INNER CODE UNIT · C

cr

lh3/bedtk · bedtk.c:506

	cr = read_bed3(argv[o.ind + 1]);
	assert(cr);
	cr_index2(cr, 1);

	fp = strcmp(argv[o.ind], "-")? gzopen(argv[o.ind], "r") : gzdopen(0, "r");
	assert(fp);
	ks = ks_init(fp);
	while (ks_getuntil(ks, KS_SEP_LINE, &str, 0) >= 0) {
		int32_t st1, en1, x;
		char *ctg, *rest;
		int64_t j;
		ctg = parse_bed3b(str.s, &st1, &en1, &rest);
		if (ctg == 0) continue;
		n_b = cr_overlap(cr, ctg, st1, en1, &b, &m_b);
		for (j = 0, x = st1; j < n_b; ++j) {
			cr_intv_t *r = &cr->r[b[j]];
			int32_t st0 = cr_st(r), en0 = cr_en(r);
			if (st0 < st1) st0 = st1;

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