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.

To run:

1. Install CCTools.
2. Install BWA and all its required dependencies. BWA can be download from:
http://bio-bwa.sourceforge.net
3. Run './wq_bwa <REFERENCE_FILE> <FASTQ_FILE>' to align sequences in <FASTQ_FILE>.
4. Start workers:
work_queue_worker -d all <HOSTNAME> <PORT>
where <HOSTNAME> is the name of the host on which the manager is running
	  <PORT> is the port number on which the manager is listening.

Alternatively, you can also specify a project name for the manager and use that
to start workers:

1. ./wq_bwa <REFERENCE_FILE> <FASTQ_FILE> -N WQBWA
2. work_queue_worker -d all -N WQBWA

For listing the command-line options, do:
./wq_bwa -h

When the alignment completes, you will find the output files in the
same directory from where wq_bwa was run.
