internal static IInterval <uint> ConvertPositionToCiInterval(
this uint position, [NotNull] IVcfVariant variant, [NotNull] string ciInfoTag)
{
if (!variant.Info.TryGetValue(ciInfoTag, out var posString))
{
return(BedInterval.Create(position > 0 ? position - 1 : 0, position == 0 ? 1 : position));
}
var split = posString.Split(WittyerConstants.InfoValueDel);
if (split.Length != 2)
{
throw VcfVariantFormatException.Create(variant.ToString(), ImmutableHashSet.Create(VcfColumn.Info),
$"Invalid {ciInfoTag} found: {posString}", variant.ToStrings().ToList().AsReadOnly());
}
var parsedStart = GetParsedAbsValue(split[0]);
if (parsedStart == null)
{
throw new InvalidOperationException($"Failed to parse {ciInfoTag}={posString}!");
}
var parsedStop = GetParsedAbsValue(split[1]);
if (parsedStop == null)
{
throw new InvalidOperationException($"Failed to parse {ciInfoTag}={posString}!");
}
var(start, stop) = ConvertPositionToCiInterval(position, (parsedStart.Value, parsedStop.Value));
return(BedInterval.Create(start, stop));
uint?GetParsedAbsValue(string val)
=> !int.TryParse(val, out var parsed) ? (uint?)null : (uint)(parsed < 0 ? -parsed : parsed);
}
internal static IWittyerVariant Create([NotNull] IVcfVariant baseVariant,
string sample, double percentageDistance, uint basepairDistance,
IReadOnlyList <uint> bins, WittyerVariantType svType)
{
if (svType == WittyerVariantType.Invalid)
{
throw new InvalidDataException(
$"Invalid {VcfConstants.SvTypeKey} in variant: \n{baseVariant}\nNot sure why you got here though. Check with a witty.er developer!");
}
var end = baseVariant.Position + baseVariant.GetSvLength();
var baseInterval = BedInterval.Create(baseVariant.Position, end);
var borderInterval =
baseVariant.Position.CalculateBorderInterval(baseInterval,
baseVariant.ParseCi(WittyerConstants.Cipos),
percentageDistance, basepairDistance);
// wittyerVariant should all have end border, it's a matter of how to find it,
// either END key in INFO field, sort out through SVLEN or other ways, details can be defined in FindEndBorder() later
var endInterval = (end - 1).CalculateBorderInterval(baseInterval,
baseVariant.ParseCi(WittyerConstants.Ciend),
percentageDistance, basepairDistance);
var posContigAndInterval =
ContigAndInterval.Create(baseVariant.Contig, borderInterval.Start, borderInterval.Stop + 1);
var endContigAndInterval =
ContigAndInterval.Create(baseVariant.Contig, endInterval.Start, endInterval.Stop + 1);
return(Create(baseVariant, baseInterval, svType, posContigAndInterval,
Winner.Create(svType, baseInterval, bins), new List <OverlapAnnotation>(),
WittyerSample.CreateOverall(baseVariant, sample, svType == WittyerVariantType.CopyNumberReference),
endContigAndInterval));
}
internal static IInterval <uint> ConvertPositionToCiInterval(
this uint position, [NotNull] IVcfVariant variant, [NotNull] string ciInfoTag)
{
if (!variant.Info.TryGetValue(ciInfoTag, out var posString))
{
return(BedInterval.Create(position > 0 ? position - 1 : 0, position == 0 ? 1 : position));
}
var split = posString.Split(WittyerConstants.InfoValueDel);
if (split.Length != 2)
{
throw VcfVariantFormatException.Create(variant.ToString(), ImmutableHashSet.Create(VcfColumn.Info),
$"Invalid {ciInfoTag} found: {posString}", variant.ToStrings().ToList().AsReadOnly());
}
var(start, stop) = ConvertPositionToCiInterval(position, (GetParsedAbsValue(split[0]), GetParsedAbsValue(split[1])));
return(BedInterval.Create(start, stop));
uint GetParsedAbsValue(string val)
{
var parsed = int.Parse(val);
return((uint)(parsed < 0 ? -parsed : parsed));
}
}
public static void WittyerVariantIntervalCorrect([NotNull] string variant, uint start, uint end,
uint posStart, uint posEnd, uint endStart, uint endEnd)
{
const string sampleName = "tumor";
var vcfVariant = VcfVariant.TryParse(variant,
VcfVariantParserSettings.Create(ImmutableList.Create("normal", sampleName), GenomeAssembly.Hg38))
.GetOrThrowDebug();
