public static SimplePosition GetSimplePosition(string[] vcfFields, IDictionary <string, IChromosome> refNameToChromosome, bool isRecomposed = false)
{
var simplePosition = new SimplePosition
{
Start = Convert.ToInt32(vcfFields[VcfCommon.PosIndex]),
Chromosome = ReferenceNameUtilities.GetChromosome(refNameToChromosome, vcfFields[VcfCommon.ChromIndex]),
RefAllele = vcfFields[VcfCommon.RefIndex]
};
simplePosition.End = vcfFields[VcfCommon.AltIndex].StartsWith("<") || vcfFields[VcfCommon.AltIndex] == "*" ? -1 : simplePosition.Start + simplePosition.RefAllele.Length - 1;
simplePosition.AltAlleles = vcfFields[VcfCommon.AltIndex].Split(",");
simplePosition.VcfFields = vcfFields;
simplePosition.IsRecomposed = isRecomposed;
simplePosition.IsDecomposed = new bool[simplePosition.AltAlleles.Length]; // fasle by default
return(simplePosition);
}
private ISimplePosition GetNextSimplePosition()
{
while (_queuedPositions.Count == 0)
{
VcfLine = _reader.ReadLine();
var simplePositions = _recomposer.ProcessSimplePosition(SimplePosition.GetSimplePosition(VcfLine, _refNameToChromosome));
foreach (var simplePosition in simplePositions)
{
_queuedPositions.Enqueue(simplePosition);
}
if (VcfLine == null)
{
break;
}
}
return(_queuedPositions.Count == 0 ? null: _queuedPositions.Dequeue());
}
private ISimplePosition GetNextSimplePosition()
{
while (_queuedPositions.Count == 0)
{
VcfLine = _vcfFilter.GetNextLine(_reader);
SimplePosition vcfPosition = null;
if (VcfLine != null)
{
string[] vcfFields = VcfLine.OptimizedSplit('\t');
var chromosome = ReferenceNameUtilities.GetChromosome(_refNameToChromosome, vcfFields[VcfCommon.ChromIndex]);
CheckVcfOrder(vcfFields[VcfCommon.ChromIndex]);
(int start, bool foundError) = vcfFields[VcfCommon.PosIndex].OptimizedParseInt32();
if (foundError)
{
throw new InvalidDataException($"Unable to convert the VCF position to an integer: {vcfFields[VcfCommon.PosIndex]}");
}
if (InconsistentSampleFields(vcfFields))
{
int sampleCount = _sampleNames?.Length ?? 0;
throw new UserErrorException($"Inconsistent number of sample fields in line:\n{VcfLine}\nExpected number of sample fields: {sampleCount}");
}
vcfPosition = SimplePosition.GetSimplePosition(chromosome, start, vcfFields, _vcfFilter);
}
IEnumerable <ISimplePosition> simplePositions = _recomposer.ProcessSimplePosition(vcfPosition);
foreach (var simplePosition in simplePositions)
{
_queuedPositions.Enqueue(simplePosition);
}
if (VcfLine == null)
{
break;
}
}
return(_queuedPositions.Count == 0 ? null : _queuedPositions.Dequeue());
}
public static SimplePosition GetSimplePosition(string[] vcfFields, IVcfFilter vcfFilter, IDictionary <string, IChromosome> refNameToChromosome, bool isRecomposed = false)
{
var simplePosition = new SimplePosition(
ReferenceNameUtilities.GetChromosome(refNameToChromosome, vcfFields[VcfCommon.ChromIndex]),
int.Parse(vcfFields[VcfCommon.PosIndex]),
vcfFields[VcfCommon.RefIndex],
vcfFields[VcfCommon.AltIndex].OptimizedSplit(','));
if (vcfFilter.PassedTheEnd(simplePosition.Chromosome, simplePosition.Start))
{
return(null);
}
simplePosition.End = vcfFields[VcfCommon.AltIndex].OptimizedStartsWith('<') || vcfFields[VcfCommon.AltIndex] == "*" ? -1 : simplePosition.Start + simplePosition.RefAllele.Length - 1;
simplePosition.VcfFields = vcfFields;
simplePosition.IsRecomposed = isRecomposed;
simplePosition.IsDecomposed = new bool[simplePosition.AltAlleles.Length]; // false by default
simplePosition.Vids = new string[simplePosition.AltAlleles.Length];
simplePosition.LinkedVids = new List <string> [simplePosition.AltAlleles.Length];
return(simplePosition);
}
internal static IPosition ParseVcfLine(string vcfLine, VariantFactory variantFactory, IDictionary <string, IChromosome> refNameToChromosome)
{
var simplePosition = SimplePosition.GetSimplePosition(vcfLine, refNameToChromosome);
return(Position.CreatFromSimplePosition(simplePosition, variantFactory));
}
