gatk-bwamem-jni

JNI code for bwa mem.

This project builds dynamic libraries with a JNI API. It allows Java code to call Heng Li's bwa mem aligner.

To build you'll need gmake, git, gcc, and Java 23.

To build and install a snapshot locally:

git clone --recursive https://github.com/umccr/gatk-bwamem-jni
./gradlew build

This will work for testing but will only include a native library for your system.