var _ = WittyerType.ParseFromVariant(vcfVariant, false, sampleName, out var type);
if (type == null)
{
throw new NotSupportedException("This test does not handle svType null");
}
var wittyerVariant = WittyerVariantInternal
.Create(vcfVariant, vcfVariant.Samples[sampleName], type, Bins, PercentDistance, BasepairDistance);
var expectedStart = ContigAndInterval.Create(vcfVariant.Contig, start, end);
var expectedPos = BedInterval.Create(posStart, posEnd);
var expectedEnd = BedInterval.Create(endStart, endEnd);
MultiAssert.Equal(expectedStart, wittyerVariant);
MultiAssert.Equal(expectedPos, wittyerVariant.CiPosInterval);
MultiAssert.Equal(expectedEnd, wittyerVariant.CiEndInterval);
MultiAssert.AssertAll();
}
private BedGraphEntry GetAlleleFrequencyEntry(string bafLine)
{
var bafFields = CSVReader.ParseCommaDelimitedLine(bafLine);
var chromosome = bafFields[0];
var oneBasedPosition = int.Parse(bafFields[1]);
var alleleFrequency = (decimal)double.Parse(bafFields[2]);
var bedPosition = new BedInterval(oneBasedPosition - 1, oneBasedPosition);
return(new BedGraphEntry(chromosome, bedPosition, alleleFrequency));
}
internal static IWittyerBnd Create([NotNull] IVcfVariant variant,
IVcfVariant secondVariant, [CanBeNull] string sampleName,
double percentageDistance, uint basepairDistance, IReadOnlyList <uint> bins)
{
var(first, second) = MiscUtils.FindBndEntriesOrder(variant, secondVariant);
var posInterval = first.CalculateBndBorderInterval(second,
first.ParseCi(WittyerConstants.Cipos), percentageDistance, basepairDistance);
var endInterval = second.CalculateBndBorderInterval(first,
second.ParseCi(WittyerConstants.Cipos), percentageDistance,
basepairDistance);
var svType = variant.ParseWittyerVariantType(sampleName);
var winner = GetWinner();
var overlapInfo = new List <OverlapAnnotation>();
var sample = WittyerSample.CreateOverall(variant, sampleName, false);
return(Create(first, posInterval, winner, endInterval, overlapInfo, sample, second, svType));
Winner GetWinner()
{
if (svType == WittyerVariantType.TranslocationBreakend)
{
return(Winner.Create(svType));
}
if (svType != WittyerVariantType.Insertion)
{
return(Winner.Create(svType, BedInterval.Create(first.Position, second.Position + 1), bins));
}
uint?end = null;
// insertion, try sequences first
if (variant.IsSimpleSequence(out var length))
{
end = length;
}
// try svlength, but if not, assume unknown length.
else if (variant.TryGetSvLength(out length) == null)
{
end = length;
}
return(Winner.Create(svType, end == null ? null : BedInterval.Create(variant.Position, variant.Position + end.Value), bins));
}
}
public static IGeneralBnd CreateFromVariant([NotNull] IVcfVariant variant)
{
var altBnd = variant.GetSingleAlt();
var thisRef = variant.Ref[0];
var mate = SimpleBreakEnd.Parse(altBnd, out var firstField, out var lastField);
var is3Prime = !string.IsNullOrWhiteSpace(firstField);
if (is3Prime && !firstField.StartsWith(thisRef) ||
!is3Prime && !lastField.EndsWith(thisRef))
{
throw new InvalidDataException(
$"Invalid breakend because neither the alt didn't start or end with ref's first base: {variant}");
}
var interval = BedInterval.Create(variant.Position - 1, variant.Position);
return(new GeneralBnd(variant, interval, is3Prime, mate));
}
internal static IInterval <uint> ToBedInterval([NotNull] this IVcfVariant baseVariant,
bool throwException, out uint endVal, out bool sharedFirstBase)
{
endVal = baseVariant.Position;
if (IsSimpleSequence(baseVariant,
out var refLenVal, out sharedFirstBase, out var sharedLastBase, false))
// first need to save the original end before normalizing
{
endVal += refLenVal;
if (baseVariant.Alts.Count > 0) // refsites don't have Alts in VariantUtils
{
baseVariant = baseVariant.TryNormalizeVariant(VariantNormalizer.TrimCommonBases, 0).GetOrThrow();
}
}
var refLen = baseVariant.GetSvLength(throwException, out sharedFirstBase, out sharedLastBase, out var endPos);
if (refLen == null) // means insertion of unknown length.
