public void Run(IFileLocation outputFile)
{
int bestNormalSampleIndex = 0;
int normalSampleCount = _controlBinnedFiles.Count();
if (normalSampleCount > 1) // find the best normal
{
List <double[]> binCountsByNormalSample = new List <double[]>();
for (int normalSampleIndex = 0; normalSampleIndex < normalSampleCount; normalSampleIndex++)
{
var controlBinnedFile = _controlBinnedFiles.ElementAt(normalSampleIndex);
var binCounts = new BinCounts(controlBinnedFile.FullName, manifest: _manifest);
List <double> counts = binCounts.OnTargetCounts;
double median = binCounts.OnTargetMedianBinCount;
// 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 weight = median > 0 ? 1.0 / median : 0;
binCountsByNormalSample.Add(counts.Select(cnt => cnt * weight).ToArray());
}
double[] tumorBinCounts;
{
var binCounts = new BinCounts(_sampleBinnedFile.FullName, manifest: _manifest);
List <double> counts = binCounts.OnTargetCounts;
double tumorMedian = binCounts.OnTargetMedianBinCount;
double tumorWeight = tumorMedian > 0 ? 1.0 / tumorMedian : 0;
tumorBinCounts = counts.Select(cnt => cnt * tumorWeight).ToArray();
}
// Find the best normal sample
bestNormalSampleIndex = -1;
double minMeanSquaredLogRatios = double.PositiveInfinity;
for (int normalSampleIndex = 0; normalSampleIndex < normalSampleCount; normalSampleIndex++)
{
// Get the sum of squared log ratios
var result = GetMeanSquaredLogRatios(tumorBinCounts, binCountsByNormalSample[normalSampleIndex]);
double meanSquaredLogRatios = result.Item1;
int ignoredBinCount = result.Item2;
// TODO: Skip a (bad) normal sample if too many bins were ignored.
// Donavan's script skips a normal sample if more than 100 log ratios is NA.
// The cut-off is likely panel-dependent.
if (meanSquaredLogRatios < minMeanSquaredLogRatios)
{
minMeanSquaredLogRatios = meanSquaredLogRatios;
bestNormalSampleIndex = normalSampleIndex;
}
}
}
// copy file
var srcBinnedFile = _controlBinnedFiles.ElementAt(bestNormalSampleIndex);
if (outputFile.Exists)
{
outputFile.Delete();
}
srcBinnedFile.CopyTo(outputFile);
}
public void Run(IFileLocation outputFile)
{
int sampleCount = _controlBinnedFiles.Count();
if (sampleCount == 1) // copy file
{
if (outputFile.Exists)
{
outputFile.Delete();
}
_controlBinnedFiles.First().CopyTo(outputFile);
}
else // merge normal samples
{
double[] weights = new double[sampleCount];
List <double>[] binCountsBySample = new List <double> [sampleCount];
for (int sampleIndex = 0; sampleIndex < sampleCount; sampleIndex++)
{
var binnedFile = _controlBinnedFiles.ElementAt(sampleIndex);
var binCounts = new BinCounts(binnedFile.FullName, 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(_controlBinnedFiles.First().FullName))
using (GzipWriter writer = new GzipWriter(outputFile.FullName))
{
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++;
}
}
}
}
/// <summary>
/// Moves an existing file to a new location, overwriting any existing file.
/// If the new location is on a different volume, this is equivalent to CopyTo + Delete
/// </summary>
/// <param name="destination">The new location of the file.</param>
/// <returns>
/// The new location of the file
/// </returns>
public IFileLocation MoveTo(IFileLocation destination)
{
if (FullName.Equals(destination.FullName)) // Doesn't handle symlinks...
return this;
if (destination.Directory != null)
destination.Directory.Create();
if (!Equals(destination))
destination.Delete();
File.Move(FullName, destination.FullName);
return destination;
}
/// <summary>
/// Copies an existing file to a new file, overwriting any existing file.
/// </summary>
/// <param name="destination">The location of the new file to copy to.</param>
/// <returns>
/// The location of the new file
/// </returns>
public IFileLocation CopyTo(IFileLocation destination)
{
if (FullName.Equals(destination.FullName)) // Doesn't handle symlinks...
return this;
destination.Delete();
File.Copy(FullName, destination.FullName);
return destination;
}
