public static void WriteToTextFile(string outfile, List<GenomicBin> bins)
{
using (GzipWriter writer = new GzipWriter(outfile))
{
foreach (GenomicBin bin in bins)
{
writer.WriteLine(string.Format("{0}\t{1}\t{2}\t{3:F2}\t{4}", bin.Chromosome, bin.Start, bin.Stop, bin.Count, bin.GC));
}
}
}
private static void GetWeightedAverageBinCount(IEnumerable<string> binnedPaths, string mergedBinnedPath,
NexteraManifest manifest = null)
{
int sampleCount = binnedPaths.Count();
if (sampleCount == 1) // copy file
{
if (File.Exists(binnedPaths.First()))
{
if (File.Exists(mergedBinnedPath)) { File.Delete(mergedBinnedPath); }
File.Copy(binnedPaths.First(), mergedBinnedPath);
}
}
else // merge normal samples
{
double[] weights = new double[sampleCount];
List<double>[] binCountsBySample = new List<double>[sampleCount];
for (int sampleIndex = 0; sampleIndex < sampleCount; sampleIndex++)
{
string binnedPath = binnedPaths.ElementAt(sampleIndex);
var binCounts = new BinCounts(binnedPath, manifest: manifest);
List<double> counts = binCounts.AllCounts;
// If a manifest is available, get the median of bins overlapping the targeted regions only.
// For small panels, there could be a lot of bins with zero count and the median would be 0 if taken over all the bins, resulting in division by zero.
double median = binCounts.OnTargetMedianBinCount;
weights[sampleIndex] = median > 0 ? 1.0 / median : 0;
binCountsBySample[sampleIndex] = counts;
}
double weightSum = weights.Sum();
for (int i = 0; i < sampleCount; i++) { weights[i] /= weightSum; } // so weights sum to 1
// Computed weighted average of bin counts across samples
using (GzipReader reader = new GzipReader(binnedPaths.First()))
using (GzipWriter writer = new GzipWriter(mergedBinnedPath))
{
string line;
string[] toks;
int lineIdx = 0;
while ((line = reader.ReadLine()) != null)
{
toks = line.Split('\t');
double weightedBinCount = 0;
for (int i = 0; i < sampleCount; i++) { weightedBinCount += weights[i] * binCountsBySample[i][lineIdx]; }
toks[3] = String.Format("{0}", weightedBinCount);
writer.WriteLine(String.Join("\t", toks));
lineIdx++;
}
}
}
}
private static void GetBinRatio(string tumorBinnedPath, string normalBinnedPath, string ratioBinnedPath,
string ploidyBedPath, NexteraManifest manifest = null)
{
PloidyInfo referencePloidy = String.IsNullOrEmpty(ploidyBedPath) ? null : PloidyInfo.LoadPloidyFromBedFile(ploidyBedPath);
double tumorMedian = (new BinCounts(tumorBinnedPath, manifest: manifest)).OnTargetMedianBinCount;
double normalMedian = (new BinCounts(normalBinnedPath, manifest: manifest)).OnTargetMedianBinCount;
double librarySizeFactor = (tumorMedian > 0 && normalMedian > 0) ? normalMedian / tumorMedian : 1;
using (GzipReader tumorReader = new GzipReader(tumorBinnedPath))
using (GzipReader normalReader = new GzipReader(normalBinnedPath))
using (GzipWriter writer = new GzipWriter(ratioBinnedPath))
{
string normalLine;
string tumorLine;
string[] normalToks;
string[] tumorToks;
double normalCount;
double tumorCount;
double ratio;
while ((normalLine = normalReader.ReadLine()) != null)
{
tumorLine = tumorReader.ReadLine();
normalToks = normalLine.Split('\t');
tumorToks = tumorLine.Split('\t');
normalCount = double.Parse(normalToks[3]);
tumorCount = double.Parse(tumorToks[3]);
// The weighted average count of a bin could be less than 1.
// Using these small counts for coverage normalization creates large ratios.
// It would be better to just drop these bins so we don't introduce too much noise into segmentation and CNV calling.
if (normalCount < 1) { continue; } // skip the bin
string chrom = normalToks[0];
int start = int.Parse(normalToks[1]);
int end = int.Parse(normalToks[2]);
// get the normal ploidy from intervalsWithPloidyByChrom
double factor = CanvasDiploidBinRatioFactor * GetPloidy(referencePloidy, chrom, start, end) / 2.0;
ratio = tumorCount / normalCount * factor * librarySizeFactor;
normalToks[3] = String.Format("{0}", ratio);
writer.WriteLine(String.Join("\t", normalToks));
}
}
}
/// <summary>
/// Step 3: Summarize results to a simple tab-delimited file.
