REQUIREMENTS:

	NAHR_finder must be run on compute nodes that are MPI-enabled and have a CUDA-capable GPU.
	Additionally, NAHR_finder utilizes the following packages.

	CUDA >= 5.5
	BOOST C++ libraries >= 1.55
		with additional packages: serialization, mpi, system, filesystem, statistical distributions
	GMP
	MPFR
	MPFRC++
	GMPFRXX
	BAMtools
	MATLAB




INSTALLATION:

	After installing the required packages, the "makefile" must be manually changed to link to these packages.
	Then, you need simply run:
			make
	


USAGE:
	detect-NAHR  [options] 

	options:
	-d	a database of segmental duplications (SDs) in the reference genome and pairwise alignments amongst homologous SDs.
		[the default database that comes with this package is for hg19 (human).]
	-R	haploid reference genome fasta file prefix for each chromsome [default: hg19_chr]
	-b	input BAM file of paired-end reads aligned to the reference genome
	-s	path to a temporary directory for temporary files
	-o	output directory
	-varpos		path to a directory which contains a file for each chromosome,
			where each file contains all of the positions in that chromosmome that are on an SD
			and are a variational position.
	-l	length of reference genome [default: 3190491286 for hg19]
	-e	base error-rate for the paired-end reads.  Context-specific error-rates adjustments will be made
		against this base error rate.  [default:  0.01]
	-p	a priori probability of no NAHR or gene conversion event occurring at a given locus [default: 0.999999]
	-compute_size	comma-separated pair of integers.  Connected components will be selected for computation
			if their compute size is within this range.  [default:  0,7000]
	-alpha	read-depth variance factor. (Let u_R = expected read-depth of a region R.  Then the likelihood of
		observing n reads from region R is N(n ; u_R, sigma^2) where sigma^2 := u_R * (1+alpha)  [default:  0.01]
	-samples	number of samples from posterior distribution to draw to estimate posterior probabilities.
	-vs	path to directory containing visitation schedules for connected components
	-gender_and_pop		file containing tab-delimited information about the gender and population of the individual
				sequenced in the BAM file.
	-G	name of individual.
	


	
	


CONTACT:

	Please direct all questions and problems to:  matthew_parks@alumni.brown.edu