--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/pyPRADA_1.2/tools/samtools-0.1.16/bedidx.c	Thu Feb 20 00:44:58 2014 -0500
@@ -0,0 +1,156 @@
+#include <stdlib.h>
+#include <stdint.h>
+#include <string.h>
+#include <stdio.h>
+#include <zlib.h>
+
+#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 (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);
+}