Package htsjdk.tribble.index.tabix

Examples of htsjdk.tribble.index.tabix.TabixIndexCreator


        if (VCFWriterArgumentTypeDescriptor.isCompressed(outFile.toString())) {
            if (type != GATKVCFUtils.DEFAULT_INDEX_TYPE || parameter != GATKVCFUtils.DEFAULT_INDEX_PARAMETER)
                logger.warn("Creating Tabix index for " + outFile + ", ignoring user-specified index type and parameter");

            if (sequenceDictionary == null)
                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;
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