SamReaderFactory抽象类介绍
SamReaderFactory 是 HTSJDK 库中的一个抽象类，用于创建 SamReader 对象。这些对象可以读取和解析各种格式的 SAM（Sequence Alignment/Map）、BAM（Binary Alignment/Map）、和 CRAM（Compressed Reference-Aligned Map）文件。SamReaderFactory 提供了配置和生成 SamReader 的多个方法，使用户可以灵活地处理不同的文件格式和选项。
内部类 SamReaderFactoryImpl
这是 SamReaderFactory 的具体实现，包含实际的文件读取逻辑和各项设置的应用。该类包括以下主要功能：
-
open(File file)方法实现文件读取逻辑，包括处理文件索引。 -
open(SamInputResource resource)方法负责根据资源类型（例如 URL、文件、SRA 访问号）创建适当的SamReader实例。 -
提供了对多种文件格式（SAM、BAM、CRAM、SRA）的支持，并根据不同的输入资源类型选择合适的读取器（如
BAMFileReader、SAMTextReader、CRAMFileReader等）。 -
各种选项（
Option）如INCLUDE_SOURCE_IN_RECORDS、CACHE_FILE_BASED_INDEXES等，控制了SamReader的行为，例如是否在记录中包含源文件信息，是否缓存索引等。
总结
SamReaderFactory 提供了一个灵活的接口来创建和配置 SAM/BAM/CRAM 文件的读取器，而具体的实现类 SamReaderFactoryImpl 则处理了实际的文件操作和选项的应用。通过这个工厂类，用户可以轻松地设置不同的选项和配置，从而控制文件读取的方式和行为。
SamReaderFactory源码
/** The MIT License** Copyright (c) 2016 The Broad Institute** Permission is hereby granted, free of charge, to any person obtaining a copy* of this software and associated documentation files (the "Software"), to deal* in the Software without restriction, including without limitation the rights* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell* copies of the Software, and to permit persons to whom the Software is* furnished to do so, subject to the following conditions:** The above copyright notice and this permission notice shall be included in* all copies or substantial portions of the Software.** THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN* THE SOFTWARE.*/package htsjdk.samtools;import htsjdk.samtools.cram.ref.CRAMReferenceSource;
import htsjdk.samtools.cram.ref.ReferenceSource;
import htsjdk.samtools.seekablestream.SeekableStream;
import htsjdk.samtools.sra.SRAAccession;
import htsjdk.samtools.util.*;
import htsjdk.samtools.util.zip.InflaterFactory;import java.io.File;
import java.io.IOException;
import java.io.InputStream;
import java.net.URISyntaxException;
import java.nio.channels.SeekableByteChannel;
import java.nio.file.Path;
import java.util.Collections;
import java.util.EnumSet;
import java.util.function.Function;
import java.util.zip.GZIPInputStream;/*** <p>Describes the functionality for producing {@link SamReader}, and offers a* handful of static generators.</p>* <pre>* SamReaderFactory.makeDefault().open(new File("/my/bam.bam");* </pre>* <p>Example: Configure a factory</p>* <pre>* final {@link SamReaderFactory} factory =* SamReaderFactory.makeDefault()* .enable({@link Option#INCLUDE_SOURCE_IN_RECORDS}, {@link Option#VALIDATE_CRC_CHECKSUMS})* .validationStringency({@link ValidationStringency#SILENT});** </pre>* <p>Example: Open two bam files from different sources, using different options</p>* <pre>* final {@link SamReaderFactory} factory =* SamReaderFactory.makeDefault()* .enable({@link Option#INCLUDE_SOURCE_IN_RECORDS}, {@link Option#VALIDATE_CRC_CHECKSUMS})* .validationStringency({@link ValidationStringency#SILENT});** // File-based bam* final {@link SamReader} fileReader = factory.open(new File("/my/bam.bam"));** // HTTP-hosted BAM with index from an arbitrary stream* final SeekableStream myBamIndexStream = ...* final {@link SamInputResource} resource =* {@link SamInputResource}.of(new URL("http://example.com/data.bam")).index(myBamIndexStream);* final {@link SamReader} complicatedReader = factory.open(resource);* </pre>** @author mccowan*/
public abstract class SamReaderFactory {private static ValidationStringency defaultValidationStringency = ValidationStringency.DEFAULT_STRINGENCY;abstract public SamReader open(final File file);/*** Open the specified path (without using any wrappers).** @param path the SAM or BAM file to open.*/public SamReader open(final Path path) {return open(path, null, null);}/*** Open the specified path, using the specified wrappers for prefetching/caching.