public void writeHeader(VCFHeader header) {
mHeader = doNotWriteGenotypes ? new VCFHeader(header.getMetaData()) : header;
try {
// the file format field needs to be written first
mWriter.write(
VCFHeader.METADATA_INDICATOR
+ VCFHeaderVersion.VCF4_1.getFormatString()
+ "="
+ VCFHeaderVersion.VCF4_1.getVersionString()
+ "\n");
for (VCFHeaderLine line : mHeader.getMetaData()) {
if (VCFHeaderVersion.isFormatString(line.getKey())) continue;
// are the records filtered (so we know what to put in the FILTER column of passing records)
// ?
if (line instanceof VCFFilterHeaderLine) filtersWereAppliedToContext = true;
mWriter.write(VCFHeader.METADATA_INDICATOR);
mWriter.write(line.toString());
mWriter.write("\n");
}
// write out the column line
mWriter.write(VCFHeader.HEADER_INDICATOR);
for (VCFHeader.HEADER_FIELDS field : mHeader.getHeaderFields()) {
mWriter.write(field.toString());
mWriter.write(VCFConstants.FIELD_SEPARATOR);
}
if (mHeader.hasGenotypingData()) {
mWriter.write("FORMAT");
for (String sample : mHeader.getGenotypeSamples()) {
mWriter.write(VCFConstants.FIELD_SEPARATOR);
mWriter.write(sample);
}
}
mWriter.write("\n");
mWriter.flush(); // necessary so that writing to an output stream will work
} catch (IOException e) {
throw new TribbleException("IOException writing the VCF header to " + locationString(), e);
}
}
