Java ReadConstants类代码示例

import org.broadinstitute.hellbender.utils.read.ReadConstants; //导入依赖的package包/类
@Test(dataProvider = "loadShardedReads", groups = "spark")
public void shardedReadsSparkSourceTest(String expectedBam, String shardedBam, String referencePath) {
    JavaSparkContext ctx = SparkContextFactory.getTestSparkContext();

    ReadsSparkSource readSource = new ReadsSparkSource(ctx);
    JavaRDD<GATKRead> rddSerialReads = getSerialReads(ctx, expectedBam, referencePath, ReadConstants.DEFAULT_READ_VALIDATION_STRINGENCY);
    JavaRDD<GATKRead> rddParallelReads = readSource.getParallelReads(shardedBam, referencePath);

    List<GATKRead> serialReads = rddSerialReads.collect();
    List<GATKRead> parallelReads = rddParallelReads.collect();
    Assert.assertEquals(parallelReads.size(), serialReads.size());
}
 

import org.broadinstitute.hellbender.utils.read.ReadConstants; //导入依赖的package包/类
/**
 * Initialize this data source with multiple SAM/BAM/CRAM files, explicit indices for those files,
 * and a custom SamReaderFactory.
 *
 * @param samPaths paths to SAM/BAM/CRAM files, not null
 * @param samIndices indices for all of the SAM/BAM/CRAM files, in the same order as samPaths. May be null,
 *                   in which case index paths are inferred automatically.
 * @param customSamReaderFactory SamReaderFactory to use, if null a default factory with no reference and validation
 *                               stringency SILENT is used.
 * @param cloudWrapper caching/prefetching wrapper for the data, if on Google Cloud.
 * @param cloudIndexWrapper caching/prefetching wrapper for the index, if on Google Cloud.
 */
public ReadsDataSource( final List<Path> samPaths, final List<Path> samIndices,
    SamReaderFactory customSamReaderFactory,
    Function<SeekableByteChannel, SeekableByteChannel> cloudWrapper,
    Function<SeekableByteChannel, SeekableByteChannel> cloudIndexWrapper) {
    Utils.nonNull(samPaths);
    Utils.nonEmpty(samPaths, "ReadsDataSource cannot be created from empty file list");

    if ( samIndices != null && samPaths.size() != samIndices.size() ) {
        throw new UserException(String.format("Must have the same number of BAM/CRAM/SAM paths and indices. Saw %d BAM/CRAM/SAMs but %d indices",
                                              samPaths.size(), samIndices.size()));
    }

    readers = new LinkedHashMap<>(samPaths.size() * 2);
    backingPaths = new LinkedHashMap<>(samPaths.size() * 2);
    indicesAvailable = true;

    final SamReaderFactory samReaderFactory =
            customSamReaderFactory == null ?
                SamReaderFactory.makeDefault().validationStringency(ReadConstants.DEFAULT_READ_VALIDATION_STRINGENCY) :
                customSamReaderFactory;

    int samCount = 0;
    for ( final Path samPath : samPaths ) {
        // Ensure each file can be read
        try {
            IOUtil.assertFileIsReadable(samPath);
        }
        catch ( SAMException|IllegalArgumentException e ) {
            throw new UserException.CouldNotReadInputFile(samPath.toString(), e);
        }

        Function<SeekableByteChannel, SeekableByteChannel> wrapper =
            (BucketUtils.isCloudStorageUrl(samPath)
                ? cloudWrapper
                : Function.identity());
        // if samIndices==null then we'll guess the index name from the file name.
        // If the file's on the cloud, then the search will only consider locations that are also
        // in the cloud.
        Function<SeekableByteChannel, SeekableByteChannel> indexWrapper =
            ((samIndices != null && BucketUtils.isCloudStorageUrl(samIndices.get(samCount))
             || (samIndices == null && BucketUtils.isCloudStorageUrl(samPath)))
                ? cloudIndexWrapper
                : Function.identity());

        SamReader reader;
        if ( samIndices == null ) {
            reader = samReaderFactory.open(samPath, wrapper, indexWrapper);
        }
        else {
            final SamInputResource samResource = SamInputResource.of(samPath, wrapper);
            Path indexPath = samIndices.get(samCount);
            samResource.index(indexPath, indexWrapper);
            reader = samReaderFactory.open(samResource);
        }

        // Ensure that each file has an index
        if ( ! reader.hasIndex() ) {
            indicesAvailable = false;
        }

        readers.put(reader, null);
        backingPaths.put(reader, samPath);
        ++samCount;
    }

    // Prepare a header merger only if we have multiple readers
    headerMerger = samPaths.size() > 1 ? createHeaderMerger() : null;
}
 

import org.broadinstitute.hellbender.utils.read.ReadConstants; //导入依赖的package包/类
@Test(expectedExceptions = UserException.MissingReference.class)
public void loadReadsNonExistentReference() {
    doLoadReads(dir + "valid.cram",
            GATKBaseTest.getSafeNonExistentFile("NonExistentReference.fasta").getAbsolutePath(),
            ReadConstants.DEFAULT_READ_VALIDATION_STRINGENCY);
}
 

import org.broadinstitute.hellbender.utils.read.ReadConstants; //导入依赖的package包/类
private void doLoadReadsTest(String bam, String referencePath) {
    doLoadReads(bam, referencePath, ReadConstants.DEFAULT_READ_VALIDATION_STRINGENCY);
}
 

import org.broadinstitute.hellbender.utils.read.ReadConstants; //导入依赖的package包/类
@Test(expectedExceptions = UserException.class, expectedExceptionsMessageRegExp = ".*Failed to read bam header from hdfs://bogus/path.bam.*")
public void readsSparkSourceUnknownHostTest() {
    JavaSparkContext ctx = SparkContextFactory.getTestSparkContext();
    ReadsSparkSource readSource = new ReadsSparkSource(ctx, ReadConstants.DEFAULT_READ_VALIDATION_STRINGENCY);
    readSource.getParallelReads("hdfs://bogus/path.bam", null);
}