
The wq_bwa program aligns sequences of genomes listed in a fastq file using
the Burrows-Wheeler Aligner. It aligns by partitioning the file into pieces
containing one or more sequences and running BWA to align them individually.
The program uses the Work Queue framework for distributed execution.

This version makes use of the JSON API and the work_queue_server.

To run:

# Build bwa code and setup input files:
make

# Start the application (and transparently the server)
./wq_bwa_json 

# Run multiple workers.  If using Condor: 
condor_submit_workers --cores 2 --memory 4000 --disk 10000 -M wq_bwa_json 10
