private SampleStats([NotNull] ISamplePair samplePair, IReadOnlyList <BasicJsonStats> overallStats,
IReadOnlyList <SvTypeJsonStats> detailedStats)
{
_samplePair = samplePair;
OverallStats = overallStats;
DetailedStats = detailedStats;
}
/// <summary>
/// Initializes a new instance of the <see cref="SampleMetrics"/> class.
/// </summary>
/// <param name="samplePair">The sample pair.</param>
/// <param name="overallStats">The overall stats.</param>
/// <param name="detailedStats">The detailed stats.</param>
private SampleMetrics([NotNull] ISamplePair samplePair,
[NotNull] IImmutableDictionary <StatsType, IStatsUnit> overallStats,
[NotNull] IImmutableDictionary <WittyerType, IBenchmarkMetrics <WittyerType> > detailedStats)
{
SamplePair = samplePair;
OverallStats = overallStats;
DetailedStats = detailedStats;
}
public static SampleMetrics Create([NotNull] ISamplePair samplePair,
[NotNull] IImmutableDictionary <StatsType, IStatsUnit> overallStats,
[NotNull] IImmutableDictionary <WittyerType, IBenchmarkMetrics <WittyerType> > detailedStats)
=> new SampleMetrics(samplePair, overallStats, detailedStats);
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);
}
}
}
