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