var cnvVcf = new Vcf(sampleSandbox.GetFileLocation("CNV.vcf.gz"));
var tempCnvDirectory = sampleSandbox.GetDirectoryLocation($"TempCNV_{sampleId}");
var variantFrequencies = tempCnvDirectory.GetFileLocation($"VFResults{sampleId}.txt.gz");
var variantFrequenciesBaf = tempCnvDirectory.GetFileLocation($"VFResults{sampleId}.txt.gz.baf");
IFileLocation coverageAndVariantFrequencies = sampleSandbox.GetFileLocation("CNV.CoverageAndVariantFrequency.txt");
IFileLocation tempStub = tempCnvDirectory.GetFileLocation($"{sampleId}");
IFileLocation partitioned = tempStub.AppendName(".partitioned");
var canvasOutput = new CanvasOutput(cnvVcf, coverageAndVariantFrequencies, variantFrequencies,
variantFrequenciesBaf, partitioned);
IFileLocation binSize = tempStub.AppendName(".binsize");
IFileLocation normalBinned = tempStub.AppendName(".normal.binned");
IFileLocation unsmoothedCnd = tempStub.AppendName(".ratio.binned.cnd");
if (!binSize.Exists)
{
binSize = null;
}
return(new CanvasEnrichmentOutput(canvasOutput, binSize, normalBinned, unsmoothedCnd));
}
private CanvasOutput GetCanvasOutput(string sampleId, IDirectoryLocation sampleSandbox)
{
var cnvVcf = new Vcf(sampleSandbox.GetFileLocation("CNV.vcf.gz"));
var tempCnvDirectory = sampleSandbox.GetDirectoryLocation($"TempCNV_{sampleId}");
var variantFrequencies = tempCnvDirectory.GetFileLocation($"VFResults{sampleId}.txt.gz");
var variantFrequenciesBaf = tempCnvDirectory.GetFileLocation($"VFResults{sampleId}.txt.gz.baf");
IFileLocation coverageAndVariantFrequencies = sampleSandbox.GetFileLocation("CNV.CoverageAndVariantFrequency.txt");
IFileLocation tempStub = tempCnvDirectory.GetFileLocation($"{sampleId}");
IFileLocation partitioned = tempStub.AppendName(".partitioned");
return(new CanvasOutput(cnvVcf, coverageAndVariantFrequencies, variantFrequencies,
variantFrequenciesBaf, partitioned));
}
private static IFileLocation GetVfSummaryPathExtension(IFileLocation stub)
{
return(stub.AppendName(".txt.gz"));
}
public static Vcf GetVcfFromStub(IFileLocation stub)
{
return new Vcf(stub.AppendName(Extension));
}
public static IFileLocation GetCoverageBigWig(IFileLocation stub)
{
return(stub.AppendName(".coverage.bigWig"));
}
public static IFileLocation GetCoverageAndVariantFrequencyOutput(IFileLocation stub)
{
return(stub.AppendName(".CoverageAndVariantFrequency.txt"));
}
private IFileLocation GetCnvVcf()
{
return(_pedigreefileNameStub.AppendName(".CNV.vcf.gz"));
}
public static IFileLocation GetVcfOutput(IFileLocation stub)
{
return(stub.AppendName(".vcf.gz"));
}
public static IFileLocation GetVfSummaryBafPath(IFileLocation stub)
{
return(stub.AppendName(".VFResults.baf"));
}
public static BgzfFile GetBAlleleBedGraph(IFileLocation stub)
{
return(new BgzfFile(stub.AppendName(".ballele.bedgraph.gz")));
}
public static BgzfFile GetCopyNumberBedGraph(IFileLocation stub)
{
return(new BgzfFile(stub.AppendName(".copynumber.bedgraph.gz")));
}
public static BgzfFile GetPartitionBedGraph(IFileLocation stub)
{
return(new BgzfFile(stub.AppendName(".partition.bedgraph.gz")));
}
public static IFileLocation GetVfSummaryPath(IFileLocation stub)
{
return(GetVfSummaryPathExtension(stub.AppendName(".VFResults")));
}
public static IFileLocation GetPartitionedPath(IFileLocation stub)
{
return(stub.AppendName(".partitioned"));
}
/// <summary>
/// Intersect bins with the targeted regions defined in callset.Manifest.
/// Assumes that the targeted regions don't intersect, the bins are sorted by genomic location and the bins don't intersect.
