Please see the GATK website, where you can download a precompiled executable, read documentation, ask questions, and receive technical support.
This repository contains the next generation of the Genome Analysis Toolkit (GATK). The contents of this repository are 100% open source and released under the BSD 3-Clause license (see LICENSE.TXT).
GATK4 aims to bring together well-established tools from the GATK and Picard codebases under a streamlined framework, and to enable selected tools to be run in a massively parallel way on local clusters or in the cloud using Apache Spark. It also contains many newly developed tools not present in earlier releases of the toolkit.
- Requirements
- Quick Start Guide
- Downloading GATK4
- Building GATK4
- Running GATK4
- For GATK Developers
- General guidelines for GATK4 developers
- Testing GATK4
- Using Git LFS to download and track large test data
- Creating a GATK project in the IntelliJ IDE
- Setting up debugging in IntelliJ
- Updating the Intellij project when dependencies change
- Setting up profiling using JProfiler
- Uploading Archives to Sonatype
- Building GATK4 Docker images
- Releasing GATK4
- Generating GATK4 documentation
- Using Zenhub to track github issues
- Further Reading on Spark
- How to contribute to GATK
- Discussions
- Authors
- License
- Java 8
- Git 2.5 or greater
- Optional, but recommended:
- Gradle 3.1 or greater, needed for building the GATK. We recommend using the
./gradlew
script which will download and use an appropriate gradle version automatically (see examples below). - Python 2.6 or greater (needed for running the
gatk
frontend script) - Python 3.6.2, along with a set of additional Python packages, are required to run some tools and workflows.
GATK uses the Conda package manager to
establish and manage the environment and dependencies required by these tools. The GATK Docker image comes
with this environment pre-configured. In order to establish an environment suitable to run these tools
outside of the Docker image, the conda gatkcondaenv.yml
file is provided. To establish the conda environment locally, Conda must first
be installed. Then, create the gatk environment by running the command
conda env -n gatk -f gatkcondaenv.yml
. To activate the environment once it has been created, run the commandsource activate gatk
. See the Conda documentation for additional information about using and managing Conda environments. - R 3.2.5 (needed for producing plots in certain tools, and for running the test suite)
- git-lfs 1.1.0 or greater (needed to download large files for the complete test suite).
Run
git lfs install
after downloading, followed bygit lfs pull
from the root of your git clone to download the large files. The download is several hundred megabytes.
- Gradle 3.1 or greater, needed for building the GATK. We recommend using the
- Alternatively, pre-packaged images with all needed dependencies installed can be found on our dockerhub repository. This requires a recent version of the docker client, which can be found on the docker website.
- Build the GATK:
./gradlew bundle
(createsgatk-VERSION.zip
inbuild/
) - Get help on running the GATK:
./gatk --help
- Get a list of available tools:
./gatk --list
- Run a tool:
./gatk PrintReads -I src/test/resources/NA12878.chr17_69k_70k.dictFix.bam -O output.bam
- Get help on a particular tool:
./gatk PrintReads --help
You can download and run pre-built versions of GATK4 from the following places:
-
A zip archive with everything you need to run GATK4 can be downloaded for each release from the github releases page.
-
You can download a GATK4 docker image from our dockerhub repository. We also host unstable nightly development builds on this dockerhub repository.
- Within the docker image, run gatk commands as usual from the default startup directory (/gatk).
-
To do a full build of GATK4, run:
./gradlew bundle
Equivalently, you can just type:
./gradlew
- This creates a zip archive in the
build/
directory with a name likegatk-VERSION.zip
containing a complete standalone GATK distribution, including our launchergatk
, both the local and spark jars, and this README. - You can also run GATK commands directly from the root of your git clone after running this command.
- This creates a zip archive in the
-
Other ways to build:
./gradlew installDist
- Does a fast build that only lets you run GATK tools from inside your git clone, and locally only (not on a cluster). Good for developers!
./gradlew installAll
- Does a semi-fast build that only lets you run GATK tools from inside your git clone, but works both locally and on a cluster. Good for developers!
./gradlew localJar
- Builds only the GATK jar used for running tools locally (not on a Spark cluster). The resulting jar will be in
build/libs
with a name likegatk-package-VERSION-local.jar
, and can be used outside of your git clone.
