Examples of VCFCodec

Examples of htsjdk.variant.vcf.VCFCodec

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            Assert.assertEquals(actualLines.get(i), expectedLines.get(i), "VCF header lines");
        }
    }

    public static void assertVCFandBCFFilesAreTheSame(final File vcfFile, final File bcfFile) throws IOException {
        final Pair<VCFHeader, GATKVCFUtils.VCIterable<LineIterator>> vcfData = GATKVCFUtils.readAllVCs(vcfFile, new VCFCodec());
        final Pair<VCFHeader, GATKVCFUtils.VCIterable<PositionalBufferedStream>> bcfData = GATKVCFUtils.readAllVCs(bcfFile, new BCF2Codec());
        assertVCFHeadersAreEqual(bcfData.getFirst(), vcfData.getFirst());
        assertVariantContextStreamsAreEqual(bcfData.getSecond(), vcfData.getSecond());
    }
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Examples of htsjdk.variant.vcf.VCFCodec

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            return String.format("Index Type %s, Index Parameter %s", type, parameter);
        }

        public Index getIndex(final File vcfFile) {
            switch (type) {
                case DYNAMIC_SEEK : return IndexFactory.createDynamicIndex(vcfFile, new VCFCodec(), IndexFactory.IndexBalanceApproach.FOR_SEEK_TIME);
                case DYNAMIC_SIZE : return IndexFactory.createDynamicIndex(vcfFile, new VCFCodec(), IndexFactory.IndexBalanceApproach.FOR_SIZE);
                case LINEAR : return IndexFactory.createLinearIndex(vcfFile, new VCFCodec(), parameter);
                case INTERVAL : return IndexFactory.createIntervalIndex(vcfFile, new VCFCodec(), parameter);
                default : throw new TestException("Invalid index type");
            }
        }
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Examples of htsjdk.variant.vcf.VCFCodec

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    }

    public void timeV14(int rep) {
        for ( int i = 0; i < rep; i++ ) {
            FunctionToBenchmark<VariantContext> func = getV14FunctionToBenchmark();
            final VCFCodec codec = new VCFCodec();
            runBenchmark(codec, func);
        }
    }
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