@Override public void start(final BCF2Encoder encoder, final VariantContext vc) throws IOException { if ( vc.getNAlleles() > BCF2Utils.MAX_ALLELES_IN_GENOTYPES ) throw new IllegalStateException("Current BCF2 encoder cannot handle sites " + "with > " + BCF2Utils.MAX_ALLELES_IN_GENOTYPES + " alleles, but you have " + vc.getNAlleles() + " at " + vc.getContig() + ":" + vc.getStart()); encodingType = BCF2Type.INT8; buildAlleleMap(vc); nValuesPerGenotype = vc.getMaxPloidy(2); super.start(encoder, vc); }
@Override public void start(final BCF2Encoder encoder, final VariantContext vc) throws IOException { if ( vc.getNAlleles() > BCF2Utils.MAX_ALLELES_IN_GENOTYPES ) throw new IllegalStateException("Current BCF2 encoder cannot handle sites " + "with > " + BCF2Utils.MAX_ALLELES_IN_GENOTYPES + " alleles, but you have " + vc.getNAlleles() + " at " + vc.getContig() + ":" + vc.getStart()); encodingType = BCF2Type.INT8; buildAlleleMap(vc); nValuesPerGenotype = vc.getMaxPloidy(2); super.start(encoder, vc); }
@Override public void start(final BCF2Encoder encoder, final VariantContext vc) throws IOException { if ( vc.getNAlleles() > BCF2Utils.MAX_ALLELES_IN_GENOTYPES ) throw new IllegalStateException("Current BCF2 encoder cannot handle sites " + "with > " + BCF2Utils.MAX_ALLELES_IN_GENOTYPES + " alleles, but you have " + vc.getNAlleles() + " at " + vc.getChr() + ":" + vc.getStart()); encodingType = BCF2Type.INT8; buildAlleleMap(vc); nValuesPerGenotype = vc.getMaxPloidy(2); super.start(encoder, vc); }