/// <summary>
/// Get the number of values expected for this header field, given the properties of VariantContext vc
///
/// If the count is a fixed count, return that. For example, a field with size of 1 in the header returns 1
/// If the count is of type A, return vc.getNAlleles - 1
/// If the count is of type G, return the expected number of genotypes given the number of alleles in VC and the
/// max ploidy among all samples. Note that if the max ploidy of the VC is 0 (there's no GT information
/// at all, then implicitly assume diploid samples when computing G values.
/// If the count is UNBOUNDED return -1
/// </summary>
/// <param name="vc">
/// @return </param>
public virtual int getCount(VariantContext vc)
{
switch (countType)
{
case Bio.VCF.VCFHeaderLineCount.INTEGER:
return(count);
case Bio.VCF.VCFHeaderLineCount.UNBOUNDED:
return(-1);
case Bio.VCF.VCFHeaderLineCount.A:
return(vc.NAlleles - 1);
case Bio.VCF.VCFHeaderLineCount.G:
int ploidy = vc.GetMaxPloidy(2);
return(GenotypeLikelihoods.numLikelihoods(vc.NAlleles, ploidy));
default:
throw new VCFParsingError("Unknown count type: " + countType);
}
}
/// <summary>
/// add the genotype data
/// </summary>
/// <param name="vc"> the variant context </param>
/// <param name="genotypeFormatKeys"> Genotype formatting string </param>
/// <param name="alleleMap"> alleles for this context </param>
/// <exception cref="IOException"> for writer </exception>
private string getGenotypeDataText(VariantContext vc, IDictionary <Allele, string> alleleMap, IList <string> genotypeFormatKeys)
{
StringBuilder sbn = new StringBuilder();
int ploidy = vc.GetMaxPloidy(2);
foreach (string sample in mHeader.GenotypeSampleNames)
{
sbn.Append(VCFConstants.FIELD_SEPARATOR);
Genotype g = vc.GetGenotype(sample);
if (g == null)
{
g = GenotypeBuilder.CreateMissing(sample, ploidy);
}
IList <string> attrs = new List <string>(genotypeFormatKeys.Count);
foreach (string field in genotypeFormatKeys)
{
if (field.Equals(VCFConstants.GENOTYPE_KEY))
{
if (!g.Available)
{
throw new Exception("GTs cannot be missing for some samples if they are available for others in the record");
}
sbn.Append(getAlleleText(g.getAllele(0), alleleMap));
for (int i = 1; i < g.Ploidy; i++)
{
sbn.Append(g.Phased ? VCFConstants.PHASED : VCFConstants.UNPHASED);
sbn.Append(getAlleleText(g.getAllele(i), alleleMap));
}
continue;
}
else
{
string outputValue;
if (field.Equals(VCFConstants.GENOTYPE_FILTER_KEY))
{
outputValue = g.Filtered ? g.Filters : VCFConstants.PASSES_FILTERS_v4;
}
else
{
IntGenotypeFieldAccessors.Accessor accessor = intGenotypeFieldAccessors.GetAccessor(field);
if (accessor != null)
{
int[] intValues = accessor.getValues(g);
if (intValues == null)
{
outputValue = VCFConstants.MISSING_VALUE_v4;
}
else if (intValues.Length == 1) // fast path
{
outputValue = Convert.ToString(intValues[0]);
}
else
{
StringBuilder sb = new StringBuilder();
sb.Append(intValues[0]);
for (int i = 1; i < intValues.Length; i++)
{
sb.Append(",");
sb.Append(intValues[i]);
}
outputValue = sb.ToString();
}
}
else
{
object val = g.HasExtendedAttribute(field) ? g.GetExtendedAttribute(field) : VCFConstants.MISSING_VALUE_v4;
VCFFormatHeaderLine metaData = mHeader.getFormatHeaderLine(field);
if (metaData != null)
{
int numInFormatField = metaData.getCount(vc);
if (numInFormatField > 1 && val.Equals(VCFConstants.MISSING_VALUE_v4))
{
// If we have a missing field but multiple values are expected, we need to construct a new string with all fields.
// For example, if Number=2, the string has to be ".,."
StringBuilder sb = new StringBuilder(VCFConstants.MISSING_VALUE_v4);
for (int i = 1; i < numInFormatField; i++)
{
sb.Append(",");
sb.Append(VCFConstants.MISSING_VALUE_v4);
}
val = sb.ToString();
}
}
// assume that if key is absent, then the given string encoding suffices
outputValue = formatVCFField(val);
}
}
if (outputValue != null)
{
attrs.Add(outputValue);
}
}
}
// strip off trailing missing values
for (int i = attrs.Count - 1; i >= 0; i--)
{
if (isMissingValue(attrs[i]))
{
attrs.RemoveAt(i);
}
else
{
break;
}
}
for (int i = 0; i < attrs.Count; i++)
{
if (i > 0 || genotypeFormatKeys.Contains(VCFConstants.GENOTYPE_KEY))
{
sbn.Append(VCFConstants.GENOTYPE_FIELD_SEPARATOR);
}
sbn.Append(attrs[i]);
}
}
return(sbn.ToString());
}
/// <summary>
/// Get the number of values expected for this header field, given the properties of VariantContext vc
///
/// If the count is a fixed count, return that. For example, a field with size of 1 in the header returns 1
/// If the count is of type A, return vc.getNAlleles - 1
/// If the count is of type G, return the expected number of genotypes given the number of alleles in VC and the
/// max ploidy among all samples. Note that if the max ploidy of the VC is 0 (there's no GT information
/// at all, then implicitly assume diploid samples when computing G values.