- Builds only the GATK jar used for running tools locally (not on a Spark cluster). The resulting jar will be in
./gradlew sparkJar
- Builds only the GATK jar used for running tools on a Spark cluster (rather than locally). The resulting jar will be in
build/libs
with a name likegatk-package-VERSION-spark.jar
, and can be used outside of your git clone. - This jar will not include Spark and Hadoop libraries, in order to allow the versions of Spark and Hadoop installed on your cluster to be used.
- Builds only the GATK jar used for running tools on a Spark cluster (rather than locally). The resulting jar will be in
-
To remove previous builds, run:
./gradlew clean
-
For faster gradle operations, add
org.gradle.daemon=true
to your~/.gradle/gradle.properties
file. This will keep a gradle daemon running in the background and avoid the ~6s gradle start up time on every command. -
Gradle keeps a cache of dependencies used to build GATK. By default this goes in
~/.gradle
. If there is insufficient free space in your home directory, you can change the location of the cache by setting theGRADLE_USER_HOME
environment variable.
-
The standard way to run GATK4 tools is via the
gatk
wrapper script located in the root directory of a clone of this repository.- Requires Python 2.6 or greater (this includes Python 3.x)
- You need to have built the GATK as described in the Building GATK4 section above before running this script.
- There are several ways
gatk
can be run:- Directly from the root of your git clone after building
- By extracting the zip archive produced by
./gradlew bundle
to a directory, and runninggatk
from there - Manually putting the
gatk
script within the same directory as fully-packaged GATK jars produced by./gradlew localJar
and/or./gradlew sparkJar
- Defining the environment variables
GATK_LOCAL_JAR
andGATK_SPARK_JAR
, and setting them to the paths to the GATK jars produced by./gradlew localJar
and/or./gradlew sparkJar
gatk
can run non-Spark tools as well as Spark tools, and can run Spark tools locally, on a Spark cluster, or on Google Cloud Dataproc.- Note: running with
java -jar
directly and bypassinggatk
causes several important system properties to not get set, including htsjdk compression level!
-
For help on using
gatk
itself, run./gatk --help
-
To print a list of available tools, run
./gatk --list
.- Spark-based tools will have a name ending in
Spark
(eg.,BaseRecalibratorSpark
). Most other tools are non-Spark-based.
- Spark-based tools will have a name ending in
-
To print help for a particular tool, run
./gatk ToolName --help
. -
To run a non-Spark tool, or to run a Spark tool locally, the syntax is:
./gatk ToolName toolArguments
. -
Tool arguments that allow multiple values, such as -I, can be supplied on the command line using a file with the extension ".args". Each line of the file should contain a single value for the argument.
-
Examples:
./gatk PrintReads -I input.bam -O output.bam
./gatk PrintReadsSpark -I input.bam -O output.bam
-
To pass JVM arguments to GATK, run
gatk
with the--java-options
argument:./gatk --java-options "-Xmx4G" <rest of command> ./gatk --java-options "-Xmx4G -XX:+PrintGCDetails" <rest of command>
- Many GATK4 tools can read BAM or VCF inputs from a Google Cloud Storage bucket. Just use the "gs://" prefix:
./gatk PrintReads -I gs://mybucket/path/to/my.bam -L 1:10000-20000 -O output.bam
- Important: You must set up your credentials first for this to work! There are three options:
- Option (a): run in a Google Cloud Engine VM
- If you are running in a Google VM then your credentials are already in the VM and will be picked up by GATK, you don't need to do anything special.
- Option (b): use your own account
- Install Google Cloud SDK
- Log into your account:
gcloud auth application-default login
- Done! GATK will use the application-default credentials you set up there.
- Option (c): use a service account
- Create a new service account on the Google Cloud web page and download the JSON key file
- Install Google Cloud SDK
- Tell gcloud about the key file:
gcloud auth activate-service-account --key-file "$PATH_TO_THE_KEY_FILE"
- Set the
GOOGLE_APPLICATION_CREDENTIALS
environment variable to point to the file
export GOOGLE_APPLICATION_CREDENTIALS="$PATH_TO_THE_KEY_FILE"
- Done! GATK will pick up the service account. You can also do this in a VM if you'd like to override the default credentials.
