/** * Decode the id field in this BCF2 file and store it in the builder * @param builder */ private void decodeID( final VariantContextBuilder builder ) throws IOException { final String id = (String)decoder.decodeTypedValue(); if ( id == null ) builder.noID(); else builder.id(id); }
/** * Decode the id field in this BCF2 file and store it in the builder * @param builder */ private void decodeID( final VariantContextBuilder builder ) throws IOException { final String id = (String)decoder.decodeTypedValue(); if ( id == null ) builder.noID(); else builder.id(id); }
/** * Decode the id field in this BCF2 file and store it in the builder * @param builder */ private void decodeID( final VariantContextBuilder builder ) throws IOException { final String id = (String)decoder.decodeTypedValue(); if ( id == null ) builder.noID(); else builder.id(id); }
builder.noID(); else { if (len > b.length) b = new byte[len];
builder.noID(); else { if (len > b.length) b = new byte[len];
builder.noID(); else { if (len > b.length) b = new byte[len];
builder.noID(); } else {
generateException("The VCF specification requires a valid ID field"); else if ( parts[2].equals(VCFConstants.EMPTY_ID_FIELD) ) builder.noID(); else builder.id(parts[2]);
generateException("The VCF specification requires a valid ID field"); else if ( parts[2].equals(VCFConstants.EMPTY_ID_FIELD) ) builder.noID(); else builder.id(parts[2]);
generateException("The VCF specification requires a valid ID field"); else if ( parts[2].equals(VCFConstants.EMPTY_ID_FIELD) ) builder.noID(); else builder.id(parts[2]);
final VariantContextBuilder baseVC = new VariantContextBuilder().chr("1").start(1).stop(1).noID().passFilters().log10PError(1).alleles("A", "C"); final GenotypeBuilder baseGT = new GenotypeBuilder("Sample1").alleles(Arrays.asList(Allele.NO_CALL, Allele.NO_CALL)); final Map<Allele, String> alleleMap = new HashMap<Allele, String>(3);
vcBuilder.noID(); vcBuilder.attribute("AC", 6); vcBuilder.attribute("AF", 1.00);
add(builder().log10PError(-1.234e6)); add(builder().noID()); add(builder().id("rsID12345"));