+++ /dev/null
-#include <ctype.h>
-#include <string.h>
-#include <stdlib.h>
-#include <stdio.h>
-#include "faidx.h"
-#include "khash.h"
-
-typedef struct {
- uint64_t len:32, line_len:16, line_blen:16;
- uint64_t offset;
-} faidx1_t;
-KHASH_MAP_INIT_STR(s, faidx1_t)
-
-#ifndef _NO_RAZF
-#include "razf.h"
-#else
-#ifdef _WIN32
-#define ftello(fp) ftell(fp)
-#define fseeko(fp, offset, whence) fseek(fp, offset, whence)
-#else
-extern off_t ftello(FILE *stream);
-extern int fseeko(FILE *stream, off_t offset, int whence);
-#endif
-#define RAZF FILE
-#define razf_read(fp, buf, size) fread(buf, 1, size, fp)
-#define razf_open(fn, mode) fopen(fn, mode)
-#define razf_close(fp) fclose(fp)
-#define razf_seek(fp, offset, whence) fseeko(fp, offset, whence)
-#define razf_tell(fp) ftello(fp)
-#endif
-#ifdef _USE_KNETFILE
-#include "knetfile.h"
-#endif
-
-struct __faidx_t {
- RAZF *rz;
- int n, m;
- char **name;
- khash_t(s) *hash;
-};
-
-#ifndef kroundup32
-#define kroundup32(x) (--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4, (x)|=(x)>>8, (x)|=(x)>>16, ++(x))
-#endif
-
-static inline void fai_insert_index(faidx_t *idx, const char *name, int len, int line_len, int line_blen, uint64_t offset)
-{
- khint_t k;
- int ret;
- faidx1_t t;
- if (idx->n == idx->m) {
- idx->m = idx->m? idx->m<<1 : 16;
- idx->name = (char**)realloc(idx->name, sizeof(void*) * idx->m);
- }
- idx->name[idx->n] = strdup(name);
- k = kh_put(s, idx->hash, idx->name[idx->n], &ret);
- t.len = len; t.line_len = line_len; t.line_blen = line_blen; t.offset = offset;
- kh_value(idx->hash, k) = t;
- ++idx->n;
-}
-
-faidx_t *fai_build_core(RAZF *rz)
-{
- char c, *name;
- int l_name, m_name, ret;
- int len, line_len, line_blen, state;
- int l1, l2;
- faidx_t *idx;
- uint64_t offset;
-
- idx = (faidx_t*)calloc(1, sizeof(faidx_t));
- idx->hash = kh_init(s);
- name = 0; l_name = m_name = 0;
- len = line_len = line_blen = -1; state = 0; l1 = l2 = -1; offset = 0;
- while (razf_read(rz, &c, 1)) {
- if (c == '\n') { // an empty line
- if (state == 1) {
- offset = razf_tell(rz);
- continue;
- } else if ((state == 0 && len < 0) || state == 2) continue;
- }
- if (c == '>') { // fasta header
- if (len >= 0)
- fai_insert_index(idx, name, len, line_len, line_blen, offset);
- l_name = 0;
- while ((ret = razf_read(rz, &c, 1)) != 0 && !isspace(c)) {
- if (m_name < l_name + 2) {
- m_name = l_name + 2;
- kroundup32(m_name);
- name = (char*)realloc(name, m_name);
- }
- name[l_name++] = c;
- }
- name[l_name] = '\0';
- if (ret == 0) {
- fprintf(stderr, "[fai_build_core] the last entry has no sequence\n");
- free(name); fai_destroy(idx);
- return 0;
- }
- if (c != '\n') while (razf_read(rz, &c, 1) && c != '\n');
- state = 1; len = 0;
- offset = razf_tell(rz);
- } else {
- if (state == 3) {
- fprintf(stderr, "[fai_build_core] inlined empty line is not allowed in sequence '%s'.\n", name);
- free(name); fai_destroy(idx);
- return 0;
- }
- if (state == 2) state = 3;
- l1 = l2 = 0;
- do {
- ++l1;
- if (isgraph(c)) ++l2;
- } while ((ret = razf_read(rz, &c, 1)) && c != '\n');
- if (state == 3 && l2) {
- fprintf(stderr, "[fai_build_core] different line length in sequence '%s'.\n", name);
