static int Main(string[] args)
{
CanvasCommon.Utilities.LogCommandLine(args);
List <string> inFiles = new List <string>();
List <string> outFiles = new List <string>();
bool needHelp = false;
bool isGermline = false;
string bedPath = null;
string commonCNVsbedPath = null;
double alpha = CBSRunner.DefaultAlpha;
double madFactor = WaveletsRunner.DefaultMadFactor;
SegmentSplitUndo undoMethod = SegmentSplitUndo.None;
Segmentation.SegmentationMethod partitionMethod = Segmentation.SegmentationMethod.Wavelets;
int maxInterBinDistInSegment = 1000000;
OptionSet p = new OptionSet()
{
{ "i|infile=", "input file - usually generated by CanvasClean", v => inFiles.Add(v) },
{ "o|outfile=", "text file to output", v => outFiles.Add(v) },
{ "h|help", "show this message and exit", v => needHelp = v != null },
{ "m|method=", "segmentation method (Wavelets/CBS). Default: " + partitionMethod, v => partitionMethod = (Segmentation.SegmentationMethod)Enum.Parse(typeof(Segmentation.SegmentationMethod), v) },
{ "a|alpha=", "alpha parameter to CBS. Default: " + alpha, v => alpha = float.Parse(v) },
{ "s|split=", "CBS split method (None/Prune/SDUndo). Default: " + undoMethod, v => undoMethod = (SegmentSplitUndo)Enum.Parse(typeof(SegmentSplitUndo), v) },
{ "f|madFactor=", "MAD factor to Wavelets. Default: " + madFactor, v => madFactor = float.Parse(v) },
{ "b|bedfile=", "bed file to exclude (don't span these intervals)", v => bedPath = v },
{ "c|commoncnvs=", "bed file with common CNVs (always include these intervals into segmentation results)", v => commonCNVsbedPath = v },
{ "g|germline", "flag indicating that input file represents germline genome", v => isGermline = v != null },
{ "d|maxInterBinDistInSegment=", "the maximum distance between adjacent bins in a segment (negative numbers turn off splitting segments after segmentation). Default: " + maxInterBinDistInSegment, v => maxInterBinDistInSegment = int.Parse(v) },
};
List <string> extraArgs = p.Parse(args);
if (needHelp)
{
ShowHelp(p);
return(0);
}
if (!inFiles.Any() || !outFiles.Any())
{
ShowHelp(p);
return(0);
}
if (inFiles.Any(inFile => !File.Exists(inFile)))
{
Console.WriteLine("CanvasPartition.exe: File {0} does not exist! Exiting.", inFiles);
return(1);
}
if (!string.IsNullOrEmpty(bedPath) && !File.Exists(bedPath))
{
Console.WriteLine("CanvasPartition.exe: File {0} does not exist! Exiting.", bedPath);
return(1);
}
if (partitionMethod != Segmentation.SegmentationMethod.HMM && outFiles.Count > 1)
{
Console.WriteLine("CanvasPartition.exe: SegmentationMethod.HMM only works for MultiSample SPW worlfow, " +
"please provide multiple -o arguments");
return(1);
}
if (partitionMethod == Segmentation.SegmentationMethod.HMM && inFiles.Count == 1)
{
Console.WriteLine("CanvasPartition.exe: method=HMM option only works when more than one input files (-i) are provided");
return(1);
}
List <Segmentation> segmentationEngine = inFiles.Select(inFile => new Segmentation(inFile, bedPath, maxInterBinDistInSegment)).ToList();
Segmentation.GenomeSegmentationResults segmentationResults;
switch (partitionMethod)
{
default: // use Wavelets if CBS is not selected
Console.WriteLine("{0} Running Wavelet Partitioning", DateTime.Now);
WaveletsRunner waveletsRunner = new WaveletsRunner(new WaveletsRunner.WaveletsRunnerParams(isGermline, commonCNVsbedPath, madFactor: madFactor, verbose: 2));
segmentationResults = new Segmentation.GenomeSegmentationResults(waveletsRunner.Run(segmentationEngine.Single()));
segmentationEngine.Single().WriteCanvasPartitionResults(outFiles.Single(), segmentationResults);
break;
case Segmentation.SegmentationMethod.CBS:
Console.WriteLine("{0} Running CBS Partitioning", DateTime.Now);
CBSRunner cbsRunner = new CBSRunner(maxInterBinDistInSegment, undoMethod, alpha);
segmentationResults = new Segmentation.GenomeSegmentationResults(cbsRunner.Run(segmentationEngine.Single(), verbose: 2));
segmentationEngine.Single().WriteCanvasPartitionResults(outFiles.Single(), segmentationResults);
break;
case Segmentation.SegmentationMethod.HMM:
Console.WriteLine("{0} Running HMM Partitioning", DateTime.Now);
