import htsjdk.samtools.BAMIndexer; //导入依赖的package包/类
/**
 * Create the BAI index.
 * @param conf the Hadoop configuration
 * @param bamFile the BAM file
 * @param indexFile the BAI file
 * @throws IOException if an error occurs while creating the index
 */
static void createIndex(final Configuration conf, final Path bamFile,
    final Path indexFile) throws IOException {

  final InputStream in = FileSystem.get(conf).open(bamFile);

  final SamReader reader = SamReaderFactory.makeDefault()
      .enable(SamReaderFactory.Option.INCLUDE_SOURCE_IN_RECORDS)
      .validationStringency(ValidationStringency.DEFAULT_STRINGENCY)
      .open(SamInputResource.of(in));

  final BAMIndexer indexer =
      new BAMIndexer(indexFile.getFileSystem(conf).create(indexFile),
          reader.getFileHeader());

  for (SAMRecord rec : reader) {
    indexer.processAlignment(rec);

  }

  indexer.finish();
}
 

import htsjdk.samtools.BAMIndexer; //导入依赖的package包/类
private static void deprecatedCreateIndex(File inputBamFile, File outputBamIndexFile) {
	// make sure that the default validation strategy for the SamReaderFactory is used here too.
	SAMFileReader.setDefaultValidationStringency(SamReaderFactory.makeDefault().validationStringency());

	try (SAMFileReader reader = new SAMFileReader(inputBamFile)) {
		BAMIndexer indexer = new BAMIndexer(outputBamIndexFile, reader.getFileHeader());

		reader.enableFileSource(true);

		// create and write the content
		for (SAMRecord rec : reader) {
			indexer.processAlignment(rec);
		}
		indexer.finish();
	}
}
 

import htsjdk.samtools.BAMIndexer; //导入依赖的package包/类
public void indexBam(File bamFile, File baiFile) {
	SAMFileReader.setDefaultValidationStringency(ValidationStringency.SILENT);
       final SamReader bam;

           // input from a normal file
           IOUtil.assertFileIsReadable(bamFile);
           bam = SamReaderFactory.makeDefault().referenceSequence(null)
                   .enable(SamReaderFactory.Option.INCLUDE_SOURCE_IN_RECORDS)
                   .open(bamFile);

       if (bam.type() != SamReader.Type.BAM_TYPE) {
           throw new SAMException("Input file must be bam file, not sam file.");
       }

       if (!bam.getFileHeader().getSortOrder().equals(SAMFileHeader.SortOrder.coordinate)) {
           throw new SAMException("Input bam file must be sorted by coordinate");
       }

       BAMIndexer.createIndex(bam, baiFile);

       CloserUtil.close(bam);
}
 

import htsjdk.samtools.BAMIndexer; //导入依赖的package包/类
/** open index a BAM file */
  private void doMenuIndexBam(final Window owner)
{
  	final FileChooser fc = newFileChooser();
  	fc.getExtensionFilters().addAll(BamStage.EXTENSION_FILTERS);
  	final List<File> files = fc.showOpenMultipleDialog(owner);
  	if(files==null) return;
  	for(final File file : files)
   	{
  		LOG.info("indexing "+file);
  		updateLastDir(file);
   	SamReader bam=null;
   	try
   		{
   		final File output=  new File(file.getAbsolutePath() + BAMIndex.BAMIndexSuffix);
   		if(output.exists())
   			{
   			throw new IOException("Bam index "+output+" already exists.");
   			}
   		bam = SamReaderFactory.makeDefault()
   				.enable(SamReaderFactory.Option.INCLUDE_SOURCE_IN_RECORDS)
   				.validationStringency(ValidationStringency.LENIENT)
                   .open(file);
   				;
   		BAMIndexer.createIndex(bam, output);
   		final Alert alert = new Alert(AlertType.CONFIRMATION, "Done. ?", ButtonType.OK);
		alert.showAndWait();
   		}
   	catch(final Exception err)
   		{
		showExceptionDialog(owner, err);
		break;
   		}
   	finally
   		{
   		CloserUtil.close(bam);
   		}
   	}
}
 

import htsjdk.samtools.BAMIndexer; //导入依赖的package包/类
/**
 * Main method for the program.  Checks that all input files are present and
 * readable and that the output file can be written to.  Then iterates through
 * all the records generating a BAM Index, then writes the bai file.
 */
protected int doWork() {

    try {
        inputUrl = new URL(INPUT);
    } catch (java.net.MalformedURLException e) {
        inputFile = new File(INPUT);
    }

