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public static HaarWavelets ( double ratio, double thresholdlower, double thresholdupper, List |
||
| ratio | double | |
| thresholdlower | double | |
| thresholdupper | double | |
| breakpoints | List |
|
| isGermline | bool | |
| return | void | |
public Dictionary <string, List <int> > LaunchWavelets(Dictionary <string, double[]> coverageByChr, Dictionary <string, uint[]> startByChr,
Dictionary <string, uint[]> endByChr, double?CV, List <double> factorOfThreeCMADs)
{
var inaByChr = new Dictionary <string, int[]>();
var finiteScoresByChr = new Dictionary <string, double[]>();
var tasks = coverageByChr.Select(scoreByChrKVP => new ThreadStart(() =>
{
string chr = scoreByChrKVP.Key;
Helper.GetFiniteIndices(scoreByChrKVP.Value, out int[] ina); // not NaN, -Inf, Inf
double[] scores;
if (ina.Length == scoreByChrKVP.Value.Length)
{
scores = scoreByChrKVP.Value;
}
else
{
Helper.ExtractValues <double>(scoreByChrKVP.Value, ina, out scores);
}
lock (finiteScoresByChr)
{
finiteScoresByChr[chr] = scores;
inaByChr[chr] = ina;
}
})).ToList();
Parallel.ForEach(tasks, task => task.Invoke());
// Quick sanity-check: If we don't have any segments, then return a dummy result.
int n = finiteScoresByChr.Values.Sum(list => list.Length);
if (n == 0)
{
return(new Dictionary <string, List <int> >());
}
var breakpointsByChr = new Dictionary <string, List <int> >();
tasks = coverageByChr.Keys.Select(chr => new ThreadStart(() =>
{
var breakpoints = new List <int>();
// to cover cases of no SNVs present (i.e. chrY) => chromosome becomes one segment
int segmentLengthByChr = Math.Max(coverageByChr[chr].Length, 1);
if (segmentLengthByChr > _parameters.MinSize)
{
WaveletSegmentation.HaarWavelets(coverageByChr[chr], _parameters.ThresholdLower,
_parameters.ThresholdUpper,
breakpoints, _parameters.IsGermline, _parameters.MadFactor,
CV, factorOfThreeCMADs, chr);
}
lock (breakpointsByChr)
{
breakpointsByChr[chr] = breakpoints;
}
})).ToList();
Console.WriteLine("{0} Launching wavelet tasks", DateTime.Now);
Parallel.ForEach(tasks, task => task.Invoke());
Console.WriteLine("{0} Completed wavelet tasks", DateTime.Now);
Console.WriteLine("{0} Segmentation results complete", DateTime.Now);
return(breakpointsByChr);
}
/// <summary>
/// Wavelets: unbalanced HAAR wavelets segmentation
/// </summary>
/// <param name="threshold">wavelets coefficient threshold</param>
private void Wavelets(bool isGermline, double thresholdLower = 5, double thresholdUpper = 80, int minSize = 10, int verbose = 1)
{
Dictionary <string, int[]> inaByChr = new Dictionary <string, int[]>();
Dictionary <string, double[]> finiteScoresByChr = new Dictionary <string, double[]>();
List <ThreadStart> tasks = new List <ThreadStart>();
foreach (KeyValuePair <string, double[]> scoreByChrKVP in ScoreByChr)
{
tasks.Add(new ThreadStart(() =>
{
string chr = scoreByChrKVP.Key;
int[] ina;
Helper.GetFiniteIndices(scoreByChrKVP.Value, out ina); // not NaN, -Inf, Inf
double[] scores;
if (ina.Length == scoreByChrKVP.Value.Length)
{
scores = scoreByChrKVP.Value;
}
else
{
Helper.ExtractValues <double>(scoreByChrKVP.Value, ina, out scores);
}
lock (finiteScoresByChr)
{
finiteScoresByChr[chr] = scores;
inaByChr[chr] = ina;
}
}));
}
Isas.Shared.Utilities.DoWorkParallelThreads(tasks);
// Quick sanity-check: If we don't have any segments, then return a dummy result.
