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Hellbender

The (eventually public) parts of the next generation of GATK/Picard/Prometheus methods engine and tools.

To build, run gradle install (gradle 2.2.1 recommended).

To run the main program, run build/install/hellbender/bin/hellbender.

To run all tests, run gradle test. Report is in build/reports/tests/index.html.

To run a single test class, run something like this, gradle test -Dtest.single=ReadUtilsUnitTest.

To run tests and compute coverage reports, run gradle jacocoTestReport. The report is then in build/reports/jacoco/test/html/index.html.

General guidelines for Hellbender developers

  • Do not put private or restricted data into the repo.

  • Try to keep datafiles under 100kb in size.

  • Untested code is considered non-existent and thus is subject to removal at any time (exception is main methods, or super corner conditions, or toString() code). New code without tests should not be accepted as pull requests.

  • Do use Java 8 features liberally, in particular streams, functional programming etc.

  • Don't override clone() unless you really know what you're doing. If you do override it, document thoroughly.

  • Don't override or call finalize() even when you think you know what you're doing.

  • Don't use toString() for anything other than human consumption (ie. don't base your code on it.)

  • When in doubt, follow the Google Java Style guide: http://google-styleguide.googlecode.com/svn/trunk/javaguide.html

  • Don't accept pull requests that introduce warnings. Warnings need to be addressed or supressed.

  • Don't accept pull requests that significantly decrease coverage (less than 1% decrease is sort of tolerable).

Creating a Hellbender project in the IntelliJ IDE:

  • Ensure that you have gradle and the Java 8 JDK installed

  • Clone the Hellbender repository using git

  • In IntelliJ, go to File -> "Import Project"

  • Select the root directory of your Hellbender clone, then "Ok"

  • Select "Import project from external model", then "Gradle", then "Next"

  • Ensure that "Gradle project" points to the build.gradle file in the root of your Hellbender clone

  • Select "Use local gradle distribution", and enter your Gradle home directory in the "Gradle home" box. This will be the directory that contains the bin directory where the actual gradle executable (not merely a symlink to it!) lives. For example, if the actual gradle executable is /usr/local/Cellar/gradle/2.2.1/libexec/bin/gradle, you would enter /usr/local/Cellar/gradle/2.2.1/libexec/ as your gradle home directory.

  • Click "Finish"

  • After downloading project dependencies, IntelliJ should open a new window with your Hellbender project

  • In File -> "Project Structure" -> "Project", set the "Project SDK" to your Java 1.8 JDK, and "Project language level" to 8 (you may need to add your Java 8 JDK under "Platform Settings" -> SDKs if it isn't there already). Then click "Apply"/"Ok".

Setting up debugging in IntelliJ

  • Follow the instructions above for creating an IntelliJ project for Hellbender

  • Go to Run -> "Edit Configurations", then click "+" and add a new "Application" configuration

  • Set the name of the new configuration to something like "Hellbender debug"

  • For "Main class", enter org.broadinstitute.hellbender.Main

  • Ensure that "Use classpath of module:" is set to use the "hellbender" module's classpath

  • Enter the Hellbender arguments for the command you want to debug in "Program Arguments"

  • Click "Apply"/"Ok"

  • Set breakpoints, etc., as desired, then select "Run" -> "Debug" -> "Hellbender debug" to start your debugging session

  • In future debugging sessions, you can simply adjust the "Program Arguments" in the "Hellbender debug" configuration as needed

Updating the Intellij project when dependencies change

If there are dependency changes in build.gradle it is necessary to refresh the gradle project. This is easily done with the following steps.

  • Open the gradle tool window ( "View" -> "Tool Windows" -> "Gradle" )
  • Click the refresh button in the Gradle tool window. It is in the top left of the gradle view and is represented by two blue arrows.