/// </summary>
/// <param name="callset"></param>
/// <param name="partitionedPath">Output of CanvasPartition. Bins are assumed to be sorted</param>
/// <returns></returns>
private IFileLocation IntersectBinsWithTargetedRegions(CanvasCallset callset, IFileLocation partitionedPath)
{
if (!partitionedPath.Exists)
{
return(partitionedPath);
}
var rawPartitionedPath = partitionedPath.AppendName(".raw");
if (rawPartitionedPath.Exists)
{
rawPartitionedPath.Delete();
}
partitionedPath.MoveTo(rawPartitionedPath);
//callset.Manifest
Dictionary <string, List <NexteraManifest.ManifestRegion> > manifestRegionsByChrom = callset.Manifest.GetManifestRegionsByChromosome();
// CanvasPartition output file is in the BED format
// start: 0-based, inclusive
// end: 0-based, exclusive
// Manifest
// start: 1-based, inclusive
// end: 1-based, inclusive
using (GzipReader reader = new GzipReader(rawPartitionedPath.FullName))
using (GzipWriter writer = new GzipWriter(partitionedPath.FullName))
{
string currentChrom = null;
int manifestRegionIdx = 0;
string line;
string[] toks;
while ((line = reader.ReadLine()) != null)
{
toks = line.Split('\t');
string chrom = toks[0];
int start = int.Parse(toks[1]) + 1; // 1-based, inclusive
int end = int.Parse(toks[2]); // 1-based, inclusive
if (chrom != currentChrom)
{
currentChrom = chrom;
manifestRegionIdx = 0;
}
if (!manifestRegionsByChrom.ContainsKey(currentChrom))
{
continue;
}
while (manifestRegionIdx < manifestRegionsByChrom[currentChrom].Count &&
manifestRegionsByChrom[currentChrom][manifestRegionIdx].End < start) // |- manifest region -| |- bin -|
{
manifestRegionIdx++;
}
if (manifestRegionIdx >= manifestRegionsByChrom[currentChrom].Count || // |- last manifest region -| |- bin -|
end < manifestRegionsByChrom[currentChrom][manifestRegionIdx].Start) // |- bin -| |- manifest region -|
{
continue; // skip bin
}
// |- bin -|
// |- manifest region -|
while (manifestRegionIdx < manifestRegionsByChrom[currentChrom].Count &&
end >= manifestRegionsByChrom[currentChrom][manifestRegionIdx].Start)
{
// calculate intersection
int intersectionStart = Math.Max(start, manifestRegionsByChrom[currentChrom][manifestRegionIdx].Start); // 1-based, inclusive
int intersectionEnd = Math.Min(end, manifestRegionsByChrom[currentChrom][manifestRegionIdx].End); // 1-based, inclusive
// start/end in BED format
toks[1] = String.Format("{0}", intersectionStart - 1); // 0-based, inclusive
toks[2] = String.Format("{0}", intersectionEnd); // 0-based, exclusive
// write intersected bin
writer.WriteLine(String.Join("\t", toks));
manifestRegionIdx++;
}
}
}
return(partitionedPath);
}
public static IFileLocation GetSingleSamplePedigreeVcfOutput(IFileLocation stub)
{
return(stub.AppendName(".vcf.gz"));
}
/// <summary>
/// Intersect bins with the targeted regions defined in callset.Manifest.
/// Assumes that the targeted regions don't intersect, the bins are sorted by genomic location and the bins don't intersect.
/// </summary>
/// <param name="callset"></param>
/// <param name="partitionedPath">Output of CanvasPartition. Bins are assumed to be sorted</param>
/// <returns></returns>
private IFileLocation IntersectBinsWithTargetedRegions(CanvasCallset callset, IFileLocation partitionedPath)
{
if (!partitionedPath.Exists) { return partitionedPath; }
var rawPartitionedPath = partitionedPath.AppendName(".raw");
if (rawPartitionedPath.Exists) { rawPartitionedPath.Delete(); }
partitionedPath.MoveTo(rawPartitionedPath);
//callset.Manifest
Dictionary<string, List<NexteraManifest.ManifestRegion>> manifestRegionsByChrom = callset.Manifest.GetManifestRegionsByChromosome();
// CanvasPartition output file is in the BED format
// start: 0-based, inclusive
// end: 0-based, exclusive
// Manifest
// start: 1-based, inclusive
// end: 1-based, inclusive
using (GzipReader reader = new GzipReader(rawPartitionedPath.FullName))
using (GzipWriter writer = new GzipWriter(partitionedPath.FullName))
{
string currentChrom = null;
int manifestRegionIdx = 0;
string line;
string[] toks;
while ((line = reader.ReadLine()) != null)
{
toks = line.Split('\t');
string chrom = toks[0];
int start = int.Parse(toks[1]) + 1; // 1-based, inclusive
int end = int.Parse(toks[2]); // 1-based, inclusive
if (chrom != currentChrom)
{
currentChrom = chrom;
manifestRegionIdx = 0;
}
if (!manifestRegionsByChrom.ContainsKey(currentChrom)) { continue; }
while (manifestRegionIdx < manifestRegionsByChrom[currentChrom].Count
&& manifestRegionsByChrom[currentChrom][manifestRegionIdx].End < start) // |- manifest region -| |- bin -|
{
manifestRegionIdx++;
}
if (manifestRegionIdx >= manifestRegionsByChrom[currentChrom].Count || // |- last manifest region -| |- bin -|
end < manifestRegionsByChrom[currentChrom][manifestRegionIdx].Start) // |- bin -| |- manifest region -|
{
continue; // skip bin
}
// |- bin -|
// |- manifest region -|
while (manifestRegionIdx < manifestRegionsByChrom[currentChrom].Count &&
end >= manifestRegionsByChrom[currentChrom][manifestRegionIdx].Start)
{
// calculate intersection
int intersectionStart = Math.Max(start, manifestRegionsByChrom[currentChrom][manifestRegionIdx].Start); // 1-based, inclusive
int intersectionEnd = Math.Min(end, manifestRegionsByChrom[currentChrom][manifestRegionIdx].End); // 1-based, inclusive
// start/end in BED format
toks[1] = String.Format("{0}", intersectionStart - 1); // 0-based, inclusive
toks[2] = String.Format("{0}", intersectionEnd); // 0-based, exclusive
// write intersected bin
writer.WriteLine(String.Join("\t", toks));
manifestRegionIdx++;
}
}
}
return partitionedPath;
}
