htsjdk库ReferenceSequenceFileFactory类介绍

ReferenceSequenceFileFactory 是 HTSJDK 库中的一个工厂类，用于创建 ReferenceSequenceFile 实例。它提供了一种方便的方式来读取和处理参考基因组文件，而不需要直接处理文件的具体格式。

ReferenceSequenceFileFactory 类主要功能

• 创建 ReferenceSequenceFile 实例：

  • 提供静态方法来创建实现了 ReferenceSequenceFile 接口的对象。具体的实现类取决于文件的格式，如 FASTA 文件的实现类 FastaSequenceFile。

• 支持多种格式：

  • 根据文件的后缀名和文件内容，ReferenceSequenceFileFactory 可以自动选择合适的 ReferenceSequenceFile 实现类（例如 FASTA 格式）。

源码：

/*
 * The MIT License
 *
 * Copyright (c) 2009 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.reference;

import htsjdk.samtools.SAMException;
import htsjdk.samtools.util.BlockCompressedInputStream;
import htsjdk.samtools.util.GZIIndex;
import htsjdk.samtools.SAMFileHeader;
import htsjdk.samtools.SAMSequenceDictionary;
import htsjdk.samtools.SAMTextHeaderCodec;
import htsjdk.samtools.seekablestream.SeekableStream;
import htsjdk.samtools.util.BufferedLineReader;
import htsjdk.samtools.util.FileExtensions;
import htsjdk.samtools.util.IOUtil;

import java.io.BufferedInputStream;
import java.io.File;
import java.io.FileNotFoundException;
import java.io.IOException;
import java.io.InputStream;
import java.nio.file.Files;
import java.nio.file.Path