//JAVA TO C# CONVERTER WARNING: 'final' parameters are not allowed in .NET:
//ORIGINAL LINE: public static VCFHeader writeHeader(VCFHeader header, final Writer writer, final boolean doNotWriteGenotypes, final String versionLine, final String streamNameForError)
public static VCFHeader writeHeader(VCFHeader header, Writer writer, bool doNotWriteGenotypes, string versionLine, string streamNameForError)
{
header = doNotWriteGenotypes ? new VCFHeader(header.MetaDataInSortedOrder) : header;
try
{
// the file format field needs to be written first
writer.write(versionLine + "\n");
foreach (VCFHeaderLine line in header.MetaDataInSortedOrder)
{
if (VCFHeaderVersion.isFormatString(line.Key))
{
continue;
}
writer.write(VCFHeader.METADATA_INDICATOR);
writer.write(line.ToString());
writer.write("\n");
}
// write out the column line
writer.write(VCFHeader.HEADER_INDICATOR);
bool isFirst = true;
foreach (string field in VCFHeader.HEADER_FIELDS)
{
if (isFirst)
{
isFirst = false; // don't write out a field separator
}
else
{
writer.write(VCFConstants.FIELD_SEPARATOR);
}
writer.write(field.ToString());
}
if (header.hasGenotypingData())
{
writer.write(VCFConstants.FIELD_SEPARATOR);
writer.write("FORMAT");
foreach (string sample in header.GenotypeSampleNames)
{
writer.write(VCFConstants.FIELD_SEPARATOR);
writer.write(sample);
}
}
writer.write("\n");
writer.flush(); // necessary so that writing to an output stream will work
}
catch (IOException e)
{
throw new Exception("IOException writing the VCF header to " + streamNameForError, e);
}
return(header);
}
/// <summary>
/// Determine which genotype fields are in use in the genotypes in VC </summary>
/// <param name="vc"> </param>
/// <returns> an ordered list of genotype fields in use in VC. If vc has genotypes this will always include GT first </returns>
//JAVA TO C# CONVERTER WARNING: 'final' parameters are not allowed in .NET:
//ORIGINAL LINE: public static List<String> calcVCFGenotypeKeys(final VariantContext vc, final VCFHeader header)
public static IList<string> calcVCFGenotypeKeys(VariantContext vc, VCFHeader header)
{
Set<string> keys = new HashSet<string>();
bool sawGoodGT = false;
bool sawGoodQual = false;
bool sawGenotypeFilter = false;
bool sawDP = false;
bool sawAD = false;
bool sawPL = false;
foreach (Genotype g in vc.Genotypes)
{
keys.addAll(g.ExtendedAttributes.Keys);
if (g.Available)
{
sawGoodGT = true;
}
if (g.hasGQ())
{
sawGoodQual = true;
}
if (g.hasDP())
{
sawDP = true;
}
if (g.hasAD())
{
sawAD = true;
}
if (g.hasPL())
{
sawPL = true;
}
if (g.Filtered)
{
sawGenotypeFilter = true;
}
}
if (sawGoodQual)
{
keys.add(VCFConstants.GENOTYPE_QUALITY_KEY);
}
if (sawDP)
{
keys.add(VCFConstants.DEPTH_KEY);
}
if (sawAD)
{
keys.add(VCFConstants.GENOTYPE_ALLELE_DEPTHS);
}
if (sawPL)
{
keys.add(VCFConstants.GENOTYPE_PL_KEY);
}
if (sawGenotypeFilter)
{
keys.add(VCFConstants.GENOTYPE_FILTER_KEY);
}
IList<string> sortedList = ParsingUtils.sortList(new List<string>(keys));
// make sure the GT is first
if (sawGoodGT)
{
IList<string> newList = new List<string>(sortedList.Count + 1);
newList.Add(VCFConstants.GENOTYPE_KEY);
newList.AddRange(sortedList);
sortedList = newList;
}
if (sortedList.Count == 0 && header.hasGenotypingData())
{
// this needs to be done in case all samples are no-calls
return Collections.singletonList(VCFConstants.GENOTYPE_KEY);
}
else
{
return sortedList;
}
}
//JAVA TO C# CONVERTER WARNING: 'final' parameters are not allowed in .NET:
//ORIGINAL LINE: public static VCFHeader writeHeader(VCFHeader header, final Writer writer, final boolean doNotWriteGenotypes, final String versionLine, final String streamNameForError)
public static VCFHeader writeHeader(VCFHeader header, Writer writer, bool doNotWriteGenotypes, string versionLine, string streamNameForError)
{
header = doNotWriteGenotypes ? new VCFHeader(header.MetaDataInSortedOrder) : header;
try
{
// the file format field needs to be written first