int n = 0;
foreach (var list in finiteScoresByChr.Values)
{
n += list.Length;
}
if (n == 0)
{
this.SegmentationResults = this.GetDummySegmentationResults();
return;
}
Dictionary <string, Segment[]> segmentByChr = new Dictionary <string, Segment[]>();
// when parallelizing we need an RNG for each chromosome to get deterministic results
Random seedGenerator = new MersenneTwister(0);
Dictionary <string, Random> perChromosomeRandom = new Dictionary <string, Random>();
foreach (string chr in this.ScoreByChr.Keys)
{
perChromosomeRandom[chr] = new MersenneTwister(seedGenerator.NextFullRangeInt32(), true);
}
tasks = new List <ThreadStart>();
foreach (string chr in ScoreByChr.Keys)
{
tasks.Add(new ThreadStart(() =>
{
int[] ina = inaByChr[chr];
List <int> breakpoints = new List <int>();
int sizeScoreByChr = this.ScoreByChr[chr].Length;
if (sizeScoreByChr > minSize)
{
WaveletSegmentation.HaarWavelets(this.ScoreByChr[chr].ToArray(), thresholdLower, thresholdUpper, breakpoints, isGermline);
}
List <int> startBreakpointsPos = new List <int>();
List <int> endBreakpointPos = new List <int>();
List <int> lengthSeg = new List <int>();
if (breakpoints.Count() >= 2 && sizeScoreByChr > 10)
{
startBreakpointsPos.Add(breakpoints[0]);
endBreakpointPos.Add(breakpoints[1] - 1);
lengthSeg.Add(breakpoints[1] - 1);
for (int i = 1; i < breakpoints.Count - 1; i++)
{
startBreakpointsPos.Add(breakpoints[i]);
endBreakpointPos.Add(breakpoints[i + 1] - 1);
lengthSeg.Add(breakpoints[i + 1] - 1 - breakpoints[i]);
}
startBreakpointsPos.Add(breakpoints[breakpoints.Count - 1]);
endBreakpointPos.Add(sizeScoreByChr - 1);
lengthSeg.Add(sizeScoreByChr - breakpoints[breakpoints.Count - 1] - 1);
}
else
{
startBreakpointsPos.Add(0);
endBreakpointPos.Add(sizeScoreByChr - 1);
lengthSeg.Add(sizeScoreByChr - 1);
}
// estimate segment means
double[] segmentMeans = new double[lengthSeg.Count()];
int ss = 0, ee = 0;
for (int i = 0; i < lengthSeg.Count(); i++)
{
ee += lengthSeg[i];
// Works even if weights == null
segmentMeans[i] = Helper.WeightedAverage(this.ScoreByChr[chr], null, iStart: ss, iEnd: ee);
ss = ee;
}
Segment[] segments = new Segment[startBreakpointsPos.Count];
for (int i = 0; i < startBreakpointsPos.Count; i++)
{
int start = startBreakpointsPos[i];
int end = endBreakpointPos[i];
segments[i] = new Segment();
segments[i].start = this.StartByChr[chr][start]; // Genomic start
segments[i].end = this.EndByChr[chr][end]; // Genomic end
segments[i].nMarkers = lengthSeg[i];
segments[i].mean = segmentMeans[i];
}
lock (segmentByChr)
{
segmentByChr[chr] = segments;
}
}));
}
Console.WriteLine("{0} Launching wavelet tasks", DateTime.Now);
Isas.Shared.Utilities.DoWorkParallelThreads(tasks);
Console.WriteLine("{0} Completed wavelet tasks", DateTime.Now);
this.SegmentationResults = new GenomeSegmentationResults(segmentByChr);
Console.WriteLine("{0} Segmentation results complete", DateTime.Now);
}
/// <summary>
/// Wavelets: unbalanced HAAR wavelets segmentation
/// </summary>
/// <param name="threshold">wavelets coefficient threshold</param>
public Dictionary <string, Segmentation.Segment[]> Run(Segmentation segmentation)
{
Dictionary <string, int[]> inaByChr = new Dictionary <string, int[]>();
Dictionary <string, double[]> finiteScoresByChr = new Dictionary <string, double[]>();
List <ThreadStart> tasks = new List <ThreadStart>();
foreach (KeyValuePair <string, double[]> scoreByChrKVP in segmentation.ScoreByChr)
{
tasks.Add(new ThreadStart(() =>
{
string chr = scoreByChrKVP.Key;
int[] ina;
Helper.GetFiniteIndices(scoreByChrKVP.Value, out ina); // not NaN, -Inf, Inf
double[] scores;
if (ina.Length == scoreByChrKVP.Value.Length)
{
scores = scoreByChrKVP.Value;
}
else
{
Helper.ExtractValues <double>(scoreByChrKVP.Value, ina, out scores);
}
lock (finiteScoresByChr)
{
finiteScoresByChr[chr] = scores;
inaByChr[chr] = ina;
}
}));
}
Parallel.ForEach(tasks, task => task.Invoke());
// Quick sanity-check: If we don't have any segments, then return a dummy result.
int n = finiteScoresByChr.Values.Sum(list => list.Length);
if (n == 0)
{
return(new Dictionary <string, Segmentation.Segment[]>());
}
Dictionary <string, Segmentation.Segment[]> segmentByChr = new Dictionary <string, Segmentation.Segment[]>();
// load common CNV segments
Dictionary <string, List <SampleGenomicBin> > commonCNVintervals = null;
if (_parameters.CommonCnVs != null)
{
commonCNVintervals = CanvasCommon.Utilities.LoadBedFile(_parameters.CommonCnVs);
CanvasCommon.Utilities.SortAndOverlapCheck(commonCNVintervals, _parameters.CommonCnVs);
}
tasks = new List <ThreadStart>();
foreach (string chr in segmentation.ScoreByChr.Keys)
{
tasks.Add(new ThreadStart(() =>
{
List <int> breakpoints = new List <int>();
int sizeScoreByChr = segmentation.ScoreByChr[chr].Length;
if (sizeScoreByChr > _parameters.MinSize)
{
WaveletSegmentation.HaarWavelets(segmentation.ScoreByChr[chr], _parameters.ThresholdLower, _parameters.ThresholdUpper,
breakpoints, _parameters.IsGermline, madFactor: _parameters.MadFactor);
}
if (_parameters.CommonCnVs != null)
{
if (commonCNVintervals.ContainsKey(chr))
{
List <SampleGenomicBin> remappedCommonCNVintervals = Segmentation.RemapCommonRegions(commonCNVintervals[chr], segmentation.StartByChr[chr], segmentation.EndByChr[chr]);
List <int> oldbreakpoints = breakpoints;
breakpoints = Segmentation.OverlapCommonRegions(oldbreakpoints, remappedCommonCNVintervals);
}
}
var segments = Segmentation.DeriveSegments(breakpoints, sizeScoreByChr, segmentation.StartByChr[chr], segmentation.EndByChr[chr]);
lock (segmentByChr)
{
segmentByChr[chr] = segments;
}
}));
}
Console.WriteLine("{0} Launching wavelet tasks", DateTime.Now);
Parallel.ForEach(tasks, task => task.Invoke());
Console.WriteLine("{0} Completed wavelet tasks", DateTime.Now);
Console.WriteLine("{0} Segmentation results complete", DateTime.Now);
return(segmentByChr);
}