public void MergeHeaderWorks()
{
string GetPrefix(string line)
=> line.Split(new[] { VcfConstants.Header.MetaInfoLines.KeyValueDelimiter[0] }, 4)
.Where(it => it.Length > 2).Skip(2).FirstOrDefault();
var queryHeader = VcfHeader
.TryCreate(Path.Combine("Resources", "VcfHeaders", "query.wit-141.vcf").ToFileInfo()).GetOrThrow();
var truthHeader = VcfHeader
.TryCreate(Path.Combine("Resources", "VcfHeaders", "truth.wit-141.vcf").ToFileInfo()).GetOrThrow();
var vcfLines = truthHeader.MergedWith(queryHeader, SamplePair.Default, null).ToList();
var merged = VcfHeader.TryCreate(vcfLines)
.GetOrThrow();
MultiAssert.True(
merged.ColumnMetaInfoLines.SampleFormatLines.ContainsKey(WittyerConstants.WittyerMetaInfoLineKeys
.What));
MultiAssert.True(
merged.ColumnMetaInfoLines.SampleFormatLines.ContainsKey(WittyerConstants.WittyerMetaInfoLineKeys
.Why));
MultiAssert.True(
merged.ColumnMetaInfoLines.SampleFormatLines.ContainsKey(WittyerConstants.WittyerMetaInfoLineKeys
.Wit));
MultiAssert.True(
merged.ColumnMetaInfoLines.InfoLines.ContainsKey(WittyerConstants.WittyerMetaInfoLineKeys
.Who));
MultiAssert.True(
merged.ColumnMetaInfoLines.InfoLines.ContainsKey(WittyerConstants.WittyerMetaInfoLineKeys
.Where));
MultiAssert.True(
merged.ColumnMetaInfoLines.InfoLines.ContainsKey(WittyerConstants.WittyerMetaInfoLineKeys
.Win));
MultiAssert.True(
merged.ColumnMetaInfoLines.InfoLines.ContainsKey(WittyerConstants.WittyerMetaInfoLineKeys
.Wow));
// 1 different because of date in
// ##bcftools_viewCommand=view -h /home/hking/manta_2by250_sv_dragen/manta_2by250_sv_dragen.sv.vcf.gz; Date=Fri Jul 19 07:39:26 2019
var diffs = queryHeader.Select(GetPrefix).Where(it => it != null).ToImmutableHashSet()
.Except(merged.Select(GetPrefix).Where(it => it != null));
MultiAssert.True(diffs.Count == 1);
// 1 different because of date in
// ##bcftools_viewCommand=view -h NA12878_pbmm_v1.0.0_pbsv_v2.2.0_hg38_20190430_witty_format.vcf.gz; Date=Fri Jul 19 07:38:56 2019
diffs = truthHeader.Select(GetPrefix).Where(it => it != null).ToImmutableHashSet()
.Except(merged.Select(GetPrefix).Where(it => it != null));
MultiAssert.True(diffs.Count == 1);
MultiAssert.AssertAll();
}
public void ComparerWorks()
{
if (MiscUtils.IsRunningAnyLinux)
{
return; // currently failing on linux :(
}
IReadOnlyList <IContigInfo> CreateHeader(string fileName) => VcfHeader
.TryCreate(Path.Combine("Resources", "VcfHeaders", fileName).ToFileInfo()).GetOrThrow()
.ColumnMetaInfoLines.ContigLines.Select(kvp => kvp.Value.Contig).ToReadOnlyList();
var comparer = WittyerVcfWriter.CreateComparer(CreateHeader("query.vcf.gz"), CreateHeader("truth.vcf.gz"));
var parser = VcfVariantParserSettings.Create(ImmutableList.Create(SampleName));
var bnd1 = VcfVariant.TryParse(Bnd1, parser).GetOrThrow();
var bnd2 = VcfVariant.TryParse(Bnd2, parser).GetOrThrow();
Assert.True(comparer.Compare(bnd1, bnd2) < 0);
}