** @param path the SAM or BAM file to open* @param dataWrapper the wrapper for the data (or null for none)* @param indexWrapper the wrapper for the index (or null for none)*/public SamReader open(final Path path,Function<SeekableByteChannel, SeekableByteChannel> dataWrapper,Function<SeekableByteChannel, SeekableByteChannel> indexWrapper) {final SamInputResource r = SamInputResource.of(path, dataWrapper);final Path indexMaybe = SamFiles.findIndex(path);if (indexMaybe != null) r.index(indexMaybe, indexWrapper);return open(r);}abstract public SamReader open(final SamInputResource resource);abstract public ValidationStringency validationStringency();abstract public CRAMReferenceSource referenceSource();/** Set this factory's {@link htsjdk.samtools.SAMRecordFactory} to the provided one, then returns itself. */abstract public SamReaderFactory samRecordFactory(final SAMRecordFactory samRecordFactory);/*** Set this factory's {@link htsjdk.samtools.util.zip.InflaterFactory} to the provided one, then returns itself.* Note: The inflaterFactory provided here is only used for BAM decompression implemented with {@link BAMFileReader},* it is not used for CRAM or other formats like a gzipped SAM file.*/abstract public SamReaderFactory inflaterFactory(final InflaterFactory inflaterFactory);/** Enables the provided {@link Option}s, then returns itself. */abstract public SamReaderFactory enable(final Option... options);/** Disables the provided {@link Option}s, then returns itself. */abstract public SamReaderFactory disable(final Option... options);/** Sets a specific Option to a boolean value. * */abstract public SamReaderFactory setOption(final Option option, boolean value);/** Sets the specified reference sequence * */abstract public SamReaderFactory referenceSequence(File referenceSequence);/** Sets the specified reference sequence. */abstract public SamReaderFactory referenceSequence(Path referenceSequence);/** Sets the specified reference sequence * */abstract public SamReaderFactory referenceSource(CRAMReferenceSource referenceSequence);/** Utility method to open the file get the header and close the file */abstract public SAMFileHeader getFileHeader(File samFile);/** Utility method to open the file get the header and close the file */abstract public SAMFileHeader getFileHeader(Path samFile);/** Reapplies any changed options to the reader * */abstract public void reapplyOptions(SamReader reader);/** Set this factory's {@link ValidationStringency} to the provided one, then returns itself. */abstract public SamReaderFactory validationStringency(final ValidationStringency validationStringency);/** Set whether readers created by this factory will use asynchronous IO.* If this methods is not called, this flag will default to the value of {@link Defaults#USE_ASYNC_IO_READ_FOR_SAMTOOLS}.* Note that this option may not be applicable to all readers returned from this factory.* Returns the factory itself. */abstract public SamReaderFactory setUseAsyncIo(final boolean asynchronousIO);private static SamReaderFactoryImpl DEFAULT =new SamReaderFactoryImpl(Option.DEFAULTS, defaultValidationStringency,DefaultSAMRecordFactory.getInstance(), BlockGunzipper.getDefaultInflaterFactory());public static void setDefaultValidationStringency(final ValidationStringency defaultValidationStringency) {SamReaderFactory.defaultValidationStringency = defaultValidationStringency;// The default may have changed, so reset the default SamReaderDEFAULT = new SamReaderFactoryImpl(Option.DEFAULTS, defaultValidationStringency,DefaultSAMRecordFactory.getInstance(), BlockGunzipper.getDefaultInflaterFactory());}/** Creates a copy of the default {@link SamReaderFactory}. */public static SamReaderFactory makeDefault() {return SamReaderFactoryImpl.copyOf(DEFAULT);}/*** Creates an "empty" factory with no enabled {@link Option}s, {@link ValidationStringency#DEFAULT_STRINGENCY},* no path wrapper, and {@link htsjdk.samtools.DefaultSAMRecordFactory}.