/**
* @param reader the line reader to take header lines from
* @return the number of header lines
*/
public Object readHeader(LineReader reader) {
List<String> headerStrings = new ArrayList<String>();
String line;
try {
boolean 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 TribbleException.InvalidHeader(
lineFields[1] + " is not a supported version");
foundHeaderVersion = true;
version = VCFHeaderVersion.toHeaderVersion(lineFields[1]);
if (version != VCFHeaderVersion.VCF3_3 && version != VCFHeaderVersion.VCF3_2)
throw new TribbleException.InvalidHeader(
"This codec is strictly for VCFv3 and does not support " + lineFields[1]);
}
headerStrings.add(line);
} else if (line.startsWith(VCFHeader.HEADER_INDICATOR)) {
if (!foundHeaderVersion) {
throw new TribbleException.InvalidHeader(
"We never saw a header line specifying VCF version");
}
return createHeader(headerStrings, line);
} else {
throw new TribbleException.InvalidHeader(
"We never saw the required CHROM header line (starting with one #) for the input VCF file");
}
}
} catch (IOException e) {
throw new RuntimeException("IO Exception ", e);
}
throw new TribbleException.InvalidHeader(
"We never saw the required CHROM header line (starting with one #) for the input VCF file");
}
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);
}
}