private static VcfHeader InternalReadHeader(StreamReader reader)
{
VcfHeader header = null;
string cline = null;
while ((cline = reader.ReadLine()) != null)
{
string line = cline.Trim();
if (line.StartsWith("##"))
{
if (line.StartsWith("##INFO=<"))
{
//parse info line, to be implemented
}
else if (line.StartsWith("##FORMAT=<"))
{
//parse format line, to be implemented
}
else if (line.StartsWith("##FILTER=<"))
{
//parse filter line, to be implemented
}
else if (line.StartsWith("##ALT=<"))
{
//parse alt line, to be implemented
}
else
{
//parse other meta information line, to be implemented
}
}
else if (line.StartsWith("#CHROM"))
{
header = new VcfHeader(line.Split('\t'));
break;
}
else if (header == null && !line.StartsWith("#"))
{
throw new Exception("Invalid VCF file. Header was not found before the data lines.");
}
else
{
break;
}
}
if (header == null)
{
throw new Exception("Invalid VCF file: header line was not found.");
}
return(header);
}
private bool Load(string fileName)
{
if (this.gzip) //I should use BGZF stream for compressed vcf.gz, use standard gzip reader here for demo purpose
{
this.stream = new GZipStream(File.OpenRead(fileName), CompressionMode.Decompress);
}
else
{
this.stream = File.OpenRead(fileName);
}
this.vcfReader = new StreamReader(this.stream);
//read header of vcf file
header = InternalReadHeader(this.vcfReader);
this.firstLinePosition = this.stream.Position;
return(true);
}