A Java API for high-throughput sequencing data (HTS) formats.
Java Other
Latest commit 55bf01b Feb 17, 2017 @tomwhite tomwhite committed with droazen Make BAMFileReader and some related classes public, and expose (#786)
methods for iterating over a part of a BAM file (needed for Hadoop-BAM,
which processes BAM files in parallel).

Also, add BAMFileSpan#removeContentsAfter method to mirror
removeContentsBefore.

README.md

Coverage Status Build Status Maven Central License Language

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.

A Java API for high-throughput sequencing data (HTS) formats.

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.

NOTE: HTSJDK does not currently support the latest Variant Call Format Specification (VCFv4.3 and BCFv2.2).

Building HTSJDK

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 -Dtest.single=TestClassName
    
    ./gradlew test --tests htsjdk.variant.variantcontext.AlleleUnitTest
    ./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
    

Create an HTSJDK project in IntelliJ

To create a project in IntelliJ IDE for htsjdk do the following:

  1. Select fom the menu: File -> New -> Project from Existing Sources
  2. In the resulting dialog, chose Import from existing model, select Gradle and Next
  3. Choose the default gradle wrapper and Finish.

From time to time if dependencies change in htsjdk you may need to refresh the project from the View -> Gradle menu.

Licensing 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.

Java Minimum Version Support Policy

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.