private static IEnumerable <IMetaInfoLine> MergeTypedMetaLines(
[NotNull] this IReadOnlyDictionary <string, ITypedMetaInfoLine> truthLines,
[NotNull] string lineKey, [NotNull] IReadOnlyDictionary <string, ITypedMetaInfoLine> queryLines)
=> MergeMetaLines(truthLines, queryLines,
(t, q) => t.Type == q.Type && t.Number == q.Number && IsDescriptionEqual(t, q),
(t, q) => TypedMetaInfoLine.Create(MetaInfoLine.Create(lineKey, t.Id, MergeDescription(t, q)),
t.Type == q.Type ? t.Type : TypeField.String, t.Number == q.Number ? t.Number : NumberField.Any));
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);
}
}
}
private static IEnumerable <IMetaInfoLine> MergeMetaInfoLines(
[NotNull] this IReadOnlyDictionary <string, IMetaInfoLine> truthLines,
[NotNull] string lineKey, [NotNull] IReadOnlyDictionary <string, IMetaInfoLine> queryLines)
=> MergeMetaLines(truthLines, queryLines, IsDescriptionEqual,
(t, q) => MetaInfoLine.Create(lineKey, t.Id, MergeDescription(t, q)));