- Option (a): run in a Google Cloud Engine VM
./gatk ToolName toolArguments -- --spark-runner SPARK --spark-master <master_url> additionalSparkArguments
-
Examples:
./gatk PrintReadsSpark -I hdfs://path/to/input.bam -O hdfs://path/to/output.bam \ -- \ --spark-runner SPARK --spark-master <master_url>
./gatk PrintReadsSpark -I hdfs://path/to/input.bam -O hdfs://path/to/output.bam \ -- \ --spark-runner SPARK --spark-master <master_url> \ --num-executors 5 --executor-cores 2 --executor-memory 4g \ --conf spark.yarn.executor.memoryOverhead=600
-
You can also omit the "--num-executors" argument to enable dynamic allocation if you configure the cluster properly (see the Spark website for instructions).
-
Note that the Spark-specific arguments are separated from the tool-specific arguments by a
--
. -
Running a Spark tool on a cluster requires Spark to have been installed from http://spark.apache.org/, since
gatk
invokes thespark-submit
tool behind-the-scenes. -
Note that the examples above use YARN but we have successfully run GATK4 on Mesos as well.
- You must have a Google cloud services account, and have spun up a Dataproc cluster in the Google Developer's console. You may need to have the "Allow API access to all Google Cloud services in the same project" option enabled (settable when you create a cluster).
- You need to have installed the Google Cloud SDK from here, since
gatk
invokes thegcloud
tool behind-the-scenes. As part of the installation, be sure that you follow thegcloud
setup instructions here. As this library is frequently updated by Google, we recommend updating your copy regularly to avoid any version-related difficulties. - Your inputs to the GATK when running on dataproc are typically in Google Cloud Storage buckets, and should be specified on
your GATK command line using the syntax
gs://my-gcs-bucket/path/to/my-file
- You can run GATK4 jobs on Dataproc from your local computer or from the VM (master node) on the cloud.
Once you're set up, you can run a Spark tool on your Dataproc cluster using a command of the form:
./gatk ToolName toolArguments -- --spark-runner GCS --cluster myGCSCluster additionalSparkArguments
-
Examples:
./gatk PrintReadsSpark \ -I gs://my-gcs-bucket/path/to/input.bam \ -O gs://my-gcs-bucket/path/to/output.bam \ -- \ --spark-runner GCS --cluster myGCSCluster
./gatk PrintReadsSpark \ -I gs://my-gcs-bucket/path/to/input.bam \ -O gs://my-gcs-bucket/path/to/output.bam \ -- \ --spark-runner GCS --cluster myGCSCluster \ --num-executors 5 --executor-cores 2 --executor-memory 4g \ --conf spark.yarn.executor.memoryOverhead=600
-
When using Dataproc you can access the web interfaces for YARN, Hadoop and HDFS. Follow these instructions to create an SSH tunnel and connect with your browser.
-
Note that the spark-specific arguments are separated from the tool-specific arguments by a
--
. -
If you want to avoid uploading the GATK jar to GCS on every run, set the
GATK_GCS_STAGING
environment variable to a bucket you have write access to (eg.,export GATK_GCS_STAGING=gs://<my_bucket>/
) -
Dataproc Spark clusters are configured with dynamic allocation so you can omit the "--num-executors" argument and let YARN handle it automatically.
- Note: Some GATK Spark tools by default require the reference file to be in 2bit format (notably
BaseRecalibratorSpark
,BQSRPipelineSpark
andReadsPipelineSpark
). You can convert your fasta to 2bit by using thefaToTwoBit
utility from UCSC - see also the documentation forfaToTwoBit
.
Certain GATK tools may optionally generate plots if R is installed. We recommend R v3.2.5 if you want to produce plots. If you are uninterested in plotting, R is still required by several of the unit tests. Plotting is currently untested and should be viewed as a convenience rather than a primary output.
R installation is not part of the gradle build. See http://cran.r-project.org/ for general information on installing R for your system.
