public virtual IVcfFileWriter <CalledAllele> CreatePhasedVcfWriter()
{
//Write header. We can do this at the beginning, it's just copying from old vcf.
List <string> header = AlleleReader.GetAllHeaderLines(_options.VcfPath);
var originalFileName = Path.GetFileName(_options.VcfPath);
string outputFileName;
if (originalFileName != null && originalFileName.EndsWith(".genome.vcf"))
{
outputFileName = originalFileName.Substring(0, originalFileName.LastIndexOf(".genome.vcf", StringComparison.Ordinal));
outputFileName = outputFileName + ".phased.genome.vcf";
}
else if (originalFileName != null && originalFileName.EndsWith(".vcf"))
{
outputFileName = originalFileName.Substring(0, originalFileName.LastIndexOf(".vcf", StringComparison.Ordinal));
outputFileName = outputFileName + ".phased.vcf";
}
else
{
throw new InvalidDataException(string.Format("Input file is not a VCF file: '{0}'", originalFileName));
}
var outFile = Path.Combine(_options.OutputDirectory, outputFileName);
var phasingCommandLine = "##Scylla_cmdline=" + _options.QuotedCommandLineArgumentsString;
return(new PhasedVcfWriter(outFile,
new VcfWriterConfig(_options.VariantCallingParams, _options.VcfWritingParams, _options.BamFilterParams, null, _options.Debug, false),
new VcfWriterInputContext(), header, phasingCommandLine));
}
public void GetHeaderTests()
{
var header = AlleleReader.GetAllHeaderLines(VcfTestFile_1);
string firstLine = "##fileformat=VCFv4.1";
string lastLine = "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tmySample";
Assert.Equal(23, header.Count);
Assert.Equal(firstLine, header[0]);
Assert.Equal(lastLine, header[22]);
}
public VcfFilter(PsaraOptions settings)
{
var vcfIn = settings.VcfPath;
var vcfName = Path.GetFileName(vcfIn);
_originalHeaderLines = AlleleReader.GetAllHeaderLines(vcfIn);
_geometricFilter = new GeometricFilter(settings.GeometricFilterParameters);
_psaraOptions = (PsaraOptions)VcfConsumerAppParsingUtils.TryToUpdateWithOriginalOptions(settings, _originalHeaderLines, vcfIn);
_outputFile = Path.Combine(settings.OutputDirectory, vcfName.Replace(".vcf", ".filtered.vcf"));
_outputFile = _outputFile.Replace(".genome.filtered.vcf", ".filtered.genome.vcf");
}
public static VQRVcfWriter GetVQRVcfFileWriter(VcfConsumerAppOptions options, string outputFilePath)
{
var vcp = options.VariantCallingParams;
var vwp = options.VcfWritingParams;
var bfp = options.BamFilterParams;
var vcfConfig = new VcfWriterConfig(vcp, vwp, bfp, null, false, false);
var headerLines = AlleleReader.GetAllHeaderLines(options.VcfPath);
var vqrCommandLineForVcfHeader = "##VQR_cmdline=" + options.QuotedCommandLineArgumentsString;
return(new VQRVcfWriter(outputFilePath, vcfConfig, new VcfWriterInputContext(), headerLines, vqrCommandLineForVcfHeader));
}
private void AdjustOptions(ref ScyllaApplicationOptions scyllaOptions)
{
List <string> vcfHeaderLines = AlleleReader.GetAllHeaderLines(scyllaOptions.VcfPath);
//where to find the Pisces options used to make the original vcf
var piscesLogDirectory = Path.Combine(Path.GetDirectoryName(scyllaOptions.VcfPath), "PiscesLogs");
if (!Directory.Exists(piscesLogDirectory))
{
piscesLogDirectory = Path.GetDirectoryName(scyllaOptions.VcfPath);
}
//figure out the original settings used, use those as the defaults.
VcfConsumerAppParsingUtils.TryToUpdateWithOriginalOptions(scyllaOptions, vcfHeaderLines, piscesLogDirectory);
//let anything input on the command line take precedence
ApplicationOptionParser.ParseArgs(scyllaOptions.CommandLineArguments);
_options.Save(Path.Combine(scyllaOptions.LogFolder, "ScyllaOptions.used.json"));
}
