/**
* Returns a list of VariantContext records from a VCF file
*
* @param vcfFile VCF file
* @throws IOException if the file does not exist or can not be opened
* @return list of VariantContext records
*/
private static List<VariantContext> getVariantContexts(final File vcfFile) throws IOException {
final VCFCodec codec = new VCFCodec();
final FileInputStream s = new FileInputStream(vcfFile);
final LineIterator lineIteratorVCF =
codec.makeSourceFromStream(new PositionalBufferedStream(s));
codec.readHeader(lineIteratorVCF);
final List<VariantContext> VCs = new ArrayList<>();
while (lineIteratorVCF.hasNext()) {
final String line = lineIteratorVCF.next();
Assert.assertFalse(line == null);
VCs.add(codec.decode(line));
}
return VCs;
}
/**
* Returns a list of attribute values from a VCF file
*
* @param vcfFile VCF file
* @param attributeName attribute name
* @throws IOException if the file does not exist or can not be opened
* @return list of attribute values
*/
private List<String> getAttributeValues(final File vcfFile, final String attributeName)
throws IOException {
final VCFCodec codec = new VCFCodec();
final FileInputStream s = new FileInputStream(vcfFile);
final LineIterator lineIteratorVCF =
codec.makeSourceFromStream(new PositionalBufferedStream(s));
codec.readHeader(lineIteratorVCF);
List<String> attributeValues = new ArrayList<String>();
while (lineIteratorVCF.hasNext()) {
final String line = lineIteratorVCF.next();
Assert.assertFalse(line == null);
final VariantContext vc = codec.decode(line);
for (final Genotype g : vc.getGenotypes()) {
if (g.hasExtendedAttribute(attributeName)) {
attributeValues.add((String) g.getExtendedAttribute(attributeName));
}
}
}
return attributeValues;
}
public static VariantContextContainer readAllVCs(final File input, final VCFCodec codec)
throws FileNotFoundException {
final LineIterator lineIterator =
new LineIteratorImpl(
LineReaderUtil.fromBufferedStream(new BufferedInputStream(new FileInputStream(input))));
final VCFHeader vcfHeader = (VCFHeader) codec.readActualHeader(lineIterator);
return new VariantContextTestProvider.VariantContextContainer(
vcfHeader,
new VariantContextTestProvider.VCIterable<LineIterator>(codec, vcfHeader) {
@Override
public boolean hasNext() {
return lineIterator.hasNext();
}
@Override
public LineIterator nextSource() {
return lineIterator;
}
});
}