- free(name); fai_destroy(idx);
- return 0;
- }
- ++l1; len += l2;
- if (l2 >= 0x10000) {
- fprintf(stderr, "[fai_build_core] line length exceeds 65535 in sequence '%s'.\n", name);
- free(name); fai_destroy(idx);
- return 0;
- }
- if (state == 1) line_len = l1, line_blen = l2, state = 0;
- else if (state == 0) {
- if (l1 != line_len || l2 != line_blen) state = 2;
- }
- }
- }
- fai_insert_index(idx, name, len, line_len, line_blen, offset);
- free(name);
- return idx;
-}
-
-void fai_save(const faidx_t *fai, FILE *fp)
-{
- khint_t k;
- int i;
- for (i = 0; i < fai->n; ++i) {
- faidx1_t x;
- k = kh_get(s, fai->hash, fai->name[i]);
- x = kh_value(fai->hash, k);
-#ifdef _WIN32
- fprintf(fp, "%s\t%d\t%ld\t%d\t%d\n", fai->name[i], (int)x.len, (long)x.offset, (int)x.line_blen, (int)x.line_len);
-#else
- fprintf(fp, "%s\t%d\t%lld\t%d\t%d\n", fai->name[i], (int)x.len, (long long)x.offset, (int)x.line_blen, (int)x.line_len);
-#endif
- }
-}
-
-faidx_t *fai_read(FILE *fp)
-{
- faidx_t *fai;
- char *buf, *p;
- int len, line_len, line_blen;
-#ifdef _WIN32
- long offset;
-#else
- long long offset;
-#endif
- fai = (faidx_t*)calloc(1, sizeof(faidx_t));
- fai->hash = kh_init(s);
- buf = (char*)calloc(0x10000, 1);
- while (!feof(fp) && fgets(buf, 0x10000, fp)) {
- for (p = buf; *p && isgraph(*p); ++p);
- *p = 0; ++p;
-#ifdef _WIN32
- sscanf(p, "%d%ld%d%d", &len, &offset, &line_blen, &line_len);
-#else
- sscanf(p, "%d%lld%d%d", &len, &offset, &line_blen, &line_len);
-#endif
- fai_insert_index(fai, buf, len, line_len, line_blen, offset);
- }
- free(buf);
- return fai;
-}
-
-void fai_destroy(faidx_t *fai)
-{
- int i;
- for (i = 0; i < fai->n; ++i) free(fai->name[i]);
- free(fai->name);
- kh_destroy(s, fai->hash);
- if (fai->rz) razf_close(fai->rz);
- free(fai);
-}
-
-int fai_build(const char *fn)
-{
- char *str;
- RAZF *rz;
- FILE *fp;
- faidx_t *fai;
- str = (char*)calloc(strlen(fn) + 5, 1);
- sprintf(str, "%s.fai", fn);
- rz = razf_open(fn, "r");
- if (rz == 0) {
- fprintf(stderr, "[fai_build] fail to open the FASTA file %s\n",fn);
- free(str);
- return -1;
- }
- fai = fai_build_core(rz);
- razf_close(rz);
- fp = fopen(str, "wb");
- if (fp == 0) {
- fprintf(stderr, "[fai_build] fail to write FASTA index %s\n",str);
- fai_destroy(fai); free(str);
- return -1;
- }
- fai_save(fai, fp);
- fclose(fp);
- free(str);
- fai_destroy(fai);
- return 0;
-}
-
-#ifdef _USE_KNETFILE
-FILE *download_and_open(const char *fn)
-{
- const int buf_size = 1 * 1024 * 1024;
- uint8_t *buf;
- FILE *fp;
- knetFile *fp_remote;
- const char *url = fn;
- const char *p;
- int l = strlen(fn);
- for (p = fn + l - 1; p >= fn; --p)
- if (*p == '/') break;
- fn = p + 1;
-
- // First try to open a local copy
- fp = fopen(fn, "r");
- if (fp)
- return fp;
-
- // If failed, download from remote and open
- fp_remote = knet_open(url, "rb");
- if (fp_remote == 0) {
- fprintf(stderr, "[download_from_remote] fail to open remote file %s\n",url);
- return NULL;
- }
- if ((fp = fopen(fn, "wb")) == 0) {
- fprintf(stderr, "[download_from_remote] fail to create file in the working directory %s\n",fn);
- knet_close(fp_remote);
- return NULL;
- }
