/// <summary>
/// sets the underlying data for the compressed sequence
/// </summary>
public void Set(int numBases, byte[] buffer, IIntervalSearch <MaskedEntry> maskedIntervalSearch, int sequenceOffset = 0)
{
NumBases = numBases;
_buffer = buffer;
_maskedIntervalSearch = maskedIntervalSearch;
_sequenceOffset = sequenceOffset;
}
private void BuildIntervalForests()
{
if (_saReaders == null || _saReaders.Count == 0)
{
return;
}
var smallVariantIntervals = new List <Interval <ISupplementaryInterval> >();
var svIntervals = new List <Interval <ISupplementaryInterval> >();
var allVariantIntervals = new List <Interval <ISupplementaryInterval> >();
foreach (var reader in _saReaders)
{
if (reader.SmallVariantIntervals != null)
{
smallVariantIntervals.AddRange(reader.SmallVariantIntervals);
}
if (reader.SvIntervals != null)
{
svIntervals.AddRange(reader.SvIntervals);
}
if (reader.AllVariantIntervals != null)
{
allVariantIntervals.AddRange(reader.AllVariantIntervals);
}
}
_smallVariantIntervalArray = CreateIntervalArray(smallVariantIntervals);
_svIntervalArray = CreateIntervalArray(svIntervals);
_allVariantIntervalArray = CreateIntervalArray(allVariantIntervals);
}
public SupplementaryAnnotationProvider(List <string> saDirs)
{
Name = "Supplementary annotation provider";
_currentUcscReferenceName = "";
_smallVariantIntervalArray = new NullIntervalSearch <ISupplementaryInterval>();
_svIntervalArray = new NullIntervalSearch <ISupplementaryInterval>();
_allVariantIntervalArray = new NullIntervalSearch <ISupplementaryInterval>();
_saDirs = saDirs.ToList();
}
internal void Set(int length, int sequenceOffset, byte[] twoBitBuffer,
IntervalArray <MaskedEntry> maskedEntryIntervalArray, Band[] cytogeneticBands)
{
Length = length;
_buffer = twoBitBuffer;
_maskedIntervalSearch = maskedEntryIntervalArray;
_sequenceOffset = sequenceOffset;
CytogeneticBands = cytogeneticBands;
_useNSequence = false;
}
private static void AddIntervals(IAnnotatedPosition annotatedPosition,
IIntervalSearch <ISupplementaryInterval> intervalArray, int begin, int end)
{
var intervals = intervalArray.GetAllOverlappingValues(begin, end);
if (intervals == null)
{
return;
}
foreach (var overlappingInterval in intervals)
{
var reciprocalOverlap = annotatedPosition.Position.Start >= annotatedPosition.Position.End
? null
: overlappingInterval.GetReciprocalOverlap(annotatedPosition.AnnotatedVariants[0].Variant);
annotatedPosition.SupplementaryIntervals.Add(
new AnnotatedSupplementaryInterval(overlappingInterval, reciprocalOverlap));
}
}
public void Set(int numBases, byte[] buffer, IIntervalSearch <MaskedEntry> maskedIntervalSearch, int sequenceOffset = 0)
{
throw new NotImplementedException();
}
public ReferenceIntervalArrayTests()
{
_refIntervalSearch = GetData();
}
