assembly.h

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/*
 * nvbio
 * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved.
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#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);
}