- for ubuntu see these ubuntu specific instructions
- for OSX we recommend installation through homebrew
brew tap homebrew/science
brew install R
The plotting R scripts require certain R packages to be installed. You can install these by running scripts/docker/gatkbase/install_R_packages.R
. Either run it as superuser to force installation into the sites library or run interactively and create a local library.
sudo Rscript scripts/docker/gatkbase/install_R_packages.R
or
R
source("scripts/docker/gatkbase/install_R_packages.R")
-
A tab completion bootstrap file for the bash shell is now included in releases. This file allows the command-line shell to complete GATK run options in a manner equivalent to built-in command-line tools (e.g. grep).
-
This tab completion functionality has only been tested in the bash shell, and is released as a beta feature.
-
To enable tab completion for the GATK, open a terminal window and source the included tab completion script:
source gatk-completion.sh
-
Sourcing this file will allow you to press the tab key twice to get a list of options available to add to your current GATK command. By default you will have to source this file once in each command-line session, then for the rest of the session the GATK tab completion functionality will be available. GATK tab completion will be available in that current command-line session only.
-
Note that you must have already started typing an invocation of the GATK (using gatk) for tab completion to initiate:
./gatk <TAB><TAB>
- We recommend adding a line to your bash settings file (i.e. your ~/.bashrc file) that sources the tab completion script. To add this line to your bash settings / bashrc file you can use the following command:
echo "source <PATH_TO>/gatk-completion.sh" >> ~/.bashrc
- Where
<PATH_TO>
is the fully qualified path to thegatk-completion.sh
script.
-
Do not put private or restricted data into the repo.
-
Try to keep datafiles under 100kb in size. Larger test files should go into
src/test/resources/large
(and subdirectories) so that they'll be stored and tracked by git-lfs as described above. -
GATK4 is BSD licensed. The license is in the top level LICENSE.TXT file. Do not add any additional license text or accept files with a license included in them.
-
Each tool should have at least one good end-to-end integration test with a check for expected output, plus high-quality unit tests for all non-trivial utility methods/classes used by the tool. Although we have no specific coverage target, coverage should be extensive enough that if tests pass, the tool is guaranteed to be in a usable state.
-
All newly written code must have good test coverage (>90%).
-
All bug fixes must be accompanied by a regression test.
-
All pull requests must be reviewed before merging to master (even documentation changes).
-
Don't issue or accept pull requests that introduce warnings. Warnings must be addressed or suppressed.
-
Don't issue or accept pull requests that significantly decrease coverage (less than 1% decrease is sort of tolerable).
-
Don't use
toString()
for anything other than human consumption (ie. don't base the logic of your code on results oftoString()
.) -
Don't override
clone()
unless you really know what you're doing. If you do override it, document thoroughly. Otherwise, prefer other means of making copies of objects. -
For logging, use org.apache.logging.log4j.Logger
-
We mostly follow the Google Java Style guide
-
Git: Don't push directly to master - make a pull request instead.
-
Git: Rebase and squash commits when merging.
-
If you push to master or mess up the commit history, you owe us 1 growler or tasty snacks at happy hour. If you break the master build, you owe 3 growlers (or lots of tasty snacks). Beer may be replaced by wine (in the color and vintage of buyer's choosing) in proportions of 1 growler = 1 bottle.
-
Before running the test suite, be sure that you've installed
git lfs
and downloaded the large test data, following the git lfs setup instructions -
To run the test suite, run
./gradlew test
.- Test report is in
build/reports/tests/test/index.html
. - What will happen depends on the value of the
TEST_TYPE
environment variable:- unset or any other value : run non-cloud unit and integration tests, this is the default
cloud
,unit
,integration
,spark
: run only the cloud, unit, integration, or Spark testsall
: run the entire test suite
- Cloud tests require being logged into
gcloud
and authenticated with a project that has access to the cloud test data. They also require setting several certain environment variables.HELLBENDER_JSON_SERVICE_ACCOUNT_KEY
: path to a local JSON file with service account credentialsHELLBENDER_TEST_PROJECT
: your google cloud projectHELLBENDER_TEST_STAGING
: a gs:// path to a writable locationHELLBENDER_TEST_INPUTS
: path to cloud test data, ex: gs://hellbender/test/resources/
- Setting the environment variable
TEST_VERBOSITY=minimal
will produce much less output from the test suite
- Test report is in
-
To run a subset of tests, use gradle's test filtering (see gradle doc):
- You can use
test.single
when you just want to run a specific test class:./gradlew test -Dtest.single=SomeSpecificTestClass
- You can also use
--tests
with a wildcard to run a specific test class, method, or to select multiple test classes:./gradlew test --tests *SomeSpecificTestClass
./gradlew test --tests *SomeTest.someSpecificTestMethod
./gradlew test --tests all.in.specific.package*
- You can use
-
To run tests and compute coverage reports, run
./gradlew jacocoTestReport
. The report is then inbuild/reports/jacoco/test/html/index.html
. (IntelliJ has a good coverage tool that is preferable for development). -
We use Travis-CI as our continuous integration provider.
