public string GetVcfString()
{
var freq = ComputingUtilities.ComputeFrequency(AllAlleleNumber, AllAlleleCount) ?? "";
var ancestralAlleleString = AncestralAllele ?? "";
return(freq + ";" + ancestralAlleleString);
}
public string GetJsonString()
{
var sb = StringBuilderCache.Acquire();
var jsonObject = new JsonObject(sb);
jsonObject.AddStringValue("ancestralAllele", AncestralAllele);
jsonObject.AddStringValue("allAf", ComputingUtilities.ComputeFrequency(AllAlleleNumber, AllAlleleCount), false);
jsonObject.AddStringValue("afrAf", ComputingUtilities.ComputeFrequency(AfrAlleleNumber, AfrAlleleCount), false);
jsonObject.AddStringValue("amrAf", ComputingUtilities.ComputeFrequency(AmrAlleleNumber, AmrAlleleCount), false);
jsonObject.AddStringValue("easAf", ComputingUtilities.ComputeFrequency(EasAlleleNumber, EasAlleleCount), false);
jsonObject.AddStringValue("eurAf", ComputingUtilities.ComputeFrequency(EurAlleleNumber, EurAlleleCount), false);
jsonObject.AddStringValue("sasAf", ComputingUtilities.ComputeFrequency(SasAlleleNumber, SasAlleleCount), false);
jsonObject.AddIntValue("allAn", AllAlleleNumber);
jsonObject.AddIntValue("afrAn", AfrAlleleNumber);
jsonObject.AddIntValue("amrAn", AmrAlleleNumber);
jsonObject.AddIntValue("easAn", EasAlleleNumber);
jsonObject.AddIntValue("eurAn", EurAlleleNumber);
jsonObject.AddIntValue("sasAn", SasAlleleNumber);
jsonObject.AddIntValue("allAc", AllAlleleCount);
jsonObject.AddIntValue("afrAc", AfrAlleleCount);
jsonObject.AddIntValue("amrAc", AmrAlleleCount);
jsonObject.AddIntValue("easAc", EasAlleleCount);
jsonObject.AddIntValue("eurAc", EurAlleleCount);
jsonObject.AddIntValue("sasAc", SasAlleleCount);
return(StringBuilderCache.GetStringAndRelease(sb));
}
public string GetJsonString()
{
var sb = StringBuilderCache.Acquire();
var jsonObject = new JsonObject(sb);
jsonObject.AddIntValue("coverage", Coverage);
if (HasFailedFilters)
{
jsonObject.AddBoolValue("failedFilter", true);
}
jsonObject.AddStringValue("allAf", ComputingUtilities.ComputeFrequency(AllAlleleNumber, AllAlleleCount), false);
jsonObject.AddIntValue("allAn", AllAlleleNumber);
jsonObject.AddIntValue("allAc", AllAlleleCount);
jsonObject.AddIntValue("allHc", AllHomCount);
jsonObject.AddStringValue("afrAf", ComputingUtilities.ComputeFrequency(AfrAlleleNumber, AfrAlleleCount), false);
jsonObject.AddIntValue("afrAn", AfrAlleleNumber);
jsonObject.AddIntValue("afrAc", AfrAlleleCount);
jsonObject.AddIntValue("afrHc", AfrHomCount);
jsonObject.AddStringValue("amrAf", ComputingUtilities.ComputeFrequency(AmrAlleleNumber, AmrAlleleCount), false);
jsonObject.AddIntValue("amrAn", AmrAlleleNumber);
jsonObject.AddIntValue("amrAc", AmrAlleleCount);
jsonObject.AddIntValue("amrHc", AmrHomCount);
jsonObject.AddStringValue("easAf", ComputingUtilities.ComputeFrequency(EasAlleleNumber, EasAlleleCount), false);
jsonObject.AddIntValue("easAn", EasAlleleNumber);
