// gactg.c

// Read in an fpc file and do a genetic algorithm to fix the named contig
//
// Genetic operators
//
// Crossover probability percentages, should add up to 100
#define CROSSOVER 25
#define MUTATION 25
#define FIXWORST 25
#define BLOCKSHIFT 25
#define MOUNTAIN 25

#define POPSIZE 20
#define NUMGENS 10000
#define NUMREPLACE 3

// Types of scoring metrics
#define RUNSCORE 1
#define NEIGHBOURSCORE 2
#define NEIGHBOURCONF 3
#define SULSTONNEIGHBOUR 4
// Which score we are using
int score_method = SULSTONNEIGHBOUR;


gactg, my new program name. cool, eh?!