- Before merging any branch make sure that all required tests pass on travis.
- Every travis build will upload the test results to our GATK Google Cloud Storage bucket.
A link to the uploaded report will appear at the very bottom of the travis log.
Look for the line that says
See the test report at
. If TestNG itself crashes there will be no report generated.
-
We use Broad Jenkins for our long-running tests and performance tests.
- To add a performance test (requires Broad-ID), you need to make a "new item" in Jenkins and make it a "copy" instead of a blank project. You need to base it on either the "-spark-" jobs or the other kind of jobs and alter the commandline.
-
To output stack traces for
UserException
set the environment variableGATK_STACKTRACE_ON_USER_EXCEPTION=true
We use git-lfs to version and distribute test data that is too large to check into our repository directly. You must install and configure it in order to be able to run our test suite.
-
After installing git-lfs, run
git lfs install
- This adds hooks to your git configuration that will cause git-lfs files to be checked out for you automatically in the future.
-
To manually retrieve the large test data, run
git lfs pull
from the root of your GATK git clone.- The download is several hundred megabytes.
-
To add a new large file to be tracked by git-lfs, simply:
- Put the new file(s) in
src/test/resources/large
(or a subdirectory) git add
the file(s), thengit commit -a
- That's it! Do not run
git lfs track
on the files manually: all files insrc/test/resources/large
are tracked by git-lfs automatically.
- Put the new file(s) in
-
Ensure that you have
gradle
and the Java 8 JDK installed -
You may need to install the TestNG and Gradle plugins (in preferences)
-
Clone the GATK repository using git
-
In IntelliJ, click on "Import Project" in the home screen or go to File -> New... -> Project From Existing Sources...
-
Select the root directory of your GATK clone, then click on "OK"
-
Select "Import project from external model", then "Gradle", then click on "Next"
-
Ensure that "Gradle project" points to the build.gradle file in the root of your GATK clone
-
Select "Use auto-import" and "Use default gradle wrapper".
-
Make sure the Gradle JVM points to Java 1.8
-
Click "Finish"
-
After downloading project dependencies, IntelliJ should open a new window with your GATK project
-
Make sure that the Java version is set correctly by going to File -> "Project Structure" -> "Project". Check that the "Project SDK" is set 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".
-
Follow the instructions above for creating an IntelliJ project for GATK
-
Go to Run -> "Edit Configurations", then click "+" and add a new "Application" configuration
-
Set the name of the new configuration to something like "GATK debug"
-
For "Main class", enter
org.broadinstitute.hellbender.Main
-
Ensure that "Use classpath of module:" is set to use the "gatk" module's classpath
-
Enter the arguments for the command you want to debug in "Program Arguments"
-
Click "Apply"/"Ok"
-
Set breakpoints, etc., as desired, then select "Run" -> "Debug" -> "GATK debug" to start your debugging session
-
In future debugging sessions, you can simply adjust the "Program Arguments" in the "GATK debug" configuration as needed
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.
-
Running JProfiler standalone:
- Build a full GATK4 jar using
./gradlew localJar
- In the "Session Settings" window, select the GATK4 jar, eg.
~/gatk/build/libs/gatk-package-4.alpha-196-gb542813-SNAPSHOT-local.jar
for "Main class or executable JAR" and enter the right "Arguments" - Under "Profiling Settings", select "sampling" as the "Method call recording" method.
- Build a full GATK4 jar using
-
Running JProfiler from within IntelliJ:
- JProfiler has great integration with IntelliJ (we're using IntelliJ Ultimate edition) so the setup is trivial.
