/*
 * nvbio
 * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved.
 * 
 * Redistribution and use in source and binary forms, with or without
 * modification, are permitted provided that the following conditions are met:
 *    * Redistributions of source code must retain the above copyright
 *      notice, this list of conditions and the following disclaimer.
 *    * Redistributions in binary form must reproduce the above copyright
 *      notice, this list of conditions and the following disclaimer in the
 *      documentation and/or other materials provided with the distribution.
 *    * Neither the name of the NVIDIA CORPORATION nor the
 *      names of its contributors may be used to endorse or promote products
 *      derived from this software without specific prior written permission.
 * 
 * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
 * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
 * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
 * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY
 * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
 * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
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 * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
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 * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 */

#pragma once

#include <nvbio/basic/types.h>
#include <nvbio/basic/vector.h>
#include <nvbio/basic/packed_vector.h>

#include "haplotype_caller.h"
#include "assembly_types.h"

using namespace nvbio;

void local_assembly(assembly_pipeline* pipeline)
{
	// [read correction]

	// create assembly graphs for given kmer size(s)
	debruijn_graph assembly_graph;
	assembly_graph.construct_graph(
			pipeline->d_seq_set,
			pipeline->d_active_region_ids,
			pipeline->kmer_size,
			false);

	printf("Constructed assembly graph for kmer size %u with %u nodes and %u edges \n",
			pipeline->kmer_size, assembly_graph.n_nodes, assembly_graph.n_edges);

	//assembly_graph.print_dot_graph(pipeline->d_seq_set);

	// check complexity

	// assembly_graph.topological_sort();

	// check for cycles
	// post-process: pruning, dangling chain recovery...

	// find best paths
	//assembly_graph.find_k_best_paths(pipeline->k_best_haplotypes);
}