import htsjdk.samtools.SAMRecordCoordinateComparator; //导入依赖的package包/类
public static void sortBamFile(File inputBamFile, File outputBamFile, File tempDirectory, final Comparator<SAMRecord> comparator) {
	try (SamReader currentReader = SamReaderFactory.makeDefault().open(inputBamFile)) {
		SAMFileHeader header = currentReader.getFileHeader();
		Iterator<SAMRecord> iter = currentReader.iterator();
		try (CloseableAndIterableIterator<SAMRecord> sortedIter = getSortedBamIterator(iter, header, tempDirectory, comparator)) {

			if (comparator.getClass().equals(SAMRecordCoordinateComparator.class)) {
				header.setSortOrder(SortOrder.coordinate);
			} else if (comparator.getClass().equals(SAMRecordQueryNameComparator.class)) {
				header.setSortOrder(SortOrder.queryname);
			} else if (comparator.getClass().equals(SAMRecordDuplicateComparator.class)) {
				header.setSortOrder(SortOrder.duplicate);
			}
			try (SAMFileWriter writer = new SAMFileWriterFactory().makeBAMWriter(header, true, outputBamFile, BAM_COMPRESSION_LEVEL)) {
				while (sortedIter.hasNext()) {
					SAMRecord nextRecord = sortedIter.next();
					writer.addAlignment(nextRecord);
				}
			}
		}
	} catch (IOException e) {
		throw new PicardException(e.getMessage(), e);
	}

}
 

import htsjdk.samtools.SAMRecordCoordinateComparator; //导入依赖的package包/类
private static void assertReadsAreSorted(SAMFileHeader header, List<GATKRead> writtenReads) {
    final SAMRecordCoordinateComparator comparator = new SAMRecordCoordinateComparator();
    // Assert that the reads are sorted.
    final int size = writtenReads.size();
    for (int i = 0; i < size-1; ++i) {
        final SAMRecord smaller = writtenReads.get(i).convertToSAMRecord(header);
        final SAMRecord larger = writtenReads.get(i + 1).convertToSAMRecord(header);
        final int compare = comparator.compare(smaller, larger);
        Assert.assertTrue(compare < 0, "Reads are out of order (compare=" + compare+"): " + smaller.getSAMString() + " and " + larger.getSAMString());
    }
}
 

import htsjdk.samtools.SAMRecordCoordinateComparator; //导入依赖的package包/类
public static SortingSAMRecordCollection newSortByCoordinateInstance(SAMRecord[] recordArray, SAMFileHeader header, int maxRecordsInRAM, String tempDir) {
	return new SortingSAMRecordCollection(recordArray, header, new SAMRecordCoordinateComparator(), maxRecordsInRAM, tempDir);
}
 

import htsjdk.samtools.SAMRecordCoordinateComparator; //导入依赖的package包/类
public MergingSamRecordIterator(final List<CloseableIterator<SAMRecord>> iterators)
{
this(new SAMRecordCoordinateComparator(),iterators);
}
 

import htsjdk.samtools.SAMRecordCoordinateComparator; //导入依赖的package包/类
/**
 * Returns the collections of reads sorted in coordinate order, according to the order defined
 * in the reads themselves
 *
 * @param reads
 * @return
 */
public final static List<GATKSAMRecord> sortReadsByCoordinate(List<GATKSAMRecord> reads) {
    final SAMRecordComparator comparer = new SAMRecordCoordinateComparator();
    Collections.sort(reads, comparer);
    return reads;
}