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 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();
}