HiddenMarkovModelsRunner hiddenMarkovModelsRunner = new HiddenMarkovModelsRunner(commonCNVsbedPath, inFiles.Count);
segmentationResults = new Segmentation.GenomeSegmentationResults(hiddenMarkovModelsRunner.Run(segmentationEngine));
for (int i = 0; i < segmentationEngine.Count; i++)
{
segmentationEngine[i].WriteCanvasPartitionResults(outFiles[i], segmentationResults);
}
break;
}
Console.WriteLine("{0} CanvasPartition results written out", DateTime.Now);
return(0);
}
static int Main(string[] args)
{
CanvasCommon.Utilities.LogCommandLine(args);
List <string> cleanedFiles = new List <string>();
List <string> outPartitionedFiles = new List <string>();
List <string> vafFiles = new List <string>();
bool needHelp = false;
bool isGermline = false;
string filterBedFile = null;
string referenceFolder = null;
string commonCNVsbedPath = null;
string evennessMetricFile = null;
SegmentSplitUndo undoMethod = SegmentSplitUndo.None;
SegmentationInput.SegmentationMethod partitionMethod = SegmentationInput.SegmentationMethod.Wavelets;
string parameterconfigPath = Path.Combine(Isas.Framework.Utilities.Utilities.GetAssemblyFolder(typeof(CanvasPartition)), "CanvasPartitionParameters.json");
string ploidyVcfPath = null;
OptionSet p = new OptionSet()
{
{ "i|infile=", "input file - usually generated by CanvasClean", v => cleanedFiles.Add(v) },
{ "v|vaffile=", "variant frequencyfiles - usually generated by CanvasSNV", v => vafFiles.Add(v) },
{ "o|outfile=", "text file to output", v => outPartitionedFiles.Add(v) },
{ "m|method=", "segmentation method (Wavelets/CBS). Default: " + partitionMethod, v => partitionMethod = (SegmentationInput.SegmentationMethod)Enum.Parse(typeof(SegmentationInput.SegmentationMethod), v) },
{ "r|reference=", "folder that contains both genome.fa and GenomeSize.xml", v => referenceFolder = v },
{ "s|split=", "CBS split method (None/Prune/SDUndo). Default: " + undoMethod, v => undoMethod = (SegmentSplitUndo)Enum.Parse(typeof(SegmentSplitUndo), v) },
{ "b|bedfile=", "bed file to exclude (don't span these intervals)", v => filterBedFile = v },
{ "c|commoncnvs=", "bed file with common CNVs (always include these intervals into segmentation results)", v => commonCNVsbedPath = v },
{ "g|germline", "flag indicating that input file represents germline genome", v => isGermline = v != null },
{ $"{CommandLineOptions.EvennessMetricFile}=", "output file for evenness metric (optional)", v => evennessMetricFile = v },
{ "p|ploidyVcfFile=", "vcf file specifying reference ploidy (e.g. for sex chromosomes) (optional)", v => ploidyVcfPath = v },
{ "config=", "parameter configuration path (default {parameterconfigPath})", v => parameterconfigPath = v },
{ "h|help", "show this message and exit", v => needHelp = v != null }
};
List <string> extraArgs = p.Parse(args);
if (extraArgs.Any())
{
throw new IlluminaException($"Unknown arguments: {string.Join(",", extraArgs)}");
}
if (needHelp)
{
ShowHelp(p);
return(0);
}
if (!cleanedFiles.Any() || !outPartitionedFiles.Any() || referenceFolder == null)
{
ShowHelp(p);
return(0);
}
if (cleanedFiles.Any(inFile => !File.Exists(inFile)))
{
Console.WriteLine("CanvasPartition.exe: File {0} does not exist! Exiting.", cleanedFiles);
return(1);
}
if (!string.IsNullOrEmpty(filterBedFile) && !File.Exists(filterBedFile))
{
Console.WriteLine("CanvasPartition.exe: File {0} does not exist! Exiting.", filterBedFile);
return(1);
}
if (!File.Exists(parameterconfigPath))
{
Console.WriteLine($"CanvasPedigreeCaller.exe: File {parameterconfigPath} does not exist! Exiting.");
return(1);
}
if (!string.IsNullOrEmpty(ploidyVcfPath) && !File.Exists(ploidyVcfPath))
{
Console.WriteLine("CanvasPartition.exe: File {0} does not exist! Exiting.", ploidyVcfPath);
return(1);
}
var parameterconfigFile = new FileLocation(parameterconfigPath);
var canvasPartitionParameters = Deserialize <CanvasPartitionParameters>(parameterconfigFile);
ILogger logger = new Logger(Console.Out.ToEnumerable(), Console.Error.ToEnumerable());
var processor = new SegmentationResultsProcessor(canvasPartitionParameters.MaxInterBinDistInSegment);
var segmentationInputs = vafFiles.Count > 0 && vafFiles.Count == cleanedFiles.Count ?
