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// A. L. Delcher
//
// File: uncovered.hh
//
// Last Modified: 10 June 2005
//
// Declarations for uncovered.cc
#ifndef __UNCOVERED_HH_INCLUDED
#define __UNCOVERED_HH_INCLUDED
#include "delcher.hh"
#include "fasta.hh"
#include "gene.hh"
struct Region_t
{
long int lo, hi; // Range of region in "between" coordinates
};
static bool Region_Cmp
(Region_t const & a, Region_t const & b)
{ return (a . lo < b . lo); }
static void Coalesce_Regions
(vector <Region_t> & list);
static void Output_Subsequence
(const string & seq, long int i, long int len,
const char * tag, long int start, long int end);
static void Output_Uncovered
(const string & seq, long int seq_len, const vector <Region_t> & list);
static void Parse_Command_Line
(int argc, char * argv []);
static void Usage
(void);
#endif
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