public IEnumerable <ISupplementaryInterval> GetSupplementaryIntervals(IChromosomeRenamer renamer)
{
if (_intervalsPosition == -1)
{
return(null);
}
var returnPosition = _stream.Position;
_stream.Position = _intervalsPosition;
var count = _reader.ReadInt32(); // how many supplementary intervals to read
if (count == 0)
{
return(null);
}
var intervalList = new List <SupplementaryInterval>(count);
for (var i = 0; i < count; i++)
{
intervalList.Add(SupplementaryInterval.Read(_reader, renamer));
}
_stream.Position = returnPosition;
return(intervalList);
}
public void Load(string ucscReferenceName, IChromosomeRenamer renamer)
{
if (_customAnnotationDirs == null || _customAnnotationDirs.Count == 0 || ucscReferenceName == _currentUcscReferenceName)
{
return;
}
_customAnnotationReaders = SupplementaryAnnotationCommon.GetReaders(_customAnnotationDirs, ucscReferenceName);
_hasCustomAnnotations = _customAnnotationReaders.Count > 0;
_currentUcscReferenceName = ucscReferenceName;
}
public void Load(string ucscReferenceName, IChromosomeRenamer renamer)
{
if (_ciDirs.Count == 0 || ucscReferenceName == _currentUcscReferenceName)
{
return;
}
var intervals = GetIntervals(ucscReferenceName);
_intervalForest = IntervalArrayFactory.CreateIntervalArray(intervals, renamer);
_hasIntervals = !(_intervalForest is NullIntervalSearch <ICustomInterval>);
_currentUcscReferenceName = ucscReferenceName;
}
public void Load(string ucscReferenceName, IChromosomeRenamer renamer)
{
if (string.IsNullOrEmpty(_saDir) || ucscReferenceName == _currentUcscReferenceName)
{
return;
}
var saPath = Path.Combine(_saDir, ucscReferenceName + ".nsa");
_saReader = File.Exists(saPath) ? new SupplementaryAnnotationReader(saPath) : null;
_intervalForest = _saReader?.GetIntervalForest(renamer);
_hasIntervals = !(_intervalForest is NullIntervalSearch <ISupplementaryInterval>);
_currentUcscReferenceName = ucscReferenceName;
}
// constructor
public SupplementaryInterval(int start, int end, string refName, string altAllele, VariantType variantType,
string source, IChromosomeRenamer renamer, Dictionary <string, int> intValues = null,
Dictionary <string, double> doubleValues = null, Dictionary <string, double> freqValues = null,
Dictionary <string, string> stringValues = null, List <string> boolValues = null,
Dictionary <string, IEnumerable <string> > stringLists = null) : base(start, end)
{
Start = start;
End = end;
AlternateAllele = altAllele;
VariantType = variantType;
Source = source;
_intValues = intValues ?? new Dictionary <string, int>();
_boolList = boolValues ?? new List <string>();
_doubleValues = doubleValues ?? new Dictionary <string, double>();
_freqValues = freqValues ?? new Dictionary <string, double>();
_stringValues = stringValues ?? new Dictionary <string, string>();
_stringLists = stringLists ?? new Dictionary <string, IEnumerable <string> >();
ReferenceName = renamer.GetEnsemblReferenceName(refName);
}
public static IIntervalForest <ISupplementaryInterval> CreateIntervalArray(
IEnumerable <ISupplementaryInterval> intervals, IChromosomeRenamer renamer)
{
if (intervals == null)
{
return(new NullIntervalSearch <ISupplementaryInterval>());
}
var numRefSeqs = renamer.NumRefSeqs;
var intervalLists = new List <IntervalArray <ISupplementaryInterval> .Interval> [numRefSeqs];
for (var i = 0; i < numRefSeqs; i++)
{
intervalLists[i] = new List <IntervalArray <ISupplementaryInterval> .Interval>();
}
foreach (var interval in intervals)
{
ushort index = renamer.GetReferenceIndex(interval.ReferenceName);
if (index == ChromosomeRenamer.UnknownReferenceIndex)
{
continue;
}
intervalLists[index].Add(new IntervalArray <ISupplementaryInterval> .Interval(interval.Start, interval.End, interval));
}
// create the interval arrays
var refIntervalArrays = new IntervalArray <ISupplementaryInterval> [numRefSeqs];
for (var i = 0; i < numRefSeqs; i++)
{
var sortedIntervals = intervalLists[i].OrderBy(x => x.Begin).ThenBy(x => x.End).ToArray();
refIntervalArrays[i] = new IntervalArray <ISupplementaryInterval>(sortedIntervals);
}
return(new IntervalForest <ISupplementaryInterval>(refIntervalArrays));
}
public static SupplementaryInterval Read(ExtendedBinaryReader reader, IChromosomeRenamer renamer)
{
var referenceName = reader.ReadAsciiString();
var start = reader.ReadOptInt32();
var end = reader.ReadOptInt32();
var alternateAllele = reader.ReadAsciiString();
var sequenceAlteration = (VariantType)reader.ReadByte();
var source = reader.ReadAsciiString();
// strings
var count = reader.ReadOptInt32();
var stringValues = new Dictionary <string, string>(count);
for (var i = 0; i < count; i++)
{
var key = reader.ReadAsciiString();
var value = reader.ReadAsciiString();
stringValues[key] = value;
}
// integers
count = reader.ReadOptInt32();
var intValues = new Dictionary <string, int>(count);
for (var i = 0; i < count; i++)
{
var key = reader.ReadAsciiString();
var value = reader.ReadOptInt32();
intValues[key] = value;
}
// booleans
count = reader.ReadOptInt32();
var boolList = new List <string>(count);
for (var i = 0; i < count; i++)
{
boolList.Add(reader.ReadAsciiString());
}
// doubles
count = reader.ReadOptInt32();
var doubleValues = new Dictionary <string, double>(count);
for (var i = 0; i < count; i++)
{
var key = reader.ReadAsciiString();
var value = reader.ReadOptDouble();
doubleValues[key] = value;
}
// frequencies
count = reader.ReadOptInt32();
var freqValues = new Dictionary <string, double>(count);
for (var i = 0; i < count; i++)
{
var key = reader.ReadAsciiString();
var value = reader.ReadOptDouble();
freqValues[key] = value;
}
//stringLists
count = reader.ReadOptInt32();
var stringLists = new Dictionary <string, IEnumerable <string> >(count);
for (var i = 0; i < count; i++)
{
var key = reader.ReadAsciiString();
var valueCount = reader.ReadOptInt32();
var values = ReadStringLists(reader, valueCount);
stringLists[key] = values;
}
return(new SupplementaryInterval(start, end, referenceName, alternateAllele, sequenceAlteration, source,
renamer, intValues, doubleValues, freqValues, stringValues, boolList, stringLists));
}
public IIntervalForest <ISupplementaryInterval> GetIntervalForest(IChromosomeRenamer renamer)
{
return(IntervalArrayFactory.CreateIntervalArray(GetSupplementaryIntervals(renamer), renamer));
}
public void Load(string ucscReferenceName, IChromosomeRenamer renamer)
{
}
public IEnumerable <ISupplementaryInterval> GetSupplementaryIntervals(IChromosomeRenamer renamer)
{
throw new NotImplementedException();
}
public IIntervalForest <ISupplementaryInterval> GetIntervalForest(IChromosomeRenamer renamer)
{
return(new NullIntervalSearch <ISupplementaryInterval>());
}