GATK FeatureInput类介绍

FeatureInput 类是 GATK（Genome Analysis Toolkit）中的一个重要组件，用于处理和管理额外的功能数据（例如变异注释或其它遗传信息），以便在基因组数据分析过程中提供更多的上下文信息。以下是 FeatureInput 类的一些关键点：

目的和功能:

• FeatureInput 主要用于传递外部功能数据（如变异注释、基因组特征等）给 GATK 工具进行处理。
• 它允许在分析中整合额外的注释信息，以增强变异调用的准确性或提供更多的生物学上下文。

使用场景:

• • 在变异调用过程中，FeatureInput 可以用于加载与变异相关的注释数据（例如基因组特征、已知的变异位点等）。
  • 可以用来指定额外的 VCF 文件、BED 文件、GFF 文件等，这些文件提供了对变异位点的更多注释信息。

源码：

package org.broadinstitute.hellbender.engine;

import com.google.common.annotations.VisibleForTesting;
import htsjdk.tribble.Feature;
import htsjdk.tribble.FeatureCodec;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.broadinstitute.hellbender.utils.Utils;
import org.broadinstitute.hellbender.utils.io.IOUtils;

import java.io.Serializable;
import java.util.*;

/**
 * Class to represent a Feature-containing input file. Tools should declare @Argument-annotated fields of
 * this type (or Collections of this type), and the Feature management system will automatically discover
 * them at runtime (provided that they are declared in the tool itself, a superclass of the tool, or an
 * ArgumentCollection of the tool).
 *
 * DO NOT ATTEMPT TO INSTANTIATE THIS CLASS DIRECTLY! FeatureInputs must be instantiated by the argument-parsing
 * system only in order to be recognized by the Feature management system. This is why the constructor is
 * marked as protected.
 *
 * If you still want to instantiate this class directly, you will have to call {@link GATKTool#addFeatureInputsAfterInitialization(String, String, Class, int)}
 *  in order to register the FeatureInput with the engine.
 *
 * FeatureInputs can be assigned logical names on the command line using the syntax:
 *
 *     --argument_name:logical_name f