From GSA

GATK Coding Standards

The Genome Analysis Toolkit generally follows java coding standards and good practices, which can be viewed at Sun's site.

The full coding standard that is used internally by the group when developing in the GATK is available as a PDF, located here, which details some of the finer points as well as an extensive 'good practices' overview.

Overview

A quick overview of the coding standards is as follows:

Function names

use uppercase words, with the first word lowercase, i.e. diffTwoFiles

Package names

lowercase, with specific functional encapsulation for each class.

Variable names

uppercase words, with the first word lowercase.

Class names

uppercase words representing a noun.

Interface names

the same as class names, no 'i' before the name.

Tab length

4 spaces, represented as spaces instead of a tab character.