cleanedFiles.Zip(vafFiles, (inFile, vafFile) => new SegmentationInput(inFile, vafFile, filterBedFile,
referenceFolder, evennessMetricFile, logger, processor)).ToList() :
cleanedFiles.Select(inFile => new SegmentationInput(inFile, null, filterBedFile,
referenceFolder, evennessMetricFile, logger, processor)).ToList();
GenomeSegmentationResults segmentationResults;
PloidyInfo referencePloidy = ploidyVcfPath != null?PloidyInfo.LoadPloidyFromVcfFileNoSampleId(ploidyVcfPath) : null;
switch (partitionMethod)
{
default: // use Wavelets if CBS is not selected
Console.WriteLine("{0} Running Wavelet Partitioning", DateTime.Now);
var waveletsRunner = new WaveletsRunner(new WaveletsRunner.WaveletsRunnerParams(isGermline,
commonCNVsbedPath, madFactor:
canvasPartitionParameters.MadFactor,
thresholdLowerMaf: canvasPartitionParameters.ThresholdLowerMaf,
evennessScoreThreshold: canvasPartitionParameters.EvennessScoreThreshold, verbose: 2));
segmentationResults = new GenomeSegmentationResults(waveletsRunner.Run(segmentationInputs.Single(),
canvasPartitionParameters.EvennessScoreWindow));
PostProcessAndWriteResults(segmentationInputs.Single(), outPartitionedFiles.Single(), referencePloidy, segmentationResults);
break;
case SegmentationInput.SegmentationMethod.CBS:
{
Console.WriteLine("{0} Running CBS Partitioning", DateTime.Now);
var cbsRunner = new CBSRunner(canvasPartitionParameters.MaxInterBinDistInSegment, undoMethod,
canvasPartitionParameters.CBSalpha);
var sampleSegmentations = new List <GenomeSegmentationResults>();
foreach (var input in segmentationInputs)
{
var segmentation = new GenomeSegmentationResults(cbsRunner.Run(input, verbose: 2));
sampleSegmentations.Add(segmentation);
}
segmentationResults = GenomeSegmentationResults.SplitOverlappingSegments(sampleSegmentations);
foreach (var(segmentationInput, outPartitionedFile) in segmentationInputs.Zip(outPartitionedFiles))
{
PostProcessAndWriteResults(segmentationInput, outPartitionedFile, referencePloidy, segmentationResults);
}
break;
}
case SegmentationInput.SegmentationMethod.HMM:
{
Console.WriteLine("{0} Running HMM Partitioning", DateTime.Now);
var hiddenMarkovModelsRunner = new HiddenMarkovModelsRunner(cleanedFiles.Count);
bool isPerSample = false;
segmentationResults =
new GenomeSegmentationResults(hiddenMarkovModelsRunner.Run(segmentationInputs, isPerSample));
for (int i = 0; i < segmentationInputs.Count; i++)
{
PostProcessAndWriteResults(segmentationInputs[i], outPartitionedFiles[i], referencePloidy, segmentationResults);
}
break;
}
case SegmentationInput.SegmentationMethod.PerSampleHMM:
{
Console.WriteLine("{0} Running Per-sample HMM Partitioning", DateTime.Now);
var hiddenMarkovModelsRunner = new HiddenMarkovModelsRunner(1);
var sampleSegmentations = new List <GenomeSegmentationResults>();
bool isPerSample = true;
foreach (var input in segmentationInputs)
{
var segmentation =
new GenomeSegmentationResults(
hiddenMarkovModelsRunner.Run(input.Yield().ToList(), isPerSample));
sampleSegmentations.Add(segmentation);
}
segmentationResults = GenomeSegmentationResults.SplitOverlappingSegments(sampleSegmentations);
foreach (var(segmentationInput, outPartitionedFile) in segmentationInputs.Zip(outPartitionedFiles))
{
PostProcessAndWriteResults(segmentationInput, outPartitionedFile, referencePloidy,
segmentationResults);
}
break;
}
}
Console.WriteLine("{0} CanvasPartition results written out", DateTime.Now);
return(0);
}