*/public static SamReaderFactory make() {return new SamReaderFactoryImpl(EnumSet.noneOf(Option.class), ValidationStringency.DEFAULT_STRINGENCY,DefaultSAMRecordFactory.getInstance(), BlockGunzipper.getDefaultInflaterFactory());}private static class SamReaderFactoryImpl extends SamReaderFactory {private final static Log LOG = Log.getInstance(SamReaderFactory.class);private final EnumSet<Option> enabledOptions;private ValidationStringency validationStringency;private boolean asynchronousIO = Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS;private SAMRecordFactory samRecordFactory;private CustomReaderFactory customReaderFactory;private CRAMReferenceSource referenceSource;private InflaterFactory inflaterFactory;private SamReaderFactoryImpl(final EnumSet<Option> enabledOptions, final ValidationStringency validationStringency, final SAMRecordFactory samRecordFactory, final InflaterFactory inflaterFactory) {this.enabledOptions = EnumSet.copyOf(enabledOptions);this.samRecordFactory = samRecordFactory;this.validationStringency = validationStringency;this.customReaderFactory = CustomReaderFactory.getInstance();this.inflaterFactory = inflaterFactory;}@Overridepublic SamReader open(final File file) {final SamInputResource r = SamInputResource.of(file);final File indexMaybe = SamFiles.findIndex(file);if (indexMaybe != null) r.index(indexMaybe);return open(r);}@Overridepublic ValidationStringency validationStringency() {return validationStringency;}@Overridepublic CRAMReferenceSource referenceSource() {return referenceSource;}@Overridepublic SamReaderFactory samRecordFactory(final SAMRecordFactory samRecordFactory) {this.samRecordFactory = samRecordFactory;return this;}@Overridepublic SamReaderFactory inflaterFactory(final InflaterFactory inflaterFactory) {this.inflaterFactory = inflaterFactory;return this;}@Overridepublic SamReaderFactory enable(final Option... options) {Collections.addAll(this.enabledOptions, options);return this;}@Overridepublic SamReaderFactory disable(final Option... options) {for (final Option option : options) {this.enabledOptions.remove(option);}return this;}@Overridepublic SamReaderFactory setOption(final Option option, final boolean value) {if (value) {return enable(option);} else {return disable(option);}}@Overridepublic SamReaderFactory referenceSequence(final File referenceSequence) {this.referenceSource = new ReferenceSource(referenceSequence);return this;}@Overridepublic SamReaderFactory referenceSequence(final Path referenceSequence) {this.referenceSource = new ReferenceSource(referenceSequence);return this;}@Overridepublic SamReaderFactory referenceSource(final CRAMReferenceSource referenceSource) {this.referenceSource = referenceSource;return this;}@Overridepublic SAMFileHeader getFileHeader(final File samFile) {final SamReader reader = open(samFile);final SAMFileHeader header = reader.getFileHeader();CloserUtil.close(reader);return header;}@Overridepublic SAMFileHeader getFileHeader(final Path samFile) {final SamReader reader = open(samFile);final SAMFileHeader header = reader.getFileHeader();CloserUtil.close(reader);return header;}@Overridepublic void reapplyOptions(final SamReader reader) {for (final Option option : enabledOptions) {option.applyTo((SamReader.PrimitiveSamReaderToSamReaderAdapter) reader);}}@Overridepublic SamReaderFactory validationStringency(final ValidationStringency validationStringency) {this.validationStringency = validationStringency;return this;}@Overridepublic SamReaderFactory setUseAsyncIo(final boolean asynchronousIO){this.asynchronousIO = asynchronousIO;return this;}@Overridepublic SamReader open(final SamInputResource resource) {final SamReader.PrimitiveSamReader primitiveSamReader;try {final InputResource data = resource.data();final InputResource indexMaybe = resource.indexMaybe();final boolean indexDefined = indexMaybe != null;final InputResource.Type type = data.type();if (type == InputResource.Type.URL) {SamReader reader = customReaderFactory.maybeOpen(data.asUrl());if (reader != null) {return reader;}}if (type == InputResource.Type.HTSGET) {primitiveSamReader = HtsgetBAMFileReader.fromHtsgetURI((HtsgetInputResource) data,false,this.validationStringency,this.samRecordFactory,this.asynchronousIO,this.inflaterFactory);} else if (type == InputResource.Type.SEEKABLE_STREAM || type == InputResource.Type.URL) {if (SamStreams.sourceLikeBam(data.asUnbufferedSeekableStream())) {final