- Follow the instructions above for creating an IntelliJ project for GATK
- Right click on a test method/class/package and select "Profile"
To upload snapshots to Sonatype you'll need the following:
-
You must have a registered account on the sonatype JIRA (and be approved as a gatk uploader)
-
You need to configure several additional properties in your
/~.gradle/gradle.properties
file -
If you want to upload a release instead of a snapshot you will additionally need to have access to the gatk signing key and password
#needed for snapshot upload
sonatypeUsername=<your sonatype username>
sonatypePassword=<your sonatype password>
#needed for signing a release
signing.keyId=<gatk key id>
signing.password=<gatk key password>
signing.secretKeyRingFile=/Users/<username>/.gnupg/secring.gpg
To perform an upload, use
./gradlew uploadArchives
Currently all builds are considered snapshots. The archive name is based off of git describe
.
Please see the the Docker README in scripts/docker
. This has instructions for the Dockerfile in the root directory.
Please see the How to release GATK4 wiki article for instructions on releasing GATK4.
To generate GATK documentation, run ./gradlew gatkDoc
- Generated docs will be in the
build/docs/gatkdoc
directory.
We use Zenhub to organize and track github issues.
-
To add Zenhub to github, go to the Zenhub home page while logged in to github, and click "Add Zenhub to Github"
-
Zenhub allows the GATK development team to assign time estimates to issues, and to mark issues as Triaged/In Progress/In Review/Blocked/etc.
Apache Spark is a fast and general engine for large-scale data processing. GATK4 can run on any Spark cluster, such as an on-premise Hadoop cluster with HDFS storage and the Spark runtime, as well as on the cloud using Google Dataproc.
In a cluster scenario, your input and output files reside on HDFS, and Spark will run in a distributed fashion on the cluster. The Spark documentation has a good overview of the architecture.
Note that if you don't have a dedicated cluster you can run Spark in standalone mode on a single machine, which exercises the distributed code paths, albeit on a single node.
While your Spark job is running, the Spark UI is an excellent place to monitor the progress.
Additionally, if you're running tests, then by adding -Dgatk.spark.debug=true
you can run a single Spark test and
look at the Spark UI (on http://localhost:4040/) as it runs.
You can find more information about tuning Spark and choosing good values for important settings such as the number of executors and memory settings at the following:
- Tuning Spark
- How-to: Tune Your Apache Spark Jobs (Part 1)
- How-to: Tune Your Apache Spark Jobs (Part 2)
(Note: section inspired by, and some text copied from, Apache Parquet)
We welcome all contributions to the GATK project. The contribution can be a issue report or a pull request. If you're not a committer, you will need to make a fork of the gatk repository and issue a pull request from your fork.
To become a committer, you need to make several high-quality code contributions and be approved by the current committers.
For ideas on what to contribute, check issues labeled "Help wanted (Community)". Comment on the issue to indicate you're interested in contibuting code and for sharing your questions and ideas.
To contribute a patch:
- Break your work into small, single-purpose patches if possible. Itβs much harder to merge in a large change with a lot of disjoint features.
- Submit the patch as a GitHub pull request against the master branch. For a tutorial, see the GitHub guides on forking a repo and sending a pull request. If applicable, include the issue number in the pull request name.
- Make sure that your code passes all our tests. You can run the tests with
./gradlew test
in the root directory. - Add tests for all new code you've written. We prefer unit tests but high quality integration tests that use small amounts of data are acceptable.
- Follow the General guidelines for GATK4 developers.
We tend to do fairly close readings of pull requests, and you may get a lot of comments. Some things to consider:
- Write tests for all new code.
- Document all classes and public methods.
- For all public methods, check validity of the arguments and throw
IllegalArgumentException
if invalid. - Use braces for control constructs,
if
,for
etc. - Make classes, variables, parameters etc
final
unless there is a strong reason not to. - Give your operators some room. Not
a+b
buta + b
and notfoo(int a,int b)
butfoo(int a, int b)
. - Generally speaking, stick to the Google Java Style guide
Thank you for getting involved!
- GATK forum for general discussions on how to use the GATK and support questions.
- Issue tracker to report errors and enhancement ideas.
- Discussions also take place in GATK pull requests
The authors list is maintained in the AUTHORS file. See also the Contributors list at github.
Licensed under the BSD License. See the LICENSE.txt file.