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 17.
git clone --recursive https://github.com/umccr/gatk-bwamem-jni
./gradlew build
This will only include a native library for your system (or CI/CD runner).