Exemple #1
0
        public override SupplementaryIntervalItem GetSupplementaryInterval()
        {
            if (!IsInterval)
            {
                return(null);
            }

            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 stringLists  = new Dictionary <string, IEnumerable <string> >();

            var suppInterval = new SupplementaryIntervalItem(Chromosome, Start, End, null, VariantType,
                                                             "ClinGen", intValues, doubleValues, freqValues, stringValues, boolValues, stringLists);

            if (Id != null)
            {
                suppInterval.AddStringValue("id", Id);
            }
            if (ClinicalInterpretation != ClinicalInterpretation.unknown)
            {
                suppInterval.AddStringValue("clinicalInterpretation", GetClinicalDescription(ClinicalInterpretation));
            }
            if (Phenotypes != null)
            {
                suppInterval.AddStringList("phenotypes", Phenotypes);
            }
            if (PhenotypeIds != null)
            {
                suppInterval.AddStringList("phenotypeIds", PhenotypeIds);
            }
            if (ObservedGains != 0)
            {
                suppInterval.AddIntValue("observedGains", ObservedGains);
            }
            if (ObservedLosses != 0)
            {
                suppInterval.AddIntValue("observedLosses", ObservedLosses);
            }
            if (Validated)
            {
                suppInterval.AddBoolValue("validated");
            }



            return(suppInterval);
        }
Exemple #2
0
        public override SupplementaryIntervalItem GetSupplementaryInterval()
        {
            if (!IsInterval)
            {
                return(null);
            }

            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 SupplementaryIntervalItem(Chromosome, Start, End, null, VariantType,
                                                             "dgv", intValues, doubleValues, freqValues, stringValues, boolValues);

            if (Id != null)
            {
                suppInterval.AddStringValue("id", Id);
            }
            if (SampleSize != 0)
            {
                suppInterval.AddIntValue("sampleSize", SampleSize);
            }
            if (ObservedGains != 0)
            {
                suppInterval.AddIntValue("observedGains", ObservedGains);
            }
            if (ObservedLosses != 0)
            {
                suppInterval.AddIntValue("observedLosses", ObservedLosses);
            }
            if (VariantFreqAll != null)
            {
                suppInterval.AddFrequencyValue("variantFreqAll", VariantFreqAll.Value);
            }

            return(suppInterval);
        }
Exemple #3
0
        public override SupplementaryIntervalItem GetSupplementaryInterval()
        {
            if (!IsInterval)
            {
                return(null);
            }

            var seqAltType = SaParseUtilities.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 SupplementaryIntervalItem(Chromosome, Start, SvEnd, AlternateAllele, seqAltType,
                                                             "1000 Genomes Project", 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);
        }