Package htsjdk.tribble.index

Examples of htsjdk.tribble.index.IndexCreator

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    }

    @Test(dataProvider = "indexCreator")
    public void testGetIndexCreator(IndexCreatorTest spec) throws Exception{
        File dummy = new File("");
        IndexCreator ic = GATKVCFUtils.getIndexCreator(spec.type, spec.parameter, dummy);
        Assert.assertEquals(ic.getClass(), spec.expectedClass, "Wrong IndexCreator type");
        if (spec.expectedDimension != null) {
            Integer dimension = (int)spec.dimensionGetter.invoke(ic);
            Assert.assertEquals(dimension, spec.expectedDimension, "Wrong dimension");
        }
    }
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        }

        FileOutputStream outputStream = new FileOutputStream(outputFile);
        EnumSet<Options> options = EnumSet.of(Options.INDEX_ON_THE_FLY);
        final IndexCreator idxCreator = GATKVCFUtils.getIndexCreator(variant_index_type, variant_index_parameter, outputFile, ref.getSequenceDictionary());
        final VariantContextWriter outputWriter = VariantContextWriterFactory.create(outputFile, outputStream, ref.getSequenceDictionary(), idxCreator, options);

        boolean firstFile = true;
        int count = 0;
        while(!priorityQueue.isEmpty() ){
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                return new TabixIndexCreator(TabixFormat.VCF);
            else
                return new TabixIndexCreator(sequenceDictionary, TabixFormat.VCF);
        }

        IndexCreator idxCreator;
        switch (type) {
            case DYNAMIC_SEEK: idxCreator = new DynamicIndexCreator(outFile, IndexFactory.IndexBalanceApproach.FOR_SEEK_TIME); break;
            case DYNAMIC_SIZE: idxCreator = new DynamicIndexCreator(outFile, IndexFactory.IndexBalanceApproach.FOR_SIZE); break;
            case LINEAR: idxCreator = new LinearIndexCreator(outFile, parameter); break;
            case INTERVAL: idxCreator = new IntervalIndexCreator(outFile, parameter); break;
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Related Classes of htsjdk.tribble.index.IndexCreator

  • org.broadinstitute.gatk.tools.CatVariants
  • org.broadinstitute.gatk.utils.variant.GATKVCFUtils
  • org.broadinstitute.gatk.utils.variant.GATKVCFUtilsUnitTest
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