Status of downstream projects automatically built on top of the current htsjdk master branch. See gatk-jenkins for detailed logs. Failure may indicate problems in htsjdk, but may also be due to expected incompatibilities between versions, or unrelated failures in downstream projects.
HTSJDK is an implementation of a unified Java library for accessing common file formats, such as SAM and VCF, used for high-throughput sequencing data. There are also an number of useful utilities for manipulating HTS data.
NOTE: HTSJDK does not currently support the latest Variant Call Format Specification (VCFv4.3 and BCFv2.2).
API documentation for all versions of HTSJDK since 1.128 are available through javadoc.io.
If you believe you have found a bug or have an issue with the library please a) search the open and recently closed issues to ensure it has not already been reported, then b) log an issue.
The project has a gitter chat room if you would like to chat with the developers and others involved in the project.
To receive announcements of releases and other significant project news please subscribe to the htsjdk-announce google group.
HTSJDK is now built using gradle.
A wrapper script (gradlew) is included which will download the appropriate version of gradle on the first invocation.
Example gradle usage from the htsjdk root directory:
- compile and build a jar
./gradlew
or
./gradlew jar
The jar will be in build/libs/htsjdk-<version>.jar where version is based on the current git commit.
- run tests, a specific test class, or run a test and wait for the debugger to connect
./gradlew test
./gradlew test --tests AlleleUnitTest
./gradlew test --tests AlleleUnitTest --debug-jvm
- run tests and collect coverage information (report will be in
build/reports/jacoco/test/html/index.html)
./gradlew jacocoTestReport
- clean the project directory
./gradlew clean
- build a monolithic jar that includes all of htsjdk's dependencies
./gradlew shadowJar
- create a snapshot and install it into your local maven repository
./gradlew install
- for an exhaustive list of all available targets
./gradlew tasks
To create a project in IntelliJ IDE for htsjdk do the following:
- Select fom the menu:
File -> New -> Project from Existing Sources - In the resulting dialog, chose
Import from existing model, selectGradleandNext - Choose the
default gradle wrapperandFinish.
From time to time if dependencies change in htsjdk you may need to refresh the project from the View -> Gradle menu.
Not all sub-packages of htsjdk are subject to the same license, so a license notice is included in each source file or sub-package as appropriate. Please check the relevant license notice whenever you start working with a part of htsjdk that you have not previously worked with to avoid any surprises. Broadly speaking the majority of the code is covered under the MIT license with the following notable exceptions:
- Much of the CRAM code is under the Apache License, Version 2
- Core
tribblecode (underlying VCF reading/writing amongst other things) is under LGPL - Code supporting the reading/writing of SRA format is uncopyrighted & public domain
Htsjdk currently targets Java 8 and is tested on both 8 and 11. We do not currently plan to support versions of Java which are not long-term-support releases (ex: 9, 10, or 12).
We will notify the community at least 6 months before we plan to stop support for Java 8.
| Java SE Major Release | End of Java SE Oracle Public Updates / OpenJDK support | Proposed End of Support in HTSJDK | Actual End of Support in HTSJDK |
|---|---|---|---|
| 6 | Feb 2013 | Aug 2013 | Oct 2015 |
| 7 | Apr 2015 | Oct 2015 | Oct 2015 |
| 8 | Jan 2019 | TBD | TBD |
| 11 | Sep 2022 | TBD | TBD |
HTSJDK is migrating to semantic versioning (http://semver.org/). We will eventually adhere to it strictly and bump our major version whenever there are breaking changes to our API, but until we more clearly define what constitutes our official API, clients should assume that every release potentially contains at least minor changes to public methods.