/// <summary>
/// returns a ClinVar object given the vcf line
/// </summary>
public static DgvItem ExtractDgvItem(string line, ChromosomeRenamer renamer)
{
var cols = line.Split('\t');
if (cols.Length < 8)
{
return(null);
}
var id = cols[0];
var chromosome = cols[1];
if (!InputFileParserUtilities.IsDesiredChromosome(chromosome, renamer))
{
return(null);
}
var start = int.Parse(cols[2]);
var end = int.Parse(cols[3]);
var variantType = cols[4];
var variantSubType = cols[5];
var sampleSize = int.Parse(cols[14]);
var observedGains = cols[15] == "" ? 0:int.Parse(cols[15]);
var observedLosses = cols[16] == "" ? 0 : int.Parse(cols[16]);
var seqAltType = SequenceAlterationUtilities.GetSequenceAlteration(variantType, variantSubType);
return(new DgvItem(id, chromosome, start, end, sampleSize, observedGains, observedLosses, seqAltType));
}
public override SupplementaryInterval GetSupplementaryInterval(ChromosomeRenamer renamer)
{
if (!IsInterval)
{
return(null);
}
var seqAltType = SequenceAlterationUtilities.GetSequenceAlteration(SvType, ObservedGains, ObservedLosses);
var intValues = new Dictionary <string, int>();
var doubleValues = new Dictionary <string, double>();
var freqValues = new Dictionary <string, double>();
var stringValues = new Dictionary <string, string>();
var boolValues = new List <string>();
var suppInterval = new SupplementaryInterval(Start, SvEnd, Chromosome, AlternateAllele, seqAltType,
"1000 Genomes Project", renamer, intValues, doubleValues, freqValues, stringValues, boolValues);
if (Id != null)
{
suppInterval.AddStringValue("id", Id);
}
if (AfrFreq != null)
{
suppInterval.AddFrequencyValue("variantFreqAfr", Convert.ToDouble(AfrFreq));
}
if (AllFreq != null)
{
suppInterval.AddFrequencyValue("variantFreqAll", Convert.ToDouble(AllFreq));
}
if (AmrFreq != null)
{
suppInterval.AddFrequencyValue("variantFreqAmr", Convert.ToDouble(AmrFreq));
}
if (EasFreq != null)
{
suppInterval.AddFrequencyValue("variantFreqEas", Convert.ToDouble(EasFreq));
}
if (EurFreq != null)
{
suppInterval.AddFrequencyValue("variantFreqEur", Convert.ToDouble(EurFreq));
}
if (SasFreq != null)
{
suppInterval.AddFrequencyValue("variantFreqSas", Convert.ToDouble(SasFreq));
}
if (AllAlleleNumber != null && AllAlleleNumber.Value > 0)
{
suppInterval.AddIntValue("sampleSize", AllAlleleNumber.Value);
}
if (AfrAlleleNumber != null && AfrAlleleNumber.Value > 0)
{
suppInterval.AddIntValue("sampleSizeAfr", AfrAlleleNumber.Value);
}
if (AmrAlleleNumber != null && AmrAlleleNumber.Value > 0)
{
suppInterval.AddIntValue("sampleSizeAmr", AmrAlleleNumber.Value);
}
if (EasAlleleNumber != null && EasAlleleNumber.Value > 0)
{
suppInterval.AddIntValue("sampleSizeEas", EasAlleleNumber.Value);
}
if (EurAlleleNumber != null && EurAlleleNumber.Value > 0)
{
suppInterval.AddIntValue("sampleSizeEur", EurAlleleNumber.Value);
}
if (SasAlleleNumber != null && SasAlleleNumber.Value > 0)
{
suppInterval.AddIntValue("sampleSizeSas", SasAlleleNumber.Value);
}
if (ObservedGains != 0)
{
suppInterval.AddIntValue("observedGains", ObservedGains);
}
if (ObservedLosses != 0)
{
suppInterval.AddIntValue("observedLosses", ObservedLosses);
}
return(suppInterval);
}
