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);
}