writer.write(versionLine + "\n");
foreach (VCFHeaderLine line in header.MetaDataInSortedOrder)
{
if (VCFHeaderVersion.isFormatString(line.Key))
{
continue;
}
writer.write(VCFHeader.METADATA_INDICATOR);
writer.write(line.ToString());
writer.write("\n");
}
// write out the column line
writer.write(VCFHeader.HEADER_INDICATOR);
bool isFirst = true;
foreach (string field in VCFHeader.HEADER_FIELDS)
{
if (isFirst)
{
isFirst = false; // don't write out a field separator
}
else
{
writer.write(VCFConstants.FIELD_SEPARATOR);
}
writer.write(field.ToString());
}
if (header.hasGenotypingData())
{
writer.write(VCFConstants.FIELD_SEPARATOR);
writer.write("FORMAT");
foreach (string sample in header.GenotypeSampleNames)
{
writer.write(VCFConstants.FIELD_SEPARATOR);
writer.write(sample);
}
}
writer.write("\n");
writer.flush(); // necessary so that writing to an output stream will work
}
catch (IOException e)
{
throw new Exception("IOException writing the VCF header to " + streamNameForError, e);
}
return header;
}
/// <summary>
/// Determine which genotype fields are in use in the genotypes in VC </summary>
/// <param name="vc"> </param>
/// <returns> an ordered list of genotype fields in use in VC. If vc has genotypes this will always include GT first </returns>
//JAVA TO C# CONVERTER WARNING: 'final' parameters are not allowed in .NET:
//ORIGINAL LINE: public static List<String> calcVCFGenotypeKeys(final VariantContext vc, final VCFHeader header)
public static IList <string> calcVCFGenotypeKeys(VariantContext vc, VCFHeader header)
{
Set <string> keys = new HashSet <string>();
bool sawGoodGT = false;
bool sawGoodQual = false;
bool sawGenotypeFilter = false;
bool sawDP = false;
bool sawAD = false;
bool sawPL = false;
foreach (Genotype g in vc.Genotypes)
{
keys.addAll(g.ExtendedAttributes.Keys);
if (g.Available)
{
sawGoodGT = true;
}
if (g.hasGQ())
{
sawGoodQual = true;
}
if (g.hasDP())
{
sawDP = true;
}
if (g.hasAD())
{
sawAD = true;
}
if (g.hasPL())
{
sawPL = true;
}
if (g.Filtered)
{
sawGenotypeFilter = true;
}
}
if (sawGoodQual)
{
keys.add(VCFConstants.GENOTYPE_QUALITY_KEY);
}
if (sawDP)
{
keys.add(VCFConstants.DEPTH_KEY);
}
if (sawAD)
{
keys.add(VCFConstants.GENOTYPE_ALLELE_DEPTHS);
}
if (sawPL)
{
keys.add(VCFConstants.GENOTYPE_PL_KEY);
}
if (sawGenotypeFilter)
{
keys.add(VCFConstants.GENOTYPE_FILTER_KEY);
}
IList <string> sortedList = ParsingUtils.sortList(new List <string>(keys));
// make sure the GT is first
if (sawGoodGT)
{
IList <string> newList = new List <string>(sortedList.Count + 1);
newList.Add(VCFConstants.GENOTYPE_KEY);
newList.AddRange(sortedList);
sortedList = newList;
}
if (sortedList.Count == 0 && header.hasGenotypingData())
{
// this needs to be done in case all samples are no-calls
return(Collections.singletonList(VCFConstants.GENOTYPE_KEY));
}
else
{
return(sortedList);
}
}
void writeHeader(VCFHeader header)
{
header = doNotWriteGenotypes ? new VCFHeader(header.MetaDataInSortedOrder) : header;
try
{
// the file format field needs to be written first
writer.Write(VERSION_LINE + "\n");
foreach (VCFHeaderLine line in header.MetaDataInSortedOrder)
{
if (VCFHeaderVersion.IsFormatString(line.Key))
{
continue;
}
writer.Write(VCFHeader.METADATA_INDICATOR);
writer.Write(line.ToString());
writer.Write("\n");
}
// write out the column line
writer.Write(VCFHeader.HEADER_INDICATOR);
bool isFirst = true;
foreach (string field in VCFHeader.HEADER_FIELDS)
{
if (isFirst)
{
isFirst = false; // don't write out a field separator
}
else
{
writer.Write(VCFConstants.FIELD_SEPARATOR);
}
writer.Write(field.ToString());
}
if (header.hasGenotypingData())
{
writer.Write(VCFConstants.FIELD_SEPARATOR);
writer.Write("FORMAT");
foreach (string sample in header.GenotypeSampleNames)
{
writer.Write(VCFConstants.FIELD_SEPARATOR);
writer.Write(sample);
}
}
writer.Write("\n");
}
catch (IOException e)
{
throw new Exception("IOException writing the VCF header." , e);
}
}