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The Intel Genomics Libary does not include the latest functional and security updates. Intel Genomics Libary Version 0.8.9 is targeted to be released in December 2021 and will include additional functional and security updates. Customers should update to the latest version as it becomes available.


[![Build Status](https://travis-ci.org/Intel-HLS/GKL.svg?branch=master)](https://travis-ci.org/Intel-HLS/GKL)
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# Genomics Kernel Library (GKL)
This repository contains optimized versions of compute kernels used in genomics applications like
[GATK](https://github.com/broadinstitute/gatk) and [HTSJDK](https://github.com/samtools/htsjdk). These kernels are
optimized to run on Intel Architecture (AVX, AVX2, AVX-512, and multicore) under 64-bit Linux and Mac OSX.

Kernels included:
* **PairHMM**
  * AVX and AVX-512 optimized versions of PairHMM used in GATK HaplotypeCaller and MuTect2. 
  * OpenMP support for multicore processors.
* **Smith-Waterman**
  * AVX2 and AVX-512 optimized versions of Smith-Waterman used in GATK HaplotypeCaller and MuTect2.
* **DEFLATE Compression/Decompression**:
  * Performance optimized Level 1 and 2 compression and decompression from Intel's [ISA-L](https://github.com/01org/isa-l) library.
  * Performance optimized Level 3 through 9 compression from Intel's [Open Source Technology Center](https://01.org/) [zlib](https://github.com/jtkukunas/zlib) library.

# Building GKL
GKL release binaries are built on CentOS 7, to enable running on most Linux distributions (see [holy-build-box](https://github.com/phusion/holy-build-box#problem-introduction) for a good discription of portability issues).

## Requirements
* Java JDK 8
* Git >= 2.5
* CMake >= 2.8.12.2
* GCC g++ >= 5.3.1
* GNU patch >= 2.6
* GNU libtool >= 2.2.6
* GNU automake >= 1.11.1
* Yasm >= 1.2.0
* zlib-devel >= 1.2.7

## Setup
Run these commands to setup the build environment on CentOS:
```
sudo yum install -y java-1.8.0-openjdk-devel git cmake patch libtool automake yasm zlib-devel centos-release-scl help2man
sudo yum install -y devtoolset-7-gcc-c++
source scl_source enable devtoolset-7
```

## Build and Test
After build requirements are met, clone, and build :
```
git clone https://github.com/Intel-HLS/GKL.git
cd GKL
./gradlew build
```
For more details check `build.sh`

# License
All code is licensed under the [MIT License](https://opensource.org/licenses/MIT), except:
* PairHMM code from GATK is licensed under the [BSD 3-Clause License](https://opensource.org/licenses/BSD-3-Clause).
* ISA-L code is licensed under the [BSD 3-Clause License](https://opensource.org/licenses/BSD-3-Clause).
* Intel Open Source Technology Center zlib (otc_zlib) code is licensed under the [Zlib License](https://opensource.org/licenses/Zlib).
* zlib code is licensed under the [Zlib License](https://opensource.org/licenses/Zlib).

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