jsonObject.AddIntValue("easAc", EasAlleleCount);
jsonObject.AddIntValue("easHc", EasHomCount);
jsonObject.AddStringValue("finAf", ComputingUtilities.ComputeFrequency(FinAlleleNumber, FinAlleleCount), false);
jsonObject.AddIntValue("finAn", FinAlleleNumber);
jsonObject.AddIntValue("finAc", FinAlleleCount);
jsonObject.AddIntValue("finHc", FinHomCount);
jsonObject.AddStringValue("nfeAf", ComputingUtilities.ComputeFrequency(NfeAlleleNumber, NfeAlleleCount), false);
jsonObject.AddIntValue("nfeAn", NfeAlleleNumber);
jsonObject.AddIntValue("nfeAc", NfeAlleleCount);
jsonObject.AddIntValue("nfeHc", NfeHomCount);
jsonObject.AddStringValue("asjAf", ComputingUtilities.ComputeFrequency(AsjAlleleNumber, AsjAlleleCount), false);
jsonObject.AddIntValue("asjAn", AsjAlleleNumber);
jsonObject.AddIntValue("asjAc", AsjAlleleCount);
jsonObject.AddIntValue("asjHc", AsjHomCount);
jsonObject.AddStringValue("sasAf", ComputingUtilities.ComputeFrequency(SasAlleleNumber, SasAlleleCount), false);
jsonObject.AddIntValue("sasAn", SasAlleleNumber);
jsonObject.AddIntValue("sasAc", SasAlleleCount);
jsonObject.AddIntValue("sasHc", SasHomCount);
jsonObject.AddStringValue("othAf", ComputingUtilities.ComputeFrequency(OthAlleleNumber, OthAlleleCount), false);
jsonObject.AddIntValue("othAn", OthAlleleNumber);
jsonObject.AddIntValue("othAc", OthAlleleCount);
jsonObject.AddIntValue("othHc", OthHomCount);
return(StringBuilderCache.GetStringAndRelease(sb));
}
public GnomadItem(IChromosome chromosome,
int position,
string refAllele,
string alternateAllele,
int?depth,
int?allAlleleNumber, int?afrAlleleNumber, int?amrAlleleNumber, int?easAlleleNumber,
int?finAlleleNumber, int?nfeAlleleNumber, int?othAlleleNumber, int?asjAlleleNumber, int?sasAlleleNumber,
int?allAlleleCount, int?afrAlleleCount, int?amrAlleleCount, int?easAlleleCount, int?finAlleleCount, int?nfeAlleleCount, int?othAlleleCount, int?asjAlleleCount, int?sasAlleleCount,
int?allHomCount, int?afrHomCount, int?amrHomCount, int?easHomCount,
int?finHomCount, int?nfeHomCount, int?othHomCount, int?asjHomCount, int?sasHomCount,
bool hasFailedFilters)
{
Chromosome = chromosome;
Start = position;
ReferenceAllele = refAllele;
AlternateAllele = alternateAllele;
if (depth != null && allAlleleNumber != null)
{
Coverage = ComputingUtilities.GetCoverage(depth.Value, allAlleleNumber.Value);
}
AllAlleleNumber = allAlleleNumber;
AfrAlleleNumber = afrAlleleNumber;
AmrAlleleNumber = amrAlleleNumber;
EasAlleleNumber = easAlleleNumber;
FinAlleleNumber = finAlleleNumber;
NfeAlleleNumber = nfeAlleleNumber;
OthAlleleNumber = othAlleleNumber;
AsjAlleleNumber = asjAlleleNumber;
SasAlleleNumber = sasAlleleNumber;
AllAlleleCount = allAlleleCount;
AfrAlleleCount = afrAlleleCount;
AmrAlleleCount = amrAlleleCount;
EasAlleleCount = easAlleleCount;
FinAlleleCount = finAlleleCount;
NfeAlleleCount = nfeAlleleCount;
OthAlleleCount = othAlleleCount;
