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);
}
}
/// <summary>
/// check our metadata for a VCF version tag, and throw an exception if the version is out of date
/// or the version is not present
/// TODO: Should only be one format line
/// </summary>
public virtual void loadVCFVersion()
{
IList <VCFHeaderLine> toRemove = new List <VCFHeaderLine>();
foreach (VCFHeaderLine line in mMetaData)
{
if (VCFHeaderVersion.IsFormatString(line.Key))
{
toRemove.Add(line);
}
}
// remove old header lines for now,
mMetaData.RemoveRange(toRemove);
}
/// <param name="reader"> the line reader to take header lines from </param>
/// <returns> the number of header lines </returns>
public virtual VCFHeader readHeader(StreamReader reader)
{
IList <string> headerStrings = new List <string>();
string line;
try
{
bool foundHeaderVersion = false;
while ((line = reader.ReadLine()) != null)
{
lineNo++;
if (line.StartsWith(VCFHeader.METADATA_INDICATOR))
{
string[] lineFields = line.Substring(2).Split('=');
if (lineFields.Length == 2 && VCFHeaderVersion.IsFormatString(lineFields[0]))
{
if (!VCFHeaderVersion.IsVersionString(lineFields[1]))
{
throw new VCFParsingError("Header: " + lineFields[1] + " is not a supported version");
}
foundHeaderVersion = true;
version = VCFHeaderVersion.ToHeaderVersion(lineFields[1]);
if (!this.AcceptableVersions.Contains(version))
{
throw new VCFParsingError("This codec is strictly for " + Name + "; please use a different codec for " + lineFields[1]);
}
}
headerStrings.Add(line);
}
else if (line.StartsWith(VCFHeader.HEADER_INDICATOR))
{//should be only one such line
if (!foundHeaderVersion)
{
throw new VCFParsingError("We never saw a header line specifying VCF version");
}
headerStrings.Add(line);
return(parseHeaderFromLines(headerStrings, version));
}
else
{
throw new VCFParsingError("We never saw the required CHROM header line (starting with one #) for the input VCF file");
}
}
}
catch (IOException e)
{
throw new Exception("IO Exception ", e);
}
throw new VCFParsingError("We never saw the required CHROM header line (starting with one #) for the input VCF file");
}
