| Unit Tests | Integration Tests | |
|---|---|---|
| Master | GATK | Picard |
 |
||
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.
Please see the HTSJDK Documentation for more information.
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.
NOTE: Effective November 24th 2015, HTSJDK has ended support of Java 7 and previous versions. Java 8 is now required.
We will support all Java SE versions supported by Oracle until at least six months after Oracle's Public Updates period has ended (see this link).
| Java SE Major Release | End of Java SE Oracle Public Updates | 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* | Mar 2017 | Sep 2017 | Sep 2017 |
- to be finalized
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.
Integration tests need to pass for any htsjdk release to be considered.
Integration tests show the 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.