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package org.broadinstitute.hellbender.tools.filediagnostics;

import htsjdk.samtools.BAMIndexer;
import org.broadinstitute.hellbender.engine.GATKPath;

import java.io.File;
import java.io.IOException;

/**
 * Analyzer for BAI files.
 */
public class BAIAnalyzer extends HTSAnalyzer {

    public BAIAnalyzer(final GATKPath inputPath, final GATKPath outputPath) {
        super(inputPath, outputPath);
    }

    /**
     * Run the analyzer for the file.
     */
    protected void doAnalysis() {
        System.out.println(String.format("\nOutput written to %s\n", outputPath));
        // note this method is not nio aware
        BAMIndexer.createAndWriteIndex(inputPath.toPath().toFile(), new File(outputPath.getRawInputString()), true);
    }

    @Override
    public void close() throws IOException {
    }

}