{
return(null);
}
if (endPos != null)
{
endVal = endPos.Value;
}
var start = sharedFirstBase || baseVariant.Position == 0 ? baseVariant.Position : baseVariant.Position - 1;
var end = start + refLen.Value;
if (sharedLastBase) // rare case
{
end--;
}
return(BedInterval.Create(start, end));
}
public void SubtractMultipleIntervalsWorks()
{
var target = BedInterval.Create(10, 20);
var subtracts = new[]
{
BedInterval.Create(16, 18), BedInterval.Create(19, 25), BedInterval.Create(27, 30),
BedInterval.Create(2, 4), BedInterval.Create(8, 11), BedInterval.Create(13, 15)
};
var expectedLengths = new List <uint>
{
// [11,13)
2,
// [15,16)
1,
// [18,19)
1
};
var intervals = target.Subtract(subtracts).ToList();
Assert.True(expectedLengths.SequenceEqual(intervals.Select(i => i.GetLength())));
}
public GenomicBin(string chromosome, BedInterval interval, int gc)
{
Chromosome = chromosome;
Interval = interval;
GC = gc;
}
public GenomicBin(string chromosome, BedInterval interval)
{
Chromosome = chromosome;
Interval = interval;
}
internal static IWittyerBnd Create([NotNull] IVcfVariant first, [CanBeNull] IVcfSample originalSample,
[NotNull] WittyerType svType, [NotNull] IReadOnlyList <uint> bins, uint bpd, double?percentageDistance,
[NotNull] IVcfVariant second)
{
if (!ReferenceEquals(first, second))
{
(first, second) = FindBndEntriesOrder(in first, in second);
}
var ciPosInterval = first.Position.ConvertPositionToCiInterval(first, WittyerConstants.Cipos);
var ciEndInterval = ReferenceEquals(first, second)
? ciPosInterval // same variant means same intervals.
: second.Position.ConvertPositionToCiInterval(second, WittyerConstants.Cipos);
IContigAndInterval posInterval, endInterval;
if (ReferenceEquals(first, second)) // insertions need trimming and stuff.
{
var trimmed = first.TryNormalizeVariant(VariantNormalizer.TrimCommonBases, 0).GetOrThrow();
var tuple = (bpd, bpd);
var(posStart, posStop) = trimmed.Position.ConvertPositionToCiInterval(tuple);
WittyerUtils.GetBetterInterval(ciPosInterval, ref posStart, ref posStop);
posInterval = endInterval = ContigAndInterval.Create(first.Contig, posStart, posStop);
}
else
{
(posInterval, endInterval) = WittyerUtils.GetPosAndEndInterval(first.Contig,
svType == WittyerType.IntraChromosomeBreakend ? percentageDistance : null, bpd,
ciPosInterval, first.Position, ciEndInterval, second.Position, second.Contig);
}
var winner = GetWinner();
var sample = WittyerSample.CreateFromVariant(first, originalSample, false);
return(new WittyerBndInternal(svType, first, posInterval, ciPosInterval,
second, endInterval, ciEndInterval, winner, sample));
(IVcfVariant first, IVcfVariant second) FindBndEntriesOrder(in IVcfVariant variantA,
in IVcfVariant variantB)
=> ContigAndPositionComparer.Default.Compare(variantA, variantB) > 0
? (variantB, variantA)
: (variantA, variantB);
Winner GetWinner()
{
if (svType == WittyerType.TranslocationBreakend)
{
return(Winner.Create(svType));
}
IInterval <uint> bedInterval;
if (svType == WittyerType.Insertion)
{
bedInterval = GetInsertionInterval(first);
}
else
{
var start = first.Position;
if (start > 0)
{
start--;
}
bedInterval = BedInterval.Create(start, second.Position);
}
return(Winner.Create(svType, bedInterval, bins));
}
}
private BedGraphEntry GetCopyNumberEntry(CanvasSegment segment)
{
var interval = new BedInterval(segment.Begin, segment.End);
return(new BedGraphEntry(segment.Chr, interval, segment.CopyNumber));
}