SeekableStream bufferedIndexStream;if (indexDefined && indexMaybe.asUnbufferedSeekableStream() != null) {bufferedIndexStream = IOUtil.maybeBufferedSeekableStream(indexMaybe.asUnbufferedSeekableStream());} else {// TODO: Throw an exception here? An index _may_ have been provided, but we're ignoring itbufferedIndexStream = null;}primitiveSamReader = new BAMFileReader(IOUtil.maybeBufferedSeekableStream(data.asUnbufferedSeekableStream()),bufferedIndexStream,false,asynchronousIO,validationStringency,this.samRecordFactory,this.inflaterFactory);} else if (SamStreams.sourceLikeCram(data.asUnbufferedSeekableStream())) {if (referenceSource == null) {referenceSource = ReferenceSource.getDefaultCRAMReferenceSource();}SeekableStream bufferedIndexStream = indexDefined ?IOUtil.maybeBufferedSeekableStream(indexMaybe.asUnbufferedSeekableStream()) :null;primitiveSamReader = new CRAMFileReader(IOUtil.maybeBufferedSeekableStream(data.asUnbufferedSeekableStream()),bufferedIndexStream, referenceSource, validationStringency);} else {// assume its a SAM file/no indexLOG.warn("Unable to detect file format from input URL or stream, assuming SAM format.");primitiveSamReader = new SAMTextReader(IOUtil.toBufferedStream(data.asUnbufferedInputStream()),validationStringency, this.samRecordFactory);}} else if (type == InputResource.Type.SRA_ACCESSION) {primitiveSamReader = new SRAFileReader(data.asSRAAccession());} else {InputStream bufferedStream =IOUtil.maybeBufferInputStream(data.asUnbufferedInputStream(),Math.max(Defaults.BUFFER_SIZE, BlockCompressedStreamConstants.MAX_COMPRESSED_BLOCK_SIZE));File sourceFile = data.asFile();// calling asFile is safe even if indexMaybe is a Google Cloud Storage bucket// (in that case we just get null)final File indexFile = indexMaybe == null ? null : indexMaybe.asFile();if (SamStreams.isBAMFile(bufferedStream)) {if (sourceFile == null || !sourceFile.isFile()) {// check whether we can seekfinal SeekableStream indexSeekable = indexMaybe == null ? null : indexMaybe.asUnbufferedSeekableStream();// do not close bufferedStream, it's the same stream we're getting here.SeekableStream sourceSeekable = data.asUnbufferedSeekableStream();if (null == sourceSeekable || null == indexSeekable) {// not seekable.// it's OK that we consumed a bit of the stream already, this ctor expects it.primitiveSamReader = new BAMFileReader(bufferedStream, indexFile, false, asynchronousIO,validationStringency, this.samRecordFactory, this.inflaterFactory);} else {// seekable.// need to return to the beginning because it's the same stream we used earlier// and read a bit from, and that form of the ctor expects the stream to start at 0.sourceSeekable.seek(0);primitiveSamReader = new BAMFileReader(sourceSeekable, indexSeekable, false, asynchronousIO, validationStringency,this.samRecordFactory, this.inflaterFactory);}} else {bufferedStream.close();primitiveSamReader = new BAMFileReader(sourceFile, indexFile, false, asynchronousIO,validationStringency, this.samRecordFactory, this.inflaterFactory);}} else if (BlockCompressedInputStream.isValidFile(bufferedStream)) {primitiveSamReader = new SAMTextReader(new BlockCompressedInputStream(bufferedStream), validationStringency, this.samRecordFactory);} else if (IOUtil.isGZIPInputStream(bufferedStream)) {primitiveSamReader = new SAMTextReader(new GZIPInputStream(bufferedStream), validationStringency, this.samRecordFactory);} else if (SamStreams.isCRAMFile(bufferedStream)) {if (referenceSource == null) {referenceSource = ReferenceSource.getDefaultCRAMReferenceSource();}if (sourceFile == null || !sourceFile.isFile()) {final SeekableStream indexSeekableStream =indexMaybe == null ?null :indexMaybe.asUnbufferedSeekableStream();final SeekableStream sourceSeekableStream = data.asUnbufferedSeekableStream();if (null == sourceSeekableStream || null == indexSeekableStream) {primitiveSamReader = new CRAMFileReader(bufferedStream, indexFile, referenceSource, validationStringency);} else {sourceSeekableStream.seek(0);primitiveSamReader = new