### Question:
BamManager implements AutoCloseable { public Path createIndex() throws IOException { String ext = ".bai"; if (bamFile.toString().endsWith(".cram")) { ext = ".crai"; } Path indexPath = bamFile.getParent().resolve(bamFile.getFileName().toString() + ext); return createIndex(indexPath); } BamManager(Path bamFilePath);  BamManager(Path bamFilePath, Path refFilePath); Path createIndex(); Path createIndex(Path outputIndex); SAMFileHeader getHeader(); Path calculateBigWigCoverage(); Path calculateBigWigCoverage(Path bigWigPath, int windowSize); String header(); byte[] compressedHeader(); List<SAMRecord> query(AlignmentFilters<SAMRecord> filters); List<SAMRecord> query(AlignmentFilters<SAMRecord> filters, AlignmentOptions options); List<T> query(AlignmentFilters<SAMRecord> filters, AlignmentOptions options, Class<T> clazz); List<SAMRecord> query(Region region); List<SAMRecord> query(Region region, AlignmentOptions options); List<SAMRecord> query(Region region, AlignmentFilters<SAMRecord> filters, AlignmentOptions options); List<T> query(Region region, AlignmentFilters<SAMRecord> filters, AlignmentOptions options, Class<T> clazz); BamIterator<SAMRecord> iterator(); BamIterator<SAMRecord> iterator(AlignmentOptions options); BamIterator<SAMRecord> iterator(AlignmentFilters<SAMRecord> filters, AlignmentOptions options); BamIterator<T> iterator(AlignmentFilters<SAMRecord> filters, AlignmentOptions options, Class<T> clazz); BamIterator<SAMRecord> iterator(Region region); BamIterator<SAMRecord> iterator(Region region, AlignmentOptions options); BamIterator<SAMRecord> iterator(Region region, AlignmentFilters<SAMRecord> filters, AlignmentOptions options); BamIterator<T> iterator(Region region, AlignmentFilters<SAMRecord> filters, AlignmentOptions options, Class<T> clazz); List<Chunk> getChunks(Region region); List<String> getBreakpoints(Region region); RegionCoverage coverage(Region region, int windowSize); RegionCoverage coverage(Region region, AlignmentFilters<SAMRecord> filters, AlignmentOptions options); AlignmentGlobalStats stats(); AlignmentGlobalStats stats(Region region, AlignmentFilters<SAMRecord> filters, AlignmentOptions options); @Override void close(); Path getBamFile(); BamManager setBamFile(Path bamFilePath); static final int DEFAULT_WINDOW_SIZE; static final int MAX_NUM_RECORDS; static final int MAX_REGION_COVERAGE; static final String COVERAGE_BIGWIG_EXTENSION; }### Answer:
@Test public void testIndex() throws IOException { try { Files.copy(inputPath, bamPath); } catch (FileAlreadyExistsException e) { System.out.println("BAM file " + bamPath + " already copied"); } System.out.println("bamPath = " + bamPath); BamManager bamManager = new BamManager(bamPath); bamManager.createIndex(); }