Align a short read against an indexed reference genome and process alignment positions against a mask
EXPERIMENTAL ALPHA VERSION
This project depends on BWA (https://github.com/lh3/bwa, to generate the index files) and JBWA (https://github.com/lindenb/jbwa, to provide Java JNI mappings for BWA).
The JBWA project provides a file named libbwajni.so which is required to run the server (it is in the /jni folder). This file must be in the in the java.library.path, or it must be specified via -Djava.library.path={path} upon starting the server (see example below).
I tend to copy that file into a new directory /usr/lib/jni and then the -Djava.library.path option is not necessary.
You can build it from source using ant and this will write the Zeuss.jar file in /dist.
The compiled server can be started:
java [-Djava.library.path={path to libbwajni.so}] -jar Zeuss.jar -l {path to index}
This will start the server on port 9221 and create a mask file in the current directory.
There are 4 possible options: '-p' port (default 9221) '-c' cores (default 4*available system cores) '-l' path&prefix to genome index files '-m' path to mask file(s) (default .)
The only URL currently availble is '/v1/proc' ("proceed - yes or no"). The sequence to me mapped is provided a query parameter 'seq'. For example:
curl http://localhost:9221/v1/proc?seq=CTCTATTATTAATACTTCTTTTGAAGCTGCAGTTGTTGCTTCTACTTCAACATTAGAATTAATGTGTA
This curretly returns a JSON response: (for example) {"Pos":[120462618],"MaskVal":[0]}
This lists the alignment position, and the mask value at that position.