#ifndef _REGION_ASSOCIATION_H
#define _REGION_ASSOCIATINO_H

#include <cstdio>
#include "region.h"

namespace cis {
  
  
  int PrintRegionAssociations(REG_MAP const& query_regions_on_dna,
                              REG_MAP const& target_regions_on_dna,
                              int max_assoc_distance,
                              int min_assoc_distance,
                              int max_regions_between,
                              int first_association_id,
                              FILE * outstream);
  
} // namespace cis

#endif // _REGION_ASSOCIATION_H