CRAMFileReader(sourceSeekableStream, indexSeekableStream, referenceSource, validationStringency);}} else {bufferedStream.close();primitiveSamReader = new CRAMFileReader(sourceFile, indexFile, referenceSource, validationStringency);}} else if (sourceFile != null && isSra(sourceFile)) {if (bufferedStream != null) {bufferedStream.close();}primitiveSamReader = new SRAFileReader(new SRAAccession(sourceFile.getPath()));} else {if (indexDefined) {bufferedStream.close();throw new RuntimeException("Cannot use index file with textual SAM file");}primitiveSamReader = new SAMTextReader(bufferedStream, sourceFile, validationStringency, this.samRecordFactory);}}// Apply the options defined by this factory to this readerfinal SamReader.PrimitiveSamReaderToSamReaderAdapter reader =new SamReader.PrimitiveSamReaderToSamReaderAdapter(primitiveSamReader, resource);for (final Option option : enabledOptions) {option.applyTo(reader);}return reader;} catch (final IOException | URISyntaxException e) {throw new RuntimeIOException(e);}}/** Attempts to detect whether the file is an SRA accessioned file. If SRA support is not available, returns false. */private boolean isSra(final File sourceFile) {try {// if SRA fails to initialize (the most common reason is a failure to find/load native libraries),// it will throw a subclass of java.lang.Error and here we only catch subclasses of java.lang.Exception//// Note: SRA initialization errors should not be ignored, but rather shown to userreturn SRAAccession.isValid(sourceFile.getPath());} catch (final Exception e) {return false;}}public static SamReaderFactory copyOf(final SamReaderFactoryImpl target) {return new SamReaderFactoryImpl(target.enabledOptions, target.validationStringency, target.samRecordFactory, target.inflaterFactory);}}/** A collection of binary {@link SamReaderFactory} options. */public enum Option {/*** The factory's {@link SamReader}s will produce populated (non-null) values when calling {@link SAMRecord#getFileSource()}.* <p/>* This option increases memory footprint slightly per {@link htsjdk.samtools.SAMRecord}.*/INCLUDE_SOURCE_IN_RECORDS {@Overridevoid applyTo(final BAMFileReader underlyingReader, final SamReader reader) {underlyingReader.enableFileSource(reader, true);}@Overridevoid applyTo(final SAMTextReader underlyingReader, final SamReader reader) {underlyingReader.enableFileSource(reader, true);}@Overridevoid applyTo(final CRAMFileReader underlyingReader, final SamReader reader) {underlyingReader.enableFileSource(reader, true);}@Overridevoid applyTo(final SRAFileReader underlyingReader, final SamReader reader) {underlyingReader.enableFileSource(reader, true);}@Overridevoid applyTo(final HtsgetBAMFileReader underlyingReader, final SamReader reader) {underlyingReader.enableFileSource(reader, true);}},/*** The factory's {@link SamReader}s' {@link SamReader#indexing()}'s calls to {@link SamReader.Indexing#getIndex()} will produce* {@link BAMIndex}es that do some caching in memory instead of reading the index from the disk for each query operation.** @see SamReader#indexing()* @see htsjdk.samtools.SamReader.Indexing#getIndex()*/CACHE_FILE_BASED_INDEXES {@Overridevoid applyTo(final BAMFileReader underlyingReader, final SamReader reader) {underlyingReader.enableIndexCaching(true);}@Overridevoid applyTo(final SAMTextReader underlyingReader, final SamReader reader) {logDebugIgnoringOption(reader, this);}@Overridevoid applyTo(final CRAMFileReader underlyingReader, final SamReader reader) {underlyingReader.enableIndexCaching(true);}@Overridevoid applyTo(final SRAFileReader underlyingReader, final SamReader reader) {underlyingReader.enableIndexCaching(true);}@Overridevoid applyTo(final HtsgetBAMFileReader underlyingReader, final SamReader reader) {logDebugIgnoringOption(reader, this);}},/*** The factory's {@link SamReader}s' will not use memory mapping for accessing index files (which is used by default). This is* slower but more scalable when accessing large numbers of BAM files sequentially.