/// </summary>
protected void WriteResults(string outputPath)
{
using (GzipWriter writer = new GzipWriter(outputPath))
{
writer.WriteLine("#Chromosome\tPosition\tRef\tAlt\tCountRef\tCountAlt");
for (int index = 0; index < this.Variants.Count; index++)
{
VcfVariant variant = this.Variants[index];
// skip HOM REF positions
if (this.VariantCounts[index] > 5) {
writer.WriteLine(string.Format("{0}\t{1}\t{2}\t{3}\t{4}\t{5}", variant.ReferenceName, variant.ReferencePosition,
variant.ReferenceAllele, variant.VariantAlleles[0], this.ReferenceCounts[index],
this.VariantCounts[index]));
}
}
}
Console.WriteLine("{0} Results written to {1}", DateTime.Now, outputPath);
}
private void WriteCanvasPartitionResults(string outPath)
{
Dictionary<string, bool> starts = new Dictionary<string, bool>();
Dictionary<string, bool> stops = new Dictionary<string, bool>();
foreach (string chr in SegmentationResults.SegmentByChr.Keys)
{
for (int segmentIndex = 0; segmentIndex < SegmentationResults.SegmentByChr[chr].Length; segmentIndex++)
{
Segment segment = SegmentationResults.SegmentByChr[chr][segmentIndex];
starts[chr + ":" + segment.start] = true;
stops[chr + ":" + segment.end] = true;
}
}
Dictionary<string, List<GenomicBin>> ExcludedIntervals = new Dictionary<string, List<GenomicBin>>();
if (!string.IsNullOrEmpty(ForbiddenIntervalBedPath))
{
ExcludedIntervals = CanvasCommon.Utilities.LoadBedFile(ForbiddenIntervalBedPath);
}
using (GzipWriter writer = new GzipWriter(outPath))
{
int segmentNum = -1;
foreach (string chr in StartByChr.Keys)
{
List<GenomicBin> excludeIntervals = null;
if (ExcludedIntervals.ContainsKey(chr)) excludeIntervals = ExcludedIntervals[chr];
int excludeIndex = 0; // Points to the first interval which *doesn't* end before our current position
uint previousBinEnd = 0;
for (int pos = 0; pos < StartByChr[chr].Length; pos++)
{
uint start = StartByChr[chr][pos];
uint end = EndByChr[chr][pos];
bool newSegment = false;
string key = chr + ":" + start;
if (starts.ContainsKey(key))
{
newSegment = true;
}
if (excludeIntervals != null)
{
while (excludeIndex < excludeIntervals.Count && excludeIntervals[excludeIndex].Stop < previousBinEnd) excludeIndex++;
if (excludeIndex < excludeIntervals.Count)
{
// Note: forbiddenZoneMid should never fall inside a bin, becuase these intervals were already excluded
// from consideration during the call to CanvasBin.
int forbiddenZoneMid = (excludeIntervals[excludeIndex].Start + excludeIntervals[excludeIndex].Stop) / 2;
if (previousBinEnd < forbiddenZoneMid && end >= forbiddenZoneMid) newSegment = true;
}
}
if (previousBinEnd > 0 && MaxInterBinDistInSegment >= 0 && previousBinEnd + MaxInterBinDistInSegment < start
&& !newSegment)
{
newSegment = true;
}
if (newSegment) segmentNum++;
writer.WriteLine(string.Format("{0}\t{1}\t{2}\t{3}\t{4}", chr, start, end, ScoreByChr[chr][pos], segmentNum));
previousBinEnd = end;
}
}
}
}
/// <summary>
/// Invoke CanvasSNV. Return null if this fails and we need to abort CNV calling for this sample.
