public static VariantContextContainer readAllVCs(final File input, final BCF2Codec codec)
throws IOException {
PositionalBufferedStream headerPbs = new PositionalBufferedStream(new FileInputStream(input));
FeatureCodecHeader header = codec.readHeader(headerPbs);
headerPbs.close();
final PositionalBufferedStream pbs = new PositionalBufferedStream(new FileInputStream(input));
pbs.skip(header.getHeaderEnd());
final VCFHeader vcfHeader = (VCFHeader) header.getHeaderValue();
return new VariantContextTestProvider.VariantContextContainer(
vcfHeader,
new VariantContextTestProvider.VCIterable(codec, vcfHeader) {
@Override
public boolean hasNext() {
try {
return !pbs.isDone();
} catch (IOException e) {
throw new RuntimeException(e);
}
}
@Override
public Object nextSource() {
return pbs;
}
});
}
/**
* Utility class to read all of the VC records from a file
*
* @param file
* @param codec
* @return
* @throws java.io.IOException
*/
public static final <SOURCE> Pair<VCFHeader, VCIterable<SOURCE>> readAllVCs(
final File file, final FeatureCodec<VariantContext, SOURCE> codec) throws IOException {
// read in the features
SOURCE source = codec.makeSourceFromStream(new FileInputStream(file));
FeatureCodecHeader header = codec.readHeader(source);
final VCFHeader vcfHeader = (VCFHeader) header.getHeaderValue();
return new Pair<>(vcfHeader, new VCIterable<>(source, codec, vcfHeader));
}
