htsjdk库FeatureCodec和Feature接口介绍

在 HTSJDK 库中，FeatureCodec 接口和 Feature 接口分别扮演不同的角色，用于处理基因组数据的不同方面。下面是这两个接口的区别和各自的功能：

FeatureCodec 接口

主要功能

• 编码和解码：FeatureCodec 接口的主要职责是定义如何将数据从文件格式解码为 Java 对象（即 Feature 对象），以及如何将 Feature 对象编码回文件格式。它提供了与数据存储和读取相关的操作。
• 支持多种格式：FeatureCodec 可以支持多种格式的数据文件，如 VCF、BED、GTF 等。实现类通常需要定义如何处理特定格式的数据。
• 格式识别：通过 canDecode 方法，FeatureCodec 可以检查它是否支持解码特定格式的文件。

实现类/接口

源码：

/*
 * Copyright (c) 2007-2010 by The Broad Institute, Inc. and the Massachusetts Institute of Technology.
 * All Rights Reserved.
 *
 * This software is licensed under the terms of the GNU Lesser General Public License (LGPL), Version 2.1 which
 * is available at http://www.opensource.org/licenses/lgpl-2.1.php.
 *
 * THE SOFTWARE IS PROVIDED "AS IS." THE BROAD AND MIT MAKE NO REPRESENTATIONS OR WARRANTIES OF
 * ANY KIND CONCERNING THE SOFTWARE, EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTIES
 * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT
 * OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE.  IN NO EVENT SHALL THE BROAD OR MIT, OR THEIR
 * RESPECTIVE TRUSTEES, DIRECTORS, OFFICERS, EMPLOYEES, AND AFFILIATES BE LIABLE FOR ANY DAMAGES OF
 * ANY KIND, INCLUDING, WITHOUT LIMITATION, INCIDENTAL OR CONSEQUENTIAL DAMAGES, ECONOMIC
 * DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER THE BROAD OR MIT SHALL
 * BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF THE
 * FOREGOING.
 */

package htsjdk.tribble;

import htsjdk.io.IOPath;
import htsjdk.samtools.util.LocationAware;
import htsjdk.tribble.index.tabix.TabixFormat;

import java.io.IOException;
import java.io.InputStream;

/**
 * The base interface for classes that read in features.
 * <p/>
 * FeatureCodecs must implement several key methods:
 * <p/>
 * <ul>
 * <li>{@link #makeSourceFromStream} Return a {@link SOURCE} for this {@link FeatureCodec} given an input stream that is buffered.
 * <li>{@link #makeIndexableSourceFromStream} Return a {@link SOURCE} for this {@link FeatureCodec} that implements {@link LocationAware},
 * and is thus suitable for use during indexing. During the indexing process, the indexer passes the {@link SOURCE} to the codec
 * to consume Features from the underlying