public void CnvOverlspTest()
{
var interval = new AnnotationInterval(16764333, 17483981);
var overlap = interval.OverlapFraction(16886175, 17054465);
Assert.Equal(0.23385150260752116, overlap);// full overlap
var variant = new AnnotationInterval(16886175, 17054465);
var variantOverlap = variant.OverlapFraction(16764333, 17483981);
Assert.Equal(1.0, variantOverlap);
}
/// <summary>
/// returns the number of transcripts within flanking distance
/// </summary>
private bool HasOverlap(VariantFeature variant)
{
// ReSharper disable once LoopCanBeConvertedToQuery
foreach (var transcript in OverlappingTranscripts)
{
var overlapInterval = new AnnotationInterval(transcript.Start - FlankingLength, transcript.End + FlankingLength);
if (variant.AlternateAlleles.Any(altAllele => overlapInterval.Overlaps(altAllele.Start, altAllele.End)))
{
return(true);
}
}
return(false);
}
public void OverlapFraction()
{
var interval = new AnnotationInterval(101, 110);
var overlap = interval.OverlapFraction(99, 110);
Assert.Equal(1.0, overlap);// full overlap
overlap = interval.OverlapFraction(90, 105);
Assert.Equal(0.50, overlap);
overlap = interval.OverlapFraction(105, 111);
Assert.Equal(0.60, overlap);
overlap = interval.OverlapFraction(101, 101);
Assert.Equal(0.10, overlap);
}
/// <summary>
/// sets both the exon and intron number strings according to which were affected by the variant [BaseTranscriptVariation.pm:474 _exon_intron_number]
/// </summary>
public static void ExonIntronNumber(CdnaCoordinateMap[] cdnaMaps, SimpleInterval[] introns, bool onReverseStrand,
TranscriptAnnotation ta, out string exonNumber, out string intronNumber)
{
int exonCount = 0;
var altAllele = ta.AlternateAllele;
var variantInterval = new AnnotationInterval(altAllele.Start, altAllele.End);
var overlappedExons = new List <int>();
var overlappedIntrons = new List <int>();
var prevExon = CdnaCoordinateMap.Null();
foreach (var exon in cdnaMaps)
{
exonCount++;
if (variantInterval.Overlaps(exon.GenomicStart, exon.GenomicEnd))
{
overlappedExons.Add(exonCount);
}
if (!prevExon.IsNull)
{
int intronStart = prevExon.GenomicEnd + 1;
int intronEnd = exon.GenomicStart - 1;
if (variantInterval.Overlaps(intronStart, intronEnd))
{
overlappedIntrons.Add(exonCount - 1);
}
}
prevExon = exon;
}
exonNumber = GetExonIntronNumber(overlappedExons, cdnaMaps.Length, onReverseStrand);
intronNumber = introns != null?GetExonIntronNumber(overlappedIntrons, introns.Length, onReverseStrand) : null;
if (overlappedExons.Count > 0)
{
ta.HasExonOverlap = true;
}
}
private void PopulateSuppIntervalFields(List <ISupplementaryInterval> suppIntervals)
{
if (suppIntervals == null)
{
return;
}
var supplementaryIntervals = new List <JsonSupplementaryInterval>();
foreach (var interval in suppIntervals)
{
var jsonSuppInterval = new JsonSupplementaryInterval(interval);
supplementaryIntervals.Add(jsonSuppInterval);
//compute reciprocal overlap
if (ReferenceBegin == null || _referenceEnd == null)
{
continue;
}
if (ReferenceBegin >= _referenceEnd)
{
continue; //do not calculate reciprocal overlap for insertion
}
if (interval.Start >= interval.End)
{
continue; //donot compute reciprocal overlap if supp interval is insertion
}
var variantInterval = new AnnotationInterval(ReferenceBegin.Value + 1, _referenceEnd.Value);
var intervalOverlap = interval.OverlapFraction(variantInterval.Start, variantInterval.End);
var variantOverlap = variantInterval.OverlapFraction(interval.Start, interval.End);
jsonSuppInterval.ReciprocalOverlap = Math.Min(intervalOverlap, variantOverlap);
}
SupplementaryIntervals = supplementaryIntervals;
}
public int Extract()
{
var count = 0;
using (_reader)
using (_writer)
{
for (var i = _begin; i <= _end; i++)
{
var sa = _reader.GetAnnotation(i) as SupplementaryAnnotationPosition;
if (sa != null)
{
count++;
_writer.Write(new SupplementaryPositionCreator(sa), i);
}
}
var miniSaInterval = new AnnotationInterval(_begin, _end);
// get the supplementary intervals overlapping the mini SA interval
var suppIntervals = new List <SupplementaryInterval>();
var readerSuppInterval = _reader.GetSupplementaryIntervals(_renamer);
if (readerSuppInterval != null)
{
foreach (var interval in readerSuppInterval)
{
if (miniSaInterval.Overlaps(interval.Start, interval.End))
{
suppIntervals.Add(interval as SupplementaryInterval);
}
}
}
Console.WriteLine("Found {0} supplementary intervals.", suppIntervals.Count);
_writer.SetIntervalList(suppIntervals);
}
return(count);
}