JNI code for minimap2
This project allows Java code to call Heng Li's minimap2 assembler. We include binaries for OSX and Linux in a maven central artifact.
To build and install locally you'll need gmake, git, gcc, and Java 8. Execute
./gradlew install
This will work for testing, but will only produce a native library for your local system.
To use this JNI binding on an architecture other than OSX or Linux:
Go into src/main/c.
Modify the Makefile to produce a library name appropriate to your system.
Type make (you'll need gmake, git, and gcc).
Move the library you built somewhere permanent on your machine.
Use -DLIBMM2_PATH=<that permanent location> when you run GATK (or other Java program).