public StringBuilder GetMultiSampleCommandLine(SampleSet <CanvasPedigreeSample> samples, GenomeMetadata genomeMetadata, Vcf vcf, IDirectoryLocation sampleSandbox)
{
StringBuilder commandLine = new StringBuilder();
foreach (var sampleKvp in samples)
{
var sampleId = sampleKvp.Key.Id;
var sample = sampleKvp.Value;
commandLine.Append($" --bam \"{sample.Bam.BamFile}\"");
if (sample.SampleType != SampleType.Other)
{
commandLine.Append($" --{sample.SampleType.GetOptionName()} {sampleId}");
}
}
IFileLocation kmerFasta = _annotationFileProvider.GetKmerFasta(genomeMetadata);
commandLine.Append($" --reference \"{kmerFasta}\"");
IDirectoryLocation wholeGenomeFasta = new FileLocation(genomeMetadata.Sequences.First().FastaPath).Directory;
commandLine.Append($" --genome-folder \"{wholeGenomeFasta}\"");
IFileLocation filterBed = _annotationFileProvider.GetFilterBed(genomeMetadata);
commandLine.Append($" --filter-bed \"{filterBed}\"");
commandLine.Append($" --output \"{sampleSandbox}\"");
return(commandLine);
}
public StringBuilder GetSingleSampleCommandLine(string sampleId, Bam bam, GenomeMetadata genomeMetadata, IDirectoryLocation sampleSandbox)
{
StringBuilder commandLine = new StringBuilder();
commandLine.Append($" --bam \"{bam.BamFile}\"");
commandLine.Append($" --sample-name \"{sampleId}\"");
IFileLocation kmerFasta = _annotationFileProvider.GetKmerFasta(genomeMetadata);
commandLine.Append($" --reference \"{kmerFasta}\"");
IDirectoryLocation wholeGenomeFasta = new FileLocation(genomeMetadata.Sequences.First().FastaPath).Directory;
commandLine.Append($" --genome-folder \"{wholeGenomeFasta}\"");
IFileLocation filterBed = _annotationFileProvider.GetFilterBed(genomeMetadata);
commandLine.Append($" --filter-bed \"{filterBed}\"");
commandLine.Append($" --output \"{sampleSandbox}\"");
return(commandLine);
}
public StringBuilder GetMultiSampleCommandLine(SampleSet <CanvasPedigreeSample> samples, GenomeMetadata genomeMetadata, Vcf vcf, IDirectoryLocation sampleSandbox)
{
StringBuilder commandLine = new StringBuilder();
// move proband to the front of collection (enum Proband gets the lowest int value )
var sortedBySampleTypeSamples = samples.OrderBy(sample => sample.Value.SampleType);
foreach (var sampleKvp in sortedBySampleTypeSamples)
{
var sampleId = sampleKvp.Key.Id;
var sample = sampleKvp.Value;
commandLine.Append($" --bam \"{sample.Bam.BamFile}\" {sample.SampleType} {sampleId}");
}
IFileLocation kmerFasta = _annotationFileProvider.GetKmerFasta(genomeMetadata);
commandLine.Append($" --reference \"{kmerFasta}\"");
IDirectoryLocation wholeGenomeFasta = new FileLocation(genomeMetadata.Contigs().First().FastaPath).Directory;
commandLine.Append($" --genome-folder \"{wholeGenomeFasta}\"");
IFileLocation filterBed = _annotationFileProvider.GetFilterBed(genomeMetadata);
commandLine.Append($" --filter-bed \"{filterBed}\"");
commandLine.Append($" --output \"{sampleSandbox}\"");
return(commandLine);
}