    // set default output file - input-file.bai
    if (OUTPUT == null) {

        final String baseFileName;
        if (inputUrl != null) {
            final String path = inputUrl.getPath();
            final int lastSlash = path.lastIndexOf('/');
            baseFileName = path.substring(lastSlash + 1, path.length());
        } else {
            baseFileName = inputFile.getAbsolutePath();
        }

        if (baseFileName.endsWith(BamFileIoUtils.BAM_FILE_EXTENSION)) {

            final int index = baseFileName.lastIndexOf('.');
            OUTPUT = new File(baseFileName.substring(0, index) + BAMIndex.BAMIndexSuffix);

        } else {
            OUTPUT = new File(baseFileName + BAMIndex.BAMIndexSuffix);
        }
    }

    IOUtil.assertFileIsWritable(OUTPUT);
    final SamReader bam;

    if (inputUrl != null) {
        // remote input
        bam = SamReaderFactory.makeDefault().referenceSequence(REFERENCE_SEQUENCE)
                .disable(SamReaderFactory.Option.EAGERLY_DECODE)
                .enable(SamReaderFactory.Option.INCLUDE_SOURCE_IN_RECORDS)
                .open(SamInputResource.of(inputUrl));
    } else {
        // input from a normal file
        IOUtil.assertFileIsReadable(inputFile);
        bam = SamReaderFactory.makeDefault().referenceSequence(REFERENCE_SEQUENCE)
                .enable(SamReaderFactory.Option.INCLUDE_SOURCE_IN_RECORDS)
                .open(inputFile);
    }

    if (bam.type() != SamReader.Type.BAM_TYPE) {
        throw new SAMException("Input file must be bam file, not sam file.");
    }

    if (!bam.getFileHeader().getSortOrder().equals(SAMFileHeader.SortOrder.coordinate)) {
        throw new SAMException("Input bam file must be sorted by coordinate");
    }

    BAMIndexer.createIndex(bam, OUTPUT);

    log.info("Successfully wrote bam index file " + OUTPUT);
    CloserUtil.close(bam);
    return 0;
}
 

import htsjdk.samtools.BAMIndexer; //导入依赖的package包/类
public static File writeBamFile(int numPairs, SAMFileHeader.SortOrder sortOrder)
    throws IOException {
  // file will be both queryname and coordinate sorted, so use one or the other
  SAMRecordSetBuilder samRecordSetBuilder = new SAMRecordSetBuilder(true, sortOrder);
  for (int i = 0; i < numPairs; i++) {
    int chr = 20;
    int start1 = (i + 1) * 1000;
    int start2 = start1 + 100;
    if (i == 5) { // add two unmapped fragments instead of a mapped pair
      samRecordSetBuilder.addFrag(String.format("test-read-%03d-1", i), chr, start1,
          false, true, null,
          null,
          -1, false);
      samRecordSetBuilder.addFrag(String.format("test-read-%03d-2", i), chr, start2,
          false, true, null,
          null,
          -1, false);
    } else {
      samRecordSetBuilder.addPair(String.format("test-read-%03d", i), chr, start1,
          start2);
    }
  }
  if (numPairs > 0) { // add two unplaced unmapped fragments if non-empty
    samRecordSetBuilder.addUnmappedFragment(String.format
        ("test-read-%03d-unplaced-unmapped", numPairs++));
    samRecordSetBuilder.addUnmappedFragment(String.format
        ("test-read-%03d-unplaced-unmapped", numPairs++));
  }

  final File bamFile = File.createTempFile("test", ".bam");
  bamFile.deleteOnExit();
  SAMFileHeader samHeader = samRecordSetBuilder.getHeader();
  final SAMFileWriter bamWriter = new SAMFileWriterFactory()
      .makeSAMOrBAMWriter(samHeader, true, bamFile);
  for (final SAMRecord rec : samRecordSetBuilder.getRecords()) {
    bamWriter.addAlignment(rec);
  }
  bamWriter.close();

  // create BAM index
  if (sortOrder.equals(SAMFileHeader.SortOrder.coordinate)) {
    SamReader samReader = SamReaderFactory.makeDefault()
        .enable(SamReaderFactory.Option.INCLUDE_SOURCE_IN_RECORDS)
        .open(bamFile);
    BAMIndexer.createIndex(samReader, new File(bamFile.getAbsolutePath()
        .replaceFirst("\\.bam$", BAMIndex.BAMIndexSuffix)));
  }

  return bamFile;
}