Package htsjdk.variant.variantcontext

Examples of htsjdk.variant.variantcontext.VariantContextBuilder.make()

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        if ( !isViolation && altAlleleCount > 0 )
            numTrueVariants++;
        builder.attribute(VCFConstants.ALLELE_COUNT_KEY, String.format("%d", altAlleleCount));
        builder.attribute(VCFConstants.ALLELE_NUMBER_KEY, String.format("%d", vContext.getCalledChrCount()));

        return builder.make();
    }

    private double hardyWeinbergCalculation(VariantContext vc) {
        //if ( popFile != null ) {
        //    throw new GATKException("We still need to implement this!");
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                builder.attribute(VariantEval.IS_SINGLETON_KEY, true);

            if ( ! hasChrCountAnnotations )
                VariantContextUtils.calculateChromosomeCounts(builder, true);

            return builder.make();
        }
    }

    /**
     * For a list of track names, bind the variant contexts to a trackName->sampleName->VariantContext mapping.
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            // re-compute chromosome counts
            VariantContextUtils.calculateChromosomeCounts(builder, false);

            if ( minimalVCF )
                GATKVariantContextUtils.pruneVariantContext(builder, Arrays.asList(SET_KEY));
            final VariantContext vc = builder.make();
            if( !EXCLUDE_NON_VARIANTS || vc.isPolymorphicInSamples() )
                vcfWriter.add(builder.make());
        }

        return vcs.isEmpty() ? 0 : 1;
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            if ( minimalVCF )
                GATKVariantContextUtils.pruneVariantContext(builder, Arrays.asList(SET_KEY));
            final VariantContext vc = builder.make();
            if( !EXCLUDE_NON_VARIANTS || vc.isPolymorphicInSamples() )
                vcfWriter.add(builder.make());
        }

        return vcs.isEmpty() ? 0 : 1;
    }
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            }
            newGenotypes.add(gtBuilder.make());
        }
        builder.genotypes(newGenotypes);

        return builder.make();
    }

    @Override public boolean hasNext() { return this.iterator.hasNext(); }
    @Override public void close() { CloserUtil.close(this.iterator); }
    @Override public void remove() { throw new UnsupportedOperationException("remove() not supported by FilterApplyingVariantIterator."); }
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