AsjAlleleCount = asjAlleleCount;
SasAlleleCount = sasAlleleCount;
AllHomCount = allHomCount;
AfrHomCount = afrHomCount;
AmrHomCount = amrHomCount;
EasHomCount = easHomCount;
FinHomCount = finHomCount;
NfeHomCount = nfeHomCount;
OthHomCount = othHomCount;
AsjHomCount = asjHomCount;
SasHomCount = sasHomCount;
HasFailedFilters = hasFailedFilters;
RemoveAlleleNumberZero();
}
public string GetJsonString()
{
var sb = new StringBuilder();
var jsonObject = new JsonObject(sb);
jsonObject.AddStringValue("allAf", ComputingUtilities.ComputeFrequency(_alleleNum, _alleleCount), false);
jsonObject.AddIntValue("allAn", _alleleNum);
jsonObject.AddIntValue("allAc", _alleleCount);
jsonObject.AddIntValue("allHc", _homCount);
if (_failedFilter)
{
jsonObject.AddBoolValue("failedFilter", true);
}
return(sb.ToString());
}
public GnomadItem(IChromosome chromosome,
int position,
string refAllele,
string alternateAllele,
int?depth,
int?allAlleleNumber, int?afrAlleleNumber, int?amrAlleleNumber, int?easAlleleNumber,
int?finAlleleNumber, int?nfeAlleleNumber, int?othAlleleNumber, int?asjAlleleNumber, int?sasAlleleNumber,
int?maleAlleleNumber, int?femaleAlleleNumber,
int?allAlleleCount, int?afrAlleleCount, int?amrAlleleCount, int?easAlleleCount, int?finAlleleCount, int?nfeAlleleCount, int?othAlleleCount, int?asjAlleleCount, int?sasAlleleCount,
int?maleAlleleCount, int?femaleAlleleCount,
int?allHomCount, int?afrHomCount, int?amrHomCount, int?easHomCount,
int?finHomCount, int?nfeHomCount, int?othHomCount, int?asjHomCount, int?sasHomCount,
int?maleHomCount, int?femaleHomCount,
int?controlsAllAlleleNumber,
int?controlsAllAlleleCount,
bool hasFailedFilters,
bool isLcr,
GnomadDataType dataType)
{
Chromosome = chromosome;
Position = position;
RefAllele = refAllele;
AltAllele = alternateAllele;
Depth = depth;
if (depth != null && allAlleleNumber != null && allAlleleNumber.Value > 0)
{
Coverage = ComputingUtilities.GetCoverage(depth.Value, allAlleleNumber.Value);
}
AllAlleleNumber = allAlleleNumber;
AfrAlleleNumber = afrAlleleNumber;
AmrAlleleNumber = amrAlleleNumber;
EasAlleleNumber = easAlleleNumber;
FinAlleleNumber = finAlleleNumber;
NfeAlleleNumber = nfeAlleleNumber;
OthAlleleNumber = othAlleleNumber;
AsjAlleleNumber = asjAlleleNumber;
SasAlleleNumber = sasAlleleNumber;
MaleAlleleNumber = maleAlleleNumber;
FemaleAlleleNumber = femaleAlleleNumber;
MaleHomCount = maleHomCount;
AllAlleleCount = allAlleleCount;
AfrAlleleCount = afrAlleleCount;
AmrAlleleCount = amrAlleleCount;
EasAlleleCount = easAlleleCount;
FinAlleleCount = finAlleleCount;
NfeAlleleCount = nfeAlleleCount;
OthAlleleCount = othAlleleCount;
AsjAlleleCount = asjAlleleCount;
SasAlleleCount = sasAlleleCount;
MaleAlleleCount = maleAlleleCount;
FemaleAlleleCount = femaleAlleleCount;
FemaleHomCount = femaleHomCount;
AllHomCount = allHomCount;
AfrHomCount = afrHomCount;
AmrHomCount = amrHomCount;
EasHomCount = easHomCount;