/// </summary>
protected void InvokeCanvasSnv(CanvasCallset callset)
{
List<UnitOfWork> jobList = new List<UnitOfWork>();
List<string> outputPaths = new List<string>();
GenomeMetadata genomeMetadata = callset.GenomeMetadata;
string tumorBamPath = callset.Bam.BamFile.FullName;
string normalVcfPath = callset.NormalVcfPath.FullName;
foreach (GenomeMetadata.SequenceMetadata chromosome in genomeMetadata.Sequences)
{
// Only invoke for autosomes + allosomes;
// don't invoke it for mitochondrial chromosome or extra contigs or decoys
if (chromosome.Type != GenomeMetadata.SequenceType.Allosome && !chromosome.IsAutosome())
continue;
UnitOfWork job = new UnitOfWork();
job.ExecutablePath = Path.Combine(_canvasFolder, "CanvasSNV.exe");
if (CrossPlatform.IsThisMono())
{
job.CommandLine = job.ExecutablePath;
job.ExecutablePath = Utilities.GetMonoPath();
}
string outputPath = Path.Combine(callset.TempFolder, string.Format("{0}-{1}.SNV.txt.gz", chromosome.Name, callset.Id));
outputPaths.Add(outputPath);
job.CommandLine += $" {chromosome.Name} {normalVcfPath} {tumorBamPath} {outputPath}";
if (_customParameters.ContainsKey("CanvasSNV"))
{
job.CommandLine = Utilities.MergeCommandLineOptions(job.CommandLine, _customParameters["CanvasSNV"], true);
}
job.LoggingFolder = _workManager.LoggingFolder.FullName;
job.LoggingStub = string.Format("CanvasSNV-{0}-{1}", callset.Id, chromosome.Name);
jobList.Add(job);
}
Console.WriteLine("Invoking {0} processor jobs...", jobList.Count);
// Invoke CanvasSNV jobs:
Console.WriteLine(">>>CanvasSNV start...");
_workManager.DoWorkParallelThreads(jobList);
Console.WriteLine(">>>CanvasSNV complete!");
// Concatenate CanvasSNV results:
using (GzipWriter writer = new GzipWriter(callset.VfSummaryPath))
{
bool headerWritten = false;
foreach (string outputPath in outputPaths)
{
if (!File.Exists(outputPath))
{
Console.WriteLine("Error: Expected output file not found at {0}", outputPath);
continue;
}
using (GzipReader reader = new GzipReader(outputPath))
{
while (true)
{
string fileLine = reader.ReadLine();
if (fileLine == null) break;
if (fileLine.Length > 0 && fileLine[0] == '#')
{
if (headerWritten) continue;
headerWritten = true;
}
writer.WriteLine(fileLine);
}
}
}
}
}
/// <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;
}
/// <summary>
/// Opens the file
/// </summary>
public override void Open(string filePath)
{
_writer = new GzipWriter(filePath, GzipCompressionLevel.BestSpeed1, Append);
FileName = filePath;
IsOpen = true;
}
/// <summary>
/// Computes fragment-based GC normalization correction factor
/// </summary>
/// <returns>An array of observed vs expected GC counts.</returns>
static float[] ComputeObservedVsExpectedGC(Dictionary<string, HitArray> observedAlignments,
Dictionary<string, byte[]> readGCContent, NexteraManifest manifest,
bool debugGC, string outFile)
{
Dictionary<string, List<NexteraManifest.ManifestRegion>> regionsByChrom = null;
if (manifest != null)
{
regionsByChrom = manifest.GetManifestRegionsByChromosome();
}
long[] expectedReadCountsByGC = new long[numberOfGCbins];
long[] observedReadCountsByGC = new long[numberOfGCbins];
foreach (KeyValuePair<string, byte[]> chromosomeReadGCContent in readGCContent)
{
string chr = chromosomeReadGCContent.Key;
if (!observedAlignments.ContainsKey(chr)) { continue; }
if (manifest == null) // look at the entire genome
{
for (int i = 0; i < chromosomeReadGCContent.Value.Length; i++)
{
expectedReadCountsByGC[chromosomeReadGCContent.Value[i]]++;
observedReadCountsByGC[chromosomeReadGCContent.Value[i]] += observedAlignments[chr].Data[i];
}
}
else // look at only the targeted regions
{
if (!regionsByChrom.ContainsKey(chr)) { continue; }
int i = -1;
foreach (var region in regionsByChrom[chr])
{
if (i < region.Start) // avoid overlapping targeted regions
{
i = region.Start - 1; // i is 0-based; manifest coordinates are 1-based.
}
for (; i < chromosomeReadGCContent.Value.Length && i < region.End; i++)
{
expectedReadCountsByGC[chromosomeReadGCContent.Value[i]]++;
observedReadCountsByGC[chromosomeReadGCContent.Value[i]] += observedAlignments[chr].Data[i];
}
}
}
}
// calculate ratio of observed to expected read counts for each read GC bin
float[] observedVsExpectedGC = new float[numberOfGCbins];
for (int i = 0; i < numberOfGCbins; i++)
observedVsExpectedGC[i] = 1;
long sumObserved = 0;
long sumExpected = 0;
foreach (long gcContent in observedReadCountsByGC)
sumObserved += gcContent;
foreach (long gcContent in expectedReadCountsByGC)
sumExpected += gcContent;
for (int binIndex = 0; binIndex < numberOfGCbins; binIndex++)
{
if (expectedReadCountsByGC[binIndex] == 0)
expectedReadCountsByGC[binIndex] = 1;
if (observedReadCountsByGC[binIndex] == 0)
observedReadCountsByGC[binIndex] = 1;
observedVsExpectedGC[binIndex] = ((float)observedReadCountsByGC[binIndex] / (float)expectedReadCountsByGC[binIndex]) * ((float)sumExpected / (float)sumObserved);
}
if (debugGC)
{
using (GzipWriter writer = new GzipWriter(outFile + ".gcstat"))
{
for (int binIndex = 0; binIndex < numberOfGCbins; binIndex++)
{
writer.WriteLine(string.Format("{0}\t{1}\t{2}", expectedReadCountsByGC[binIndex], observedReadCountsByGC[binIndex], observedVsExpectedGC[binIndex]));
}
}
}
return observedVsExpectedGC;
}