git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/SICtools@109238 bc3139a8-67e5-0310-9ffc-ced21a209358
James Hester authored on 06/10/2015 17:15:15
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new file mode 100644 |
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+#include <stdlib.h> |
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+#include <stdint.h> |
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+#include <string.h> |
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+#include <stdio.h> |
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+#include <zlib.h> |
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+ |
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+#ifdef _WIN32 |
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+#define drand48() ((double)rand() / RAND_MAX) |
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+#endif |
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+ |
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+#include "ksort.h" |
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+KSORT_INIT_GENERIC(uint64_t) |
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+ |
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+#include "kseq.h" |
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+KSTREAM_INIT(gzFile, gzread, 8192) |
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+ |
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+typedef struct {
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+ int n, m; |
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+ uint64_t *a; |
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+ int *idx; |
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+} bed_reglist_t; |
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+ |
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+#include "khash.h" |
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+KHASH_MAP_INIT_STR(reg, bed_reglist_t) |
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+ |
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+#define LIDX_SHIFT 13 |
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+ |
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+typedef kh_reg_t reghash_t; |
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+ |
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+int *bed_index_core(int n, uint64_t *a, int *n_idx) |
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+{
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+ int i, j, m, *idx; |
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+ m = *n_idx = 0; idx = 0; |
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+ for (i = 0; i < n; ++i) {
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+ int beg, end; |
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+ beg = a[i]>>32 >> LIDX_SHIFT; end = ((uint32_t)a[i]) >> LIDX_SHIFT; |
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+ if (m < end + 1) {
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+ int oldm = m; |
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+ m = end + 1; |
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+ kroundup32(m); |
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+ idx = realloc(idx, m * sizeof(int)); |
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+ for (j = oldm; j < m; ++j) idx[j] = -1; |
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+ } |
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+ if (beg == end) {
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+ if (idx[beg] < 0) idx[beg] = i; |
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+ } else {
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+ for (j = beg; j <= end; ++j) |
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+ if (idx[j] < 0) idx[j] = i; |
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+ } |
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+ *n_idx = end + 1; |
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+ } |
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+ return idx; |
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+} |
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+ |
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+void bed_index(void *_h) |
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+{
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+ reghash_t *h = (reghash_t*)_h; |
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+ khint_t k; |
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+ for (k = 0; k < kh_end(h); ++k) {
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+ if (kh_exist(h, k)) {
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+ bed_reglist_t *p = &kh_val(h, k); |
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+ if (p->idx) free(p->idx); |
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+ ks_introsort(uint64_t, p->n, p->a); |
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+ p->idx = bed_index_core(p->n, p->a, &p->m); |
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+ } |
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+ } |
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+} |
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+ |
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+int bed_overlap_core(const bed_reglist_t *p, int beg, int end) |
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+{
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+ int i, min_off; |
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+ if (p->n == 0) return 0; |
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+ min_off = (beg>>LIDX_SHIFT >= p->n)? p->idx[p->n-1] : p->idx[beg>>LIDX_SHIFT]; |
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+ if (min_off < 0) { // TODO: this block can be improved, but speed should not matter too much here
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+ int n = beg>>LIDX_SHIFT; |
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+ if (n > p->n) n = p->n; |
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+ for (i = n - 1; i >= 0; --i) |
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+ if (p->idx[i] >= 0) break; |
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+ min_off = i >= 0? p->idx[i] : 0; |
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+ } |
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+ for (i = min_off; i < p->n; ++i) {
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+ if ((int)(p->a[i]>>32) >= end) break; // out of range; no need to proceed |
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+ if ((int32_t)p->a[i] > beg && (int32_t)(p->a[i]>>32) < end) |
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+ return 1; // find the overlap; return |
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+ } |
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+ return 0; |
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+} |
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+ |
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+int bed_overlap(const void *_h, const char *chr, int beg, int end) |
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+{
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+ const reghash_t *h = (const reghash_t*)_h; |
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+ khint_t k; |
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+ if (!h) return 0; |
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+ k = kh_get(reg, h, chr); |
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+ if (k == kh_end(h)) return 0; |
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+ return bed_overlap_core(&kh_val(h, k), beg, end); |
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+} |
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+ |
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+void *bed_read(const char *fn) |
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+{
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+ reghash_t *h = kh_init(reg); |
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+ gzFile fp; |
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+ kstream_t *ks; |
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+ int dret; |
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+ kstring_t *str; |
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+ // read the list |
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+ fp = strcmp(fn, "-")? gzopen(fn, "r") : gzdopen(fileno(stdin), "r"); |
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+ if (fp == 0) return 0; |
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+ str = calloc(1, sizeof(kstring_t)); |
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+ ks = ks_init(fp); |
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+ while (ks_getuntil(ks, 0, str, &dret) >= 0) { // read the chr name
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+ int beg = -1, end = -1; |
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+ bed_reglist_t *p; |
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+ khint_t k = kh_get(reg, h, str->s); |
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+ if (k == kh_end(h)) { // absent from the hash table
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+ int ret; |
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+ char *s = strdup(str->s); |
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+ k = kh_put(reg, h, s, &ret); |
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+ memset(&kh_val(h, k), 0, sizeof(bed_reglist_t)); |
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+ } |
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+ p = &kh_val(h, k); |
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+ if (dret != '\n') { // if the lines has other characters
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+ if (ks_getuntil(ks, 0, str, &dret) > 0 && isdigit(str->s[0])) {
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+ beg = atoi(str->s); // begin |
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+ if (dret != '\n') {
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+ if (ks_getuntil(ks, 0, str, &dret) > 0 && isdigit(str->s[0])) {
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+ end = atoi(str->s); // end |
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+ if (end < beg) end = -1; |
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+ } |
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+ } |
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+ } |
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+ } |
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+ if (dret != '\n') while ((dret = ks_getc(ks)) > 0 && dret != '\n'); // skip the rest of the line |
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+ if (end < 0 && beg > 0) end = beg, beg = beg - 1; // if there is only one column |
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+ if (beg >= 0 && end > beg) {
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+ if (p->n == p->m) {
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+ p->m = p->m? p->m<<1 : 4; |
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+ p->a = realloc(p->a, p->m * 8); |
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+ } |
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+ p->a[p->n++] = (uint64_t)beg<<32 | end; |
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+ } |
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+ } |
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+ ks_destroy(ks); |
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+ gzclose(fp); |
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+ free(str->s); free(str); |
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+ bed_index(h); |
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+ return h; |
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+} |
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+ |
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+void bed_destroy(void *_h) |
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+{
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+ reghash_t *h = (reghash_t*)_h; |
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+ khint_t k; |
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+ for (k = 0; k < kh_end(h); ++k) {
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+ if (kh_exist(h, k)) {
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+ free(kh_val(h, k).a); |
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+ free(kh_val(h, k).idx); |
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+ free((char*)kh_key(h, k)); |
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+ } |
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+ } |
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+ kh_destroy(reg, h); |
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+} |