** @see SamReader#indexing()* @see htsjdk.samtools.SamReader.Indexing#getIndex()*/DONT_MEMORY_MAP_INDEX {@Overridevoid applyTo(final BAMFileReader underlyingReader, final SamReader reader) {underlyingReader.enableIndexMemoryMapping(false);}@Overridevoid applyTo(final SAMTextReader underlyingReader, final SamReader reader) {logDebugIgnoringOption(reader, this);}@Overridevoid applyTo(final CRAMFileReader underlyingReader, final SamReader reader) {underlyingReader.enableIndexMemoryMapping(false);}@Overridevoid applyTo(final SRAFileReader underlyingReader, final SamReader reader) {underlyingReader.enableIndexMemoryMapping(false);}@Overridevoid applyTo(final HtsgetBAMFileReader underlyingReader, final SamReader reader) {logDebugIgnoringOption(reader, this);}},/*** Eagerly decode {@link htsjdk.samtools.SamReader}'s {@link htsjdk.samtools.SAMRecord}s, which can reduce memory footprint if many* fields are being read per record, or if fields are going to be updated.*/EAGERLY_DECODE {@Overridevoid applyTo(final BAMFileReader underlyingReader, final SamReader reader) {underlyingReader.setEagerDecode(true);}@Overridevoid applyTo(final SAMTextReader underlyingReader, final SamReader reader) {logDebugIgnoringOption(reader, this);}@Overridevoid applyTo(final CRAMFileReader underlyingReader, final SamReader reader) {logDebugIgnoringOption(reader, this);}@Overridevoid applyTo(final SRAFileReader underlyingReader, final SamReader reader) {logDebugIgnoringOption(reader, this);}@Overridevoid applyTo(final HtsgetBAMFileReader underlyingReader, final SamReader reader) {underlyingReader.setEagerDecode(true);}},/*** For {@link htsjdk.samtools.SamReader}s backed by block-compressed streams, enable CRC validation of those streams. This is an* expensive operation, but serves to ensure validity of the stream.*/VALIDATE_CRC_CHECKSUMS {@Overridevoid applyTo(final BAMFileReader underlyingReader, final SamReader reader) {underlyingReader.enableCrcChecking(true);}@Overridevoid applyTo(final SAMTextReader underlyingReader, final SamReader reader) {logDebugIgnoringOption(reader, this);}@Overridevoid applyTo(final CRAMFileReader underlyingReader, final SamReader reader) {logDebugIgnoringOption(reader, this);}@Overridevoid applyTo(final SRAFileReader underlyingReader, final SamReader reader) {logDebugIgnoringOption(reader, this);}@Overridevoid applyTo(final HtsgetBAMFileReader underlyingReader, final SamReader reader) {underlyingReader.enableCrcChecking(true);}};public static final EnumSet<Option> DEFAULTS = EnumSet.noneOf(Option.class);/** Applies this option to the provided reader, if applicable. */void applyTo(final SamReader.PrimitiveSamReaderToSamReaderAdapter reader) {final SamReader.PrimitiveSamReader underlyingReader = reader.underlyingReader();if (underlyingReader instanceof BAMFileReader) {applyTo((BAMFileReader) underlyingReader, reader);} else if (underlyingReader instanceof SAMTextReader) {applyTo((SAMTextReader) underlyingReader, reader);} else if (underlyingReader instanceof CRAMFileReader) {applyTo((CRAMFileReader) underlyingReader, reader);} else if (underlyingReader instanceof SRAFileReader) {applyTo((SRAFileReader) underlyingReader, reader);} else if (underlyingReader instanceof HtsgetBAMFileReader) {applyTo((HtsgetBAMFileReader) underlyingReader, reader);} else {throw new IllegalArgumentException(String.format("Unrecognized reader type: %s.", underlyingReader.getClass()));}}private static void logDebugIgnoringOption(final SamReader r, final Option option) {LOG.debug(String.format("Ignoring %s option; does not apply to %s readers.", option, r.getClass().getSimpleName()));}private final static Log LOG = Log.getInstance(Option.class);abstract void applyTo(final BAMFileReader underlyingReader, final SamReader reader);abstract void applyTo(final SAMTextReader underlyingReader, final SamReader reader);abstract void applyTo(final CRAMFileReader underlyingReader, final SamReader reader);abstract void applyTo(final SRAFileReader underlyingReader, final SamReader reader);abstract void applyTo(final HtsgetBAMFileReader underlyingReader, final SamReader reader);}
}
)
