GATK GATKPath类介绍

GATKPath类是GATK（基因组分析工具包）中的一个专门类，它扩展了HtsPath并实现了TaggedArgument。它提供了一种处理文件路径的方法，这些路径可以位于不同的存储系统上，如本地文件系统、谷歌云存储（GCS）或Hadoop分布式文件系统（HDFS）。此外，它还支持对命令行参数进行标记。

Key Components of GATKPath Class

1. Fields and Constants:

   • HDFS_SCHEME: A constant for identifying HDFS URLs.
   • tagName: Holds the tag name for the path.
   • tagAttributes: A map of attributes associated with the tag.

2. Constructors:

   • GATKPath(String uriString): Initializes with a URI string.
   • GATKPath(GATKPath sourceGATKPath): Copies an existing GATKPath and propagates its tag and attributes.

3. Methods:

   • toPath(): Converts the GATKPath to a Path object. Handles GCS paths specially by using BucketUtils.getPathOnGcs() and falls back to using FileSystems if the path is not found.
   • getInputStream(): Returns an InputStream for reading from the path. Handles different schemes like HDFS and local file systems.
   • getOutputStream(): Returns an OutputStream for writing to the path. Supports HDFS and local file systems.
   • isHadoopURL(): Checks if the path uses the HDFS scheme.
   • setTag(String tagName): Sets the tag name.
   • getTag(): Gets the tag name.
   • setTagAttributes(Map<String, String> attributes): Sets the tag attributes.
   • getTagAttributes(): Gets the tag attributes.
   • toString(): Returns a string representation of the path including any tags and attributes.
   • equals(Ob