FinHomCount = finHomCount;
NfeHomCount = nfeHomCount;
OthHomCount = othHomCount;
AsjHomCount = asjHomCount;
SasHomCount = sasHomCount;
//controls
ControlsAllAlleleNumber = controlsAllAlleleNumber;
ControlsAllAlleleCount = controlsAllAlleleCount;
HasFailedFilters = hasFailedFilters;
IsLowComplexityRegion = isLcr;
DataType = dataType;
RemoveAlleleNumberZero();
}
public string GetJsonString()
{
var sb = StringBuilderCache.Acquire();
var jsonObject = new JsonObject(sb);
jsonObject.AddIntValue("coverage", Coverage);
jsonObject.AddStringValue("allAf", ComputingUtilities.ComputeFrequency(AllAlleleNumber, AllAlleleCount), false);
jsonObject.AddStringValue("afrAf", ComputingUtilities.ComputeFrequency(AfrAlleleNumber, AfrAlleleCount), false);
jsonObject.AddStringValue("amrAf", ComputingUtilities.ComputeFrequency(AmrAlleleNumber, AmrAlleleCount), false);
jsonObject.AddStringValue("easAf", ComputingUtilities.ComputeFrequency(EasAlleleNumber, EasAlleleCount), false);
jsonObject.AddStringValue("finAf", ComputingUtilities.ComputeFrequency(FinAlleleNumber, FinAlleleCount), false);
jsonObject.AddStringValue("nfeAf", ComputingUtilities.ComputeFrequency(NfeAlleleNumber, NfeAlleleCount), false);
jsonObject.AddStringValue("sasAf", ComputingUtilities.ComputeFrequency(SasAlleleNumber, SasAlleleCount), false);
jsonObject.AddStringValue("othAf", ComputingUtilities.ComputeFrequency(OthAlleleNumber, OthAlleleCount), false);
if (AllAlleleNumber != null)
{
jsonObject.AddIntValue("allAn", AllAlleleNumber.Value);
}
if (AfrAlleleNumber != null)
{
jsonObject.AddIntValue("afrAn", AfrAlleleNumber.Value);
}
if (AmrAlleleNumber != null)
{
jsonObject.AddIntValue("amrAn", AmrAlleleNumber.Value);
}
if (EasAlleleNumber != null)
{
jsonObject.AddIntValue("easAn", EasAlleleNumber.Value);
}
if (FinAlleleNumber != null)
{
jsonObject.AddIntValue("finAn", FinAlleleNumber.Value);
}
if (NfeAlleleNumber != null)
{
jsonObject.AddIntValue("nfeAn", NfeAlleleNumber.Value);
}
if (SasAlleleNumber != null)
{
jsonObject.AddIntValue("sasAn", SasAlleleNumber.Value);
}
if (OthAlleleNumber != null)
{
jsonObject.AddIntValue("othAn", OthAlleleNumber.Value);
}
if (AllAlleleCount != null)
{
jsonObject.AddIntValue("allAc", AllAlleleCount.Value);
}
if (AfrAlleleCount != null)
{
jsonObject.AddIntValue("afrAc", AfrAlleleCount.Value);
}
if (AmrAlleleCount != null)
{
jsonObject.AddIntValue("amrAc", AmrAlleleCount.Value);
}
if (EasAlleleCount != null)
{
jsonObject.AddIntValue("easAc", EasAlleleCount.Value);
}
if (FinAlleleCount != null)
{
jsonObject.AddIntValue("finAc", FinAlleleCount.Value);
}
if (NfeAlleleCount != null)
{
jsonObject.AddIntValue("nfeAc", NfeAlleleCount.Value);
}
if (SasAlleleCount != null)
{
jsonObject.AddIntValue("sasAc", SasAlleleCount.Value);
}
if (OthAlleleCount != null)
{
jsonObject.AddIntValue("othAc", OthAlleleCount.Value);
}
return(StringBuilderCache.GetStringAndRelease(sb));
}