private VariantContext decodeLine(string line, bool includeGenotypes)
{
// the same line reader is not used for parsing the header and parsing lines, if we see a #, we've seen a header line
if (line.StartsWith(VCFHeader.HEADER_INDICATOR))
{
//TODO: Possibly raise exception? At least in one scenario, the VCF header has already been parsed before this is called
//seems like this should always be true based on statement below
throw new VCFParsingError("While decoding genotype lines came across a commented header line. Problem is with line:\n " + line);
}
// our header cannot be null, we need the genotype sample names and counts
if (header == null)
{
throw new VCFParsingError("VCF Header cannot be null when decoding a record");
}
//I think this is not necessary
int parseSize = Math.Min(header.ColumnCount, NUM_STANDARD_FIELDS + 1);
//TODO: Original bit of code here could do lazy genotype initalization and so could split off the
//first 8 columns, leaving any genotype data still lumped together in the 9th column (if present).
// string[] parts=line.Split(VCFConstants.FIELD_SEPARATOR_CHAR_AS_ARRAY,parseSize,StringSplitOptions.None);
string[] parts = FastStringUtils.Split(line, VCFConstants.FIELD_SEPARATOR_CHAR, parseSize, StringSplitOptions.None);
//ND - Modified this heavily, as it is imposssible for header to be null at this stage.
// if we have don't have a header, or we have a header with no genotyping data check that we have eight columns.
// Otherwise check that we have nine (normal colummns + genotyping data)
if ((!header.hasGenotypingData() && parts.Length != NUM_STANDARD_FIELDS) ||
(header.hasGenotypingData() && parts.Length != (NUM_STANDARD_FIELDS + 1)))
{
throw new VCFParsingError("Line " + lineNo + ": there aren't enough columns for line " + line + " (we expected " + (header == null ? NUM_STANDARD_FIELDS : NUM_STANDARD_FIELDS + 1) + " tokens, and saw " + parts.Length + " )");
}
return(parseVCFLine(parts, includeGenotypes));
}
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);
}
}