// Copyright 2013 Martin C. Frith

// This routine reads alignments of query sequences to a genome, and
// estimates which alignment parts represent the source of each query.
// It allows different parts of one query to come from different parts
// of the genome.

// The input should be in MAF format
// (http://genome.ucsc.edu/FAQ/FAQformat.html#format5).  It must
// include a header of the sort written by lastal, with score
// parameters and genome size.

#ifndef LAST_SPLIT_HH
#define LAST_SPLIT_HH

#include <stddef.h>  // size_t
#include <string>
#include <vector>

struct LastSplitOptions {
  int format;
  bool isTopSeqQuery;
  std::string genome;
  int direction;
  double cis;
  double trans;
  double mean;
  double sdev;
  double mismap;
  int score;
  bool no_split;
  size_t bytes;
  bool verbose;
  bool isSplicedAlignment;
  std::vector<std::string> inputFileNames;
};

void lastSplit(LastSplitOptions& opts);

#endif
