public static WittyerResult Create([NotNull] IVcfHeader vcfHeader, [NotNull] string sampleName,
[NotNull] IReadOnlyList <IContigInfo> contigs, bool isTruth,
[NotNull] IReadOnlyDictionary <WittyerType, IReadOnlyList <IWittyerVariant> > variants,
[NotNull] IReadOnlyDictionary <WittyerType, IReadOnlyList <IWittyerBnd> > breakendPairsAndInsertions,
[NotNull] IReadOnlyCollection <IVcfVariant> notAssessedVariants)
=> new WittyerResult(vcfHeader, sampleName, contigs, isTruth, variants, breakendPairsAndInsertions,
notAssessedVariants);
internal static IEnumerable <IBasicMetaLine> MergeMetaLines([NotNull] this IVcfHeader truthHeader,
[CanBeNull] string cmdLine, [NotNull] IVcfHeader queryHeader)
{
var truthMetaLines = truthHeader.ColumnMetaInfoLines;
var queryMetaLines = queryHeader.ColumnMetaInfoLines;
var altLines = MergeMetaInfoLines(truthMetaLines.AltLines, Alt, queryMetaLines.AltLines);
var filterLines = MergeMetaInfoLines(truthMetaLines.FilterLines, Filter, queryMetaLines.FilterLines);
var contigLines = MergeContigLines(queryMetaLines.ContigLines, truthMetaLines.ContigLines);
var infoLines = MergeTypedMetaLines(truthMetaLines.InfoLines, Info, queryMetaLines.InfoLines);
var sampleFormatLines =
MergeTypedMetaLines(truthMetaLines.SampleFormatLines, SampleFormat, queryMetaLines.SampleFormatLines);
var sampleMetaLines = MergeTypedMetaLines(truthMetaLines.SampleMetaLines, Meta, queryMetaLines.SampleMetaLines);
var builder = VcfHeader.CreateBuilder(truthHeader.Version)
.AddSampleColumn(DefaultTruthSampleName).AddSampleColumn(DefaultQuerySampleName);
truthHeader.ReferenceGenome.DoOnSuccess(r => builder.SetReference(r));
foreach (var line in altLines.Concat(filterLines).Concat(contigLines).Concat(sampleMetaLines)
.Concat(GenerateWittyerLines(infoLines, sampleFormatLines, cmdLine)))
{
yield return(line);
}
}
internal MutableWittyerResult([CanBeNull] string sampleName, bool isTruth, [NotNull] IVcfHeader vcfHeader)
{
// ReSharper disable once AssignNullToNotNullAttribute
SampleName = sampleName ?? (isTruth
? SamplePair.Default.TruthSampleName
: SamplePair.Default.QuerySampleName);
IsTruth = isTruth;
VcfHeader = vcfHeader;
}
private WittyerResult([NotNull] IVcfHeader vcfHeader, [NotNull] string sampleName,
[NotNull] IReadOnlyList <IContigInfo> contigs, bool isTruth,
[NotNull] IReadOnlyDictionary <WittyerType, IReadOnlyList <IWittyerVariant> > variants,
[NotNull] IReadOnlyDictionary <WittyerType, IReadOnlyList <IWittyerBnd> > breakendPairsAndInsertions,
[NotNull] IReadOnlyCollection <IVcfVariant> notAssessedVariants)
{
VcfHeader = vcfHeader;
SampleName = sampleName;
Contigs = contigs;
IsTruth = isTruth;
Variants = variants;
BreakendPairsAndInsertions = breakendPairsAndInsertions;
NotAssessedVariants = notAssessedVariants;
}
internal static IEnumerable <string> MergedWith([NotNull] this IVcfHeader truthHeader,
[NotNull] IVcfHeader queryHeader, [NotNull] ISamplePair pair, [CanBeNull] string cmdLine)
{
var mergedMetaLines = truthHeader.MergeMetaLines(cmdLine, queryHeader);
return(ToWittyBuilder()
.AddSampleMetaInfo(truthHeader, pair, queryHeader, mergedMetaLines)
.Build().ToStrings());
VcfHeader.Builder ToWittyBuilder()
{
var builder = VcfHeader.CreateBuilder(truthHeader.Version)
.AddSampleColumn(DefaultTruthSampleName).AddSampleColumn(DefaultQuerySampleName);
truthHeader.ReferenceGenome.DoOnSuccess(r => builder.SetReference(r));
return(builder);
}
}
internal static VcfHeader.Builder AddSampleMetaInfo([NotNull] this VcfHeader.Builder builder,
[NotNull] IVcfHeader truthHeader, [CanBeNull] ISamplePair samplePair,
[NotNull] IVcfHeader queryHeader, [NotNull] IEnumerable <IBasicMetaLine> mergedMetaLines)
{
// todo: for vcf 4.3, this has ids, so should be merged via AddSampleMetaInfo.
// get rid of pedigree lines since we don't have all the sample columns
//builder = truthHeader.PedigreeLines.Concat(queryHeader.PedigreeLines)
// .Aggregate(builder, (acc, line) => acc.AddPedigreeLine(line));
var truth = samplePair?.TruthSampleName ?? truthHeader.SampleNames.FirstOrDefault();
var query = samplePair?.QuerySampleName ?? queryHeader.SampleNames.FirstOrDefault();
if (truth != query && truth != null) // only add sample lines that are not the same sample names otherwise, error out.
{
AddSampleLine(truth, DefaultTruthSampleName);
AddSampleLine(query, DefaultQuerySampleName);
}
return(mergedMetaLines
.Aggregate(builder, (acc, line) => acc.AddLine(line)));
void AddSampleLine(string sampleName, string defaultSampleName)
{
if (sampleName == null)
{
return;
}
builder.AddOtherLine(MetaInfoLine.Create(OriginalSampleNameLineKey, defaultSampleName, sampleName));
var truthLine = truthHeader.ColumnMetaInfoLines.SampleLines
.FirstOrException(l => sampleName.Equals(l.Value.Id)).GetOrNull()?.Value;
if (truthLine != null)
{
builder.AddLine(truthLine);
}
}
}
internal static TruthForest Create([CanBeNull] string sampleName, [NotNull] IVcfHeader vcfHeader) => new TruthForest(sampleName, vcfHeader);
private TruthForest([CanBeNull] string sampleName, [NotNull] IVcfHeader vcfHeader) => _baseResult = new MutableWittyerResult(sampleName, true, vcfHeader);
