case -2: builder.unfiltered(); break; case -1: builder.passFilters(); break; default:
case -2: builder.unfiltered(); break; case -1: builder.passFilters(); break; default:
case -2: builder.unfiltered(); break; case -1: builder.passFilters(); break; default:
/** * Decode the filter field of this BCF2 file and store the result in the builder * @param builder */ private void decodeFilter( final VariantContextBuilder builder ) throws IOException { final Object value = decoder.decodeTypedValue(); if ( value == null ) builder.unfiltered(); else { if ( value instanceof Integer ) { // fast path for single integer result final String filterString = getDictionaryString((Integer)value); if ( VCFConstants.PASSES_FILTERS_v4.equals(filterString)) builder.passFilters(); else builder.filter(filterString); } else { for ( final int offset : (List<Integer>)value ) builder.filter(getDictionaryString(offset)); } } }
/** * Decode the filter field of this BCF2 file and store the result in the builder * @param builder */ private void decodeFilter( final VariantContextBuilder builder ) throws IOException { final Object value = decoder.decodeTypedValue(); if ( value == null ) builder.unfiltered(); else { if ( value instanceof Integer ) { // fast path for single integer result final String filterString = getDictionaryString((Integer)value); if ( VCFConstants.PASSES_FILTERS_v4.equals(filterString)) builder.passFilters(); else builder.filter(filterString); } else { for ( final int offset : (List<Integer>)value ) builder.filter(getDictionaryString(offset)); } } }
/** * Decode the filter field of this BCF2 file and store the result in the builder * @param builder */ private void decodeFilter( final VariantContextBuilder builder ) throws IOException { final Object value = decoder.decodeTypedValue(); if ( value == null ) builder.unfiltered(); else { if ( value instanceof Integer ) { // fast path for single integer result final String filterString = getDictionaryString((Integer)value); if ( VCFConstants.PASSES_FILTERS_v4.equals(filterString)) builder.passFilters(); else builder.filter(filterString); } else { for ( final int offset : (List<Integer>)value ) builder.filter(getDictionaryString(offset)); } } }
builder.unfiltered(); break; builder.unfiltered();
.genotypes(genotypes).unfiltered().attributes(new TreeMap<>(attributes)).log10PError(CommonInfo.NO_LOG10_PERROR); // we will need to re-genotype later
builder.passFilters(); } else if(filterString.equals(VCFConstants.UNFILTERED)) { builder.unfiltered(); } else { builder.filters(filterString);
.log10PError(VariantContext.NO_LOG10_PERROR) .genotypes(gt) .unfiltered().make(); } catch (IllegalArgumentException e) { throw new IllegalArgumentException(String.format("Trouble creating variant at %s-%d", snp.getChrom(), snp.getPos()), e);
.log10PError(VariantContext.NO_LOG10_PERROR) .genotypes(gt) .unfiltered().make(); } catch (IllegalArgumentException e) { throw new IllegalArgumentException(String.format("Trouble creating variant at %s-%d", snp.getChrom(), snp.getPos()), e);
rootBuilder.loc("1", 10, 10); rootBuilder.alleles("A", "C"); rootBuilder.unfiltered(); ROOT = rootBuilder.make(); add(builder().unfiltered()); add(builder().passFilters()); add(builder().filters("FILTER1"));