/// <summary>
/// Add a record to the file
/// </summary>
/// <param name="vc">The Variant Context object </param>
protected string getVariantLinetoWrite(VariantContext vc)
{
if (doNotWriteGenotypes)
{
vc = (new VariantContextBuilder(vc)).noGenotypes().make();
}
try
{
//Convert alleles to 1,2,3,etc. numbering
IDictionary <Allele, string> alleleMap = buildAlleleMap(vc);
// CHROM
StringBuilder lineToWrite = new StringBuilder();
//Add chr, pos, id, ref
lineToWrite.Append(String.Join(VCFConstants.FIELD_SEPARATOR, vc.Chr, vc.Start.ToString(), vc.ID, vc.Reference.DisplayString));
// ALT
if (vc.Variant)
{
Allele altAllele = vc.GetAlternateAllele(0);
string alt = altAllele.DisplayString;
lineToWrite.Append(alt);
for (int i = 1; i < vc.AlternateAlleles.Count; i++)
{
altAllele = vc.GetAlternateAllele(i);
alt = altAllele.DisplayString;
lineToWrite.Append(",");
lineToWrite.Append(alt);
}
}
else
{
lineToWrite.Append(VCFConstants.EMPTY_ALTERNATE_ALLELE_FIELD);
}
lineToWrite.Append(VCFConstants.FIELD_SEPARATOR);
// QUAL
if (!vc.HasLog10PError)
{
lineToWrite.Append(VCFConstants.MISSING_VALUE_v4);
}
else
{
lineToWrite.Append(formatQualValue(vc.PhredScaledQual));
}
lineToWrite.Append(VCFConstants.FIELD_SEPARATOR);
// FILTER
string filters = getFilterString(vc);
lineToWrite.Append(filters);
lineToWrite.Append(VCFConstants.FIELD_SEPARATOR);
// INFO
IDictionary <string, string> infoFields = new SortedDictionary <string, string>();
foreach (KeyValuePair <string, object> field in vc.Attributes)
{
string key = field.Key;
if (!mHeader.hasInfoLine(key))
{
fieldIsMissingFromHeaderError(vc, key, "INFO");
}
string outputValue = formatVCFField(field.Value);
if (outputValue != null)
{
infoFields[key] = outputValue;
}
}
lineToWrite.Append(getInfoString(infoFields));;
// FORMAT
GenotypesContext gc = vc.Genotypes;
if (gc.LazyWithData && ((LazyGenotypesContext)gc).UnparsedGenotypeData is string)
{
lineToWrite.Append(VCFConstants.FIELD_SEPARATOR);
lineToWrite.Append(((LazyGenotypesContext)gc).UnparsedGenotypeData.ToString());
}
else
{
IList <string> genotypeAttributeKeys = calcVCFGenotypeKeys(vc);
if (genotypeAttributeKeys.Count > 0)
{
foreach (String format in genotypeAttributeKeys)
{
if (!mHeader.hasFormatLine(format))
{
fieldIsMissingFromHeaderError(vc, format, "FORMAT");
}
}
string genotypeFormatString = String.Join(VCFConstants.GENOTYPE_FIELD_SEPARATOR, genotypeAttributeKeys);
lineToWrite.Append(VCFConstants.FIELD_SEPARATOR);
lineToWrite.Append(genotypeFormatString);
lineToWrite.Append(getGenotypeDataText(vc, alleleMap, genotypeAttributeKeys));
}
}
lineToWrite.Append("\n");
return(lineToWrite.ToString());
}
catch (IOException e)
{
throw new Exception("Unable to write the VCF object:\n " + vc.ToString() + "\n", e);
}
}
/// <summary>
/// Add a record to the file
/// </summary>
/// <param name="vc">The Variant Context object </param>
protected string getVariantLinetoWrite(VariantContext vc)
{
if (doNotWriteGenotypes)
{
vc = (new VariantContextBuilder(vc)).noGenotypes().make();
}
try
{
//Convert alleles to 1,2,3,etc. numbering
IDictionary<Allele, string> alleleMap = buildAlleleMap(vc);
// CHROM
StringBuilder lineToWrite = new StringBuilder();
//Add chr, pos, id, ref
lineToWrite.Append(String.Join(VCFConstants.FIELD_SEPARATOR, vc.Chr, vc.Start.ToString(), vc.ID, vc.Reference.DisplayString));
// ALT
if (vc.Variant)
{
Allele altAllele = vc.GetAlternateAllele(0);
string alt = altAllele.DisplayString;
lineToWrite.Append(alt);
for (int i = 1; i < vc.AlternateAlleles.Count; i++)
{
altAllele = vc.GetAlternateAllele(i);
alt = altAllele.DisplayString;
lineToWrite.Append(",");
lineToWrite.Append(alt);
}
}
else
{
lineToWrite.Append(VCFConstants.EMPTY_ALTERNATE_ALLELE_FIELD);
}
lineToWrite.Append(VCFConstants.FIELD_SEPARATOR);
// QUAL
if (!vc.HasLog10PError)
{
lineToWrite.Append(VCFConstants.MISSING_VALUE_v4);
}
else
{
lineToWrite.Append(formatQualValue(vc.PhredScaledQual));
}
lineToWrite.Append(VCFConstants.FIELD_SEPARATOR);
// FILTER
string filters = getFilterString(vc);
lineToWrite.Append(filters);
lineToWrite.Append(VCFConstants.FIELD_SEPARATOR);
// INFO
IDictionary<string, string> infoFields = new SortedDictionary<string, string>();
foreach (KeyValuePair<string, object> field in vc.Attributes)
{
string key = field.Key;
if (!mHeader.hasInfoLine(key))
{
fieldIsMissingFromHeaderError(vc, key, "INFO");
}
string outputValue = formatVCFField(field.Value);
if (outputValue != null)
{
infoFields[key] = outputValue;
}
}
lineToWrite.Append(getInfoString(infoFields)); ;
// FORMAT
GenotypesContext gc = vc.Genotypes;
if (gc.LazyWithData && ((LazyGenotypesContext)gc).UnparsedGenotypeData is string)
{
lineToWrite.Append(VCFConstants.FIELD_SEPARATOR);
lineToWrite.Append(((LazyGenotypesContext)gc).UnparsedGenotypeData.ToString());
}
else
{
IList<string> genotypeAttributeKeys = calcVCFGenotypeKeys(vc);
if (genotypeAttributeKeys.Count > 0)
{
foreach (String format in genotypeAttributeKeys)
{
if (!mHeader.hasFormatLine(format))
{
fieldIsMissingFromHeaderError(vc, format, "FORMAT");
}
}
string genotypeFormatString = String.Join(VCFConstants.GENOTYPE_FIELD_SEPARATOR, genotypeAttributeKeys);
lineToWrite.Append(VCFConstants.FIELD_SEPARATOR);
lineToWrite.Append(genotypeFormatString);
lineToWrite.Append(getGenotypeDataText(vc, alleleMap, genotypeAttributeKeys));
}
}
lineToWrite.Append("\n");
return lineToWrite.ToString();
}
catch (IOException e)
{
throw new Exception("Unable to write the VCF object:\n " + vc.ToString() + "\n", e);
}
}
