#include <stdlib.h>
 #include <stdint.h>
 #include <string.h>
 #include <stdio.h>
 #include <zlib.h>
 
 #ifdef _WIN32
 #define drand48() ((double)rand() / RAND_MAX)
 #endif
 
 #include "ksort.h"
 KSORT_INIT_GENERIC(uint64_t)
 
 #include "kseq.h"
 KSTREAM_INIT(gzFile, gzread, 8192)
 
 typedef struct {
 	int n, m;
 	uint64_t *a;
 	int *idx;
 } bed_reglist_t;
 
 #include "khash.h"
 KHASH_MAP_INIT_STR(reg, bed_reglist_t)
 
 #define LIDX_SHIFT 13
 
 typedef kh_reg_t reghash_t;
 
 int *bed_index_core(int n, uint64_t *a, int *n_idx)
 {
 	int i, j, m, *idx;
 	m = *n_idx = 0; idx = 0;
 	for (i = 0; i < n; ++i) {
 		int beg, end;
 		beg = a[i]>>32 >> LIDX_SHIFT; end = ((uint32_t)a[i]) >> LIDX_SHIFT;
 		if (m < end + 1) {
 			int oldm = m;
 			m = end + 1;
 			kroundup32(m);
 			idx = realloc(idx, m * sizeof(int));
 			for (j = oldm; j < m; ++j) idx[j] = -1;
 		}
 		if (beg == end) {
 			if (idx[beg] < 0) idx[beg] = i;
 		} else {
 			for (j = beg; j <= end; ++j)
 				if (idx[j] < 0) idx[j] = i;
 		}
 		*n_idx = end + 1;
 	}
 	return idx;
 }
 
 void bed_index(void *_h)
 {
 	reghash_t *h = (reghash_t*)_h;
 	khint_t k;
 	for (k = 0; k < kh_end(h); ++k) {
 		if (kh_exist(h, k)) {
 			bed_reglist_t *p = &kh_val(h, k);
 			if (p->idx) free(p->idx);
 			ks_introsort(uint64_t, p->n, p->a);
 			p->idx = bed_index_core(p->n, p->a, &p->m);
 		}
 	}
 }
 
 int bed_overlap_core(const bed_reglist_t *p, int beg, int end)
 {
 	int i, min_off;
 	if (p->n == 0) return 0;
 	min_off = (beg>>LIDX_SHIFT >= p->n)? p->idx[p->n-1] : p->idx[beg>>LIDX_SHIFT];
 	if (min_off < 0) { // TODO: this block can be improved, but speed should not matter too much here
 		int n = beg>>LIDX_SHIFT;
 		if (n > p->n) n = p->n;
 		for (i = n - 1; i >= 0; --i)
 			if (p->idx[i] >= 0) break;
 		min_off = i >= 0? p->idx[i] : 0;
 	}
 	for (i = min_off; i < p->n; ++i) {
 		if ((int)(p->a[i]>>32) >= end) break; // out of range; no need to proceed
 		if ((int32_t)p->a[i] > beg && (int32_t)(p->a[i]>>32) < end)
 			return 1; // find the overlap; return
 	}
 	return 0;
 }
 
 int bed_overlap(const void *_h, const char *chr, int beg, int end)
 {
 	const reghash_t *h = (const reghash_t*)_h;
 	khint_t k;
 	if (!h) return 0;
 	k = kh_get(reg, h, chr);
 	if (k == kh_end(h)) return 0;
 	return bed_overlap_core(&kh_val(h, k), beg, end);
 }
 
 void *bed_read(const char *fn)
 {
 	reghash_t *h = kh_init(reg);
 	gzFile fp;
 	kstream_t *ks;
 	int dret;
 	kstring_t *str;
 	// read the list
 	fp = strcmp(fn, "-")? gzopen(fn, "r") : gzdopen(fileno(stdin), "r");
 	if (fp == 0) return 0;
 	str = calloc(1, sizeof(kstring_t));
 	ks = ks_init(fp);
 	while (ks_getuntil(ks, 0, str, &dret) >= 0) { // read the chr name
 		int beg = -1, end = -1;
 		bed_reglist_t *p;
 		khint_t k = kh_get(reg, h, str->s);
 		if (k == kh_end(h)) { // absent from the hash table
 			int ret;
 			char *s = strdup(str->s);
 			k = kh_put(reg, h, s, &ret);
 			memset(&kh_val(h, k), 0, sizeof(bed_reglist_t));
 		}
 		p = &kh_val(h, k);
 		if (dret != '\n') { // if the lines has other characters
 			if (ks_getuntil(ks, 0, str, &dret) > 0 && isdigit(str->s[0])) {
 				beg = atoi(str->s); // begin
 				if (dret != '\n') {
 					if (ks_getuntil(ks, 0, str, &dret) > 0 && isdigit(str->s[0])) {
 						end = atoi(str->s); // end
 						if (end < beg) end = -1;
 					}
 				}
 			}
 		}
 		if (dret != '\n') while ((dret = ks_getc(ks)) > 0 && dret != '\n'); // skip the rest of the line
 		if (end < 0 && beg > 0) end = beg, beg = beg - 1; // if there is only one column
 		if (beg >= 0 && end > beg) {
 			if (p->n == p->m) {
 				p->m = p->m? p->m<<1 : 4;
 				p->a = realloc(p->a, p->m * 8);
 			}
 			p->a[p->n++] = (uint64_t)beg<<32 | end;
 		}
 	}
 	ks_destroy(ks);
 	gzclose(fp);
 	free(str->s); free(str);
 	bed_index(h);
 	return h;
 }
 
 void bed_destroy(void *_h)
 {
 	reghash_t *h = (reghash_t*)_h;
 	khint_t k;
 	for (k = 0; k < kh_end(h); ++k) {
 		if (kh_exist(h, k)) {
 			free(kh_val(h, k).a);
 			free(kh_val(h, k).idx);
 			free((char*)kh_key(h, k));
 		}
 	}
 	kh_destroy(reg, h);
 }