internal MutableWittyerResult GetQueryset([CanBeNull] string sampleName, GenomeType genomeType)
{
var query = new MutableWittyerResult(sampleName, false, _vcfReader.Header);
GetResult(sampleName, query, genomeType);
return(query);
}
public static BaseGenome CreateGenome(GenomeType type, int length)
{
switch (type) {
case GenomeType.BinaryString: return new GenomeBinaryString(length);
case GenomeType.RawBinaryString32: return new GenomeBinaryStringRaw32(length);
case GenomeType.RawBinaryString64: return new GenomeBinaryStringRaw64(length);
case GenomeType.FloatString: return new GenomeFloatString(length);
}
DebugAux.Assert(false, "There is no such genome type");
return null;
}
public static BaseGenome CreateGenome(GenomeType type, int length)
{
switch (type)
{
case GenomeType.BinaryString: return(new GenomeBinaryString(length));
case GenomeType.RawBinaryString32: return(new GenomeBinaryStringRaw32(length));
case GenomeType.RawBinaryString64: return(new GenomeBinaryStringRaw64(length));
case GenomeType.FloatString: return(new GenomeFloatString(length));
}
DebugAux.Assert(false, "There is no such genome type");
return(null);
}
internal static IVcfVariant ConvertGenomeType([NotNull] this IVcfVariant variant, GenomeType type)
{
switch (type)
{
case GenomeType.Ucsc:
return(variant.ToUcscStyleVariant());
case GenomeType.Grch:
return(variant.ToGrchStyleVariant());
case GenomeType.Unknown:
return(variant);
default:
throw new InvalidDataException(
$"Not sure why there's a genometype {type.ToString()} in vcf which we are not supporting!");
}
}
private GenomeType?GetResult([CanBeNull] string sampleName,
[NotNull] IMutableWittyerResult mutableResult, GenomeType targetType)
{
var bndSet = new Dictionary <IGeneralBnd, IVcfVariant>(BreakendPairComparer.Default);
var errorList = new List <string>();
GenomeType?genomeType = null;
foreach (var baseVariant in _baseVariants)
{
if (genomeType == null)
{
genomeType = baseVariant.Contig.GetGenomeType();
}
var sample = sampleName == null ? null : baseVariant.Samples[sampleName];
var result = CreateVariant(baseVariant.ConvertGenomeType(targetType),
sample, mutableResult.IsTruth, sampleName, _inputSpec, bndSet, errorList,
_mode == EvaluationMode.CrossTypeAndSimpleCounting);
switch (result)
{
//ugly implementation, first of breakend pair will return left as IGeneralBnd
case IGeneralBnd _:
continue;
case IVcfVariant vcfVariant:
mutableResult.AddUnsupported(vcfVariant);
break;
case IMutableWittyerSimpleVariant simpleVariant:
mutableResult.AddTarget(simpleVariant);
break;
}
}
if (errorList.Count > 0)
{
var msg = (errorList.Count > MaxNonSupportedVariantToPrint
? errorList.Take(MaxNonSupportedVariantToPrint)
: errorList).StringJoin("\n");
Console.Error.WriteLine(
$"Fail to parse {errorList.Count} variants from truth, check first {MaxNonSupportedVariantToPrint} or less: \n{msg}");
}
if (bndSet.Count == 0)
{
return(genomeType ?? GenomeType.Unknown);
}
Console.Error.WriteLine(
$"Found single breakend in truth!!!! Those entries will be completely exclude from stats. First {MaxNonSupportedVariantToPrint} or less:");
Console.Error.WriteLine(bndSet.Values.Take(MaxNonSupportedVariantToPrint).StringJoin("\n"));
foreach (var kvp in bndSet)
{
mutableResult.AddUnsupported(CreateUnsupportedVariant(kvp.Value,
sampleName == null ? null : kvp.Value.Samples[sampleName], FailedReason.UnpairedBnd, mutableResult.IsTruth));
}
return(genomeType ?? GenomeType.Unknown);
}
private static ContigMetaInfoLine ConvertGenomeType([NotNull] this ContigMetaInfoLine line, GenomeType type)
{
var contig = line.Contig;
if (contig.GetGenomeType() == type)
{
return(ContigMetaInfoLine.Create(contig));
}
switch (type)
{
// since toGrchStyle()/toUcscStyle() does not preserve length information, this is to best preserve length
case GenomeType.Grch:
contig = contig.ToGrchStyle();
break;
case GenomeType.Ucsc:
contig = contig.ToUcscStyle();
break;
}
return(ContigMetaInfoLine.Create(contig));
}
/// <summary>
/// Create a new instance of Genome with the specified
/// name and GenomeType.
/// </summary>
/// <param name="name">The name of this Genome.</param>
/// <param name="genomeType">The type of the genome test.</param>
public GenomeOld(string name, GenomeType genomeType) {
this.Name = name;
this.GenomeTestType = genomeType;
}