/// If the count is UNBOUNDED return -1
/// </summary>
/// <param name="vc">
/// @return </param>
public virtual int getCount(VariantContext vc)
{
switch (countType)
{
case Bio.VCF.VCFHeaderLineCount.INTEGER:
return count;
case Bio.VCF.VCFHeaderLineCount.UNBOUNDED:
return -1;
case Bio.VCF.VCFHeaderLineCount.A:
return vc.NAlleles - 1;
case Bio.VCF.VCFHeaderLineCount.G:
int ploidy = vc.GetMaxPloidy(2);
return GenotypeLikelihoods.numLikelihoods(vc.NAlleles, ploidy);
default:
throw new VCFParsingError("Unknown count type: " + countType);
}
}
/// <summary>
/// add the genotype data
/// </summary>
/// <param name="vc"> the variant context </param>
/// <param name="genotypeFormatKeys"> Genotype formatting string </param>
/// <param name="alleleMap"> alleles for this context </param>
/// <exception cref="IOException"> for writer </exception>
private string getGenotypeDataText(VariantContext vc, IDictionary<Allele, string> alleleMap, IList<string> genotypeFormatKeys)
{
StringBuilder sbn = new StringBuilder();
int ploidy = vc.GetMaxPloidy(2);
foreach (string sample in mHeader.GenotypeSampleNames)
{
sbn.Append(VCFConstants.FIELD_SEPARATOR);
Genotype g = vc.GetGenotype(sample);
if (g == null)
{
g = GenotypeBuilder.CreateMissing(sample, ploidy);
}
IList<string> attrs = new List<string>(genotypeFormatKeys.Count);
foreach (string field in genotypeFormatKeys)
{
if (field.Equals(VCFConstants.GENOTYPE_KEY))
{
if (!g.Available)
{
throw new Exception("GTs cannot be missing for some samples if they are available for others in the record");
}
sbn.Append(getAlleleText(g.getAllele(0), alleleMap));
for (int i = 1; i < g.Ploidy; i++)
{
sbn.Append(g.Phased ? VCFConstants.PHASED : VCFConstants.UNPHASED);
sbn.Append(getAlleleText(g.getAllele(i), alleleMap));
}
continue;
}
else
{
string outputValue;
if (field.Equals(VCFConstants.GENOTYPE_FILTER_KEY))
{
outputValue = g.Filtered ? g.Filters : VCFConstants.PASSES_FILTERS_v4;
}
else
{
IntGenotypeFieldAccessors.Accessor accessor = intGenotypeFieldAccessors.GetAccessor(field);
if (accessor != null)
{
int[] intValues = accessor.getValues(g);
if (intValues == null)
{
outputValue = VCFConstants.MISSING_VALUE_v4;
}
else if (intValues.Length == 1) // fast path
{
outputValue = Convert.ToString(intValues[0]);
}
else
{
StringBuilder sb = new StringBuilder();
sb.Append(intValues[0]);
for (int i = 1; i < intValues.Length; i++)
{
sb.Append(",");
sb.Append(intValues[i]);
}
outputValue = sb.ToString();
}
}
else
{
object val = g.HasExtendedAttribute(field) ? g.GetExtendedAttribute(field) : VCFConstants.MISSING_VALUE_v4;
VCFFormatHeaderLine metaData = mHeader.getFormatHeaderLine(field);
if (metaData != null)
{
int numInFormatField = metaData.getCount(vc);
if (numInFormatField > 1 && val.Equals(VCFConstants.MISSING_VALUE_v4))
{
// If we have a missing field but multiple values are expected, we need to construct a new string with all fields.
// For example, if Number=2, the string has to be ".,."
StringBuilder sb = new StringBuilder(VCFConstants.MISSING_VALUE_v4);
for (int i = 1; i < numInFormatField; i++)
{
sb.Append(",");
sb.Append(VCFConstants.MISSING_VALUE_v4);
}
val = sb.ToString();
}
}
// assume that if key is absent, then the given string encoding suffices
outputValue = formatVCFField(val);
}
}
if (outputValue != null)
{
attrs.Add(outputValue);
}
}
}
// strip off trailing missing values
for (int i = attrs.Count - 1; i >= 0; i--)
{
if (isMissingValue(attrs[i]))
{
attrs.RemoveAt(i);
}
else
{
break;
}
}
for (int i = 0; i < attrs.Count; i++)
{
if (i > 0 || genotypeFormatKeys.Contains(VCFConstants.GENOTYPE_KEY))
{
sbn.Append(VCFConstants.GENOTYPE_FIELD_SEPARATOR);
}
sbn.Append(attrs[i]);
}
}
return sbn.ToString();
}
