/* strip_rpts.c -- strip repeat eleements from a sequence */#include "util.h"#include "seq.h"#define BUF_SIZE 1000int main(int argc, char **argv){	SEQ *sf;	uchar *s;	int len, b, e, i, col, old_b;	char buf[500];	FILE *fp;	if (argc != 3)		fatal("args: sequence %:repeats-file");	sf = seq_get(argv[1]);	s = SEQ_CHARS(sf);	len = SEQ_LEN(sf);	fp = ckopen(argv[2], "r");	if (fgets(buf, BUF_SIZE, fp) == NULL ||	    !same_string(buf, "%:repeats\n"))		fatalf("%s is not a %:repeats file", argv[2]);	old_b = 0;	for (old_b = 0; fgets(buf, BUF_SIZE, fp); old_b = b) {		if (sscanf(buf, "%d %d", &b, &e) != 2)			fatalf("bad repeats line in %s: %s", argv[2], buf);		if (b < old_b)			fatalf("out-of-order line in %s: %s", argv[2], buf);		if (b > e || b < 1 || e > len)			fatalf("begin = %d, end = %d, seq_len = %d\n",			  b, e, len);		for (i = b-1; i < e; ++i)			s[i] = 'Z';	}	printf(">%s, minus lineage-specific repeats\n", SEQ_HEAD(sf));	for (i = col = 0; i < len; ++i)		if (s[i] != 'Z') {			putchar(s[i]);			if (++col == 50) {				putchar('\n');				col = 0;			}		}	if (col)		putchar('\n');	return 0;}