April 2022
Beginner to intermediate
486 pages
10h 22m
Chinese
Content preview from 云端基因组学
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128
｜
第
5
章
上述命令中的
java
激活你机器上的
Java
系统，创建一台
Java
虚拟机（
JVM
）。
JVM
是一个虚拟环境，你的程序就在里面运行。我们接着往后看，参数
-jar
指
定
JAR
文件；
JAR
代表
Java ARchive
，它是一组用
ZIP
工具打包为单个文件的
Java
代
码。上述命令的最后是程序运行所需参数。
然而，自
4.0
版本起，
GATK
团队提供一个
Python
封装脚本，以简化
GATK
命令的
编写方式。你用
GATK
命令行编写命令，无需考虑
Java
句法。封装脚本负责调用合
适的
JAR
文件，并设置某些你原本可能要手动指定的参数。
因此，我们不用上述句法运行
GATK
命令，而用以下基本句法：
$ gatk ToolName [tool arguments]
其中，
ToolName
是你想运行的工具名，例如，种系短变异发现工具
Haplotype
Caller
。工具名这个参数对位置敏感，即它必须是提供给
GATK
命令的所有参数中
的第一个。该参数之后，其他内容通常对位置不敏感，但有几个例外：一些工具的
参数成对出现需放在一起，
Spark
相关参数（稍后讲）总是放在最后。工具名和参
数对大小写敏感。
在某些情况下，你也许得为
JVM
指定参数，例如它在你系统所能占用的最大内存。
普通
Java
命令，
JVM
参数放在
java
和
-jar
之间，例如：
$ java -Xmx4G -XX:+PrintGCDetails -jar program.jar [program arguments]
在
GATK
命令中，你可通过一个新参数
--java-options ...
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O’Reilly covers everything we've got, with content to help us build a world-class technology community, upgrade the capabilities and competencies of our teams, and improve overall team performance as well as their engagement.Julian F.
I wanted to learn C and C++, but it didn't click for me until I picked up an O'Reilly book. When I went on the O’Reilly platform, I was astonished to find all the books there, plus live events and sandboxes so you could play around with the technology.Addison B.
I’ve been on the O’Reilly platform for more than eight years. I use a couple of learning platforms, but I'm on O'Reilly more than anybody else. When you're there, you start learning. I'm never disappointed.Amir M.
I'm always learning. So when I got on to O'Reilly, I was like a kid in a candy store. There are playlists. There are answers. There's on-demand training. It's worth its weight in gold, in terms of what it allows me to do.