- buf = (uint8_t*)calloc(buf_size, 1);
- while ((l = knet_read(fp_remote, buf, buf_size)) != 0)
- fwrite(buf, 1, l, fp);
- free(buf);
- fclose(fp);
- knet_close(fp_remote);
-
- return fopen(fn, "r");
-}
-#endif
-
-faidx_t *fai_load(const char *fn)
-{
- char *str;
- FILE *fp;
- faidx_t *fai;
- str = (char*)calloc(strlen(fn) + 5, 1);
- sprintf(str, "%s.fai", fn);
-
-#ifdef _USE_KNETFILE
- if (strstr(fn, "ftp://") == fn || strstr(fn, "http://") == fn)
- {
- fp = download_and_open(str);
- if ( !fp )
- {
- fprintf(stderr, "[fai_load] failed to open remote FASTA index %s\n", str);
- free(str);
- return 0;
- }
- }
- else
-#endif
- fp = fopen(str, "rb");
- if (fp == 0) {
- fprintf(stderr, "[fai_load] build FASTA index.\n");
- fai_build(fn);
- fp = fopen(str, "rb");
- if (fp == 0) {
- fprintf(stderr, "[fai_load] fail to open FASTA index.\n");
- free(str);
- return 0;
- }
- }
-
- fai = fai_read(fp);
- fclose(fp);
-
- fai->rz = razf_open(fn, "rb");
- free(str);
- if (fai->rz == 0) {
- fprintf(stderr, "[fai_load] fail to open FASTA file.\n");
- return 0;
- }
- return fai;
-}
-
-char *fai_fetch(const faidx_t *fai, const char *str, int *len)
-{
- char *s, *p, c;
- int i, l, k;
- khiter_t iter;
- faidx1_t val;
- khash_t(s) *h;
- int beg, end;
-
- beg = end = -1;
- h = fai->hash;
- l = strlen(str);
- p = s = (char*)malloc(l+1);
- /* squeeze out "," */
- for (i = k = 0; i != l; ++i)
- if (str[i] != ',' && !isspace(str[i])) s[k++] = str[i];
- s[k] = 0;
- for (i = 0; i != k; ++i) if (s[i] == ':') break;
- s[i] = 0;
- iter = kh_get(s, h, s); /* get the ref_id */
- if (iter == kh_end(h)) {
- *len = 0;
- free(s); return 0;
- }
- val = kh_value(h, iter);
- if (i == k) { /* dump the whole sequence */
- beg = 0; end = val.len;
- } else {
- for (p = s + i + 1; i != k; ++i) if (s[i] == '-') break;
- beg = atoi(p);
- if (i < k) {
- p = s + i + 1;
- end = atoi(p);
- } else end = val.len;
- }
- if (beg > 0) --beg;
- if (beg >= val.len) beg = val.len;
- if (end >= val.len) end = val.len;
- if (beg > end) beg = end;
- free(s);
-
- // now retrieve the sequence
- l = 0;
- s = (char*)malloc(end - beg + 2);
- razf_seek(fai->rz, val.offset + beg / val.line_blen * val.line_len + beg % val.line_blen, SEEK_SET);
- while (razf_read(fai->rz, &c, 1) == 1 && l < end - beg && !fai->rz->z_err)
- if (isgraph(c)) s[l++] = c;
- s[l] = '\0';
- *len = l;
- return s;
-}
-
-int faidx_main(int argc, char *argv[])
-{
- if (argc == 1) {
- fprintf(stderr, "Usage: faidx <in.fasta> [<reg> [...]]\n");
- return 1;
- } else {
- if (argc == 2) fai_build(argv[1]);
- else {
- int i, j, k, l;
- char *s;
- faidx_t *fai;
- fai = fai_load(argv[1]);
- if (fai == 0) return 1;
- for (i = 2; i != argc; ++i) {
- printf(">%s\n", argv[i]);
- s = fai_fetch(fai, argv[i], &l);
- for (j = 0; j < l; j += 60) {
- for (k = 0; k < 60 && k < l - j; ++k)
- putchar(s[j + k]);
- putchar('\n');
- }
- free(s);
- }
- fai_destroy(fai);
- }
- }
- return 0;
-}
-
-int faidx_fetch_nseq(const faidx_t *fai)
-{
- return fai->n;
-}
-
-char *faidx_fetch_seq(const faidx_t *fai, char *c_name, int p_beg_i, int p_end_i, int *len)
-{
- int l;
- char c;
- khiter_t iter;
- faidx1_t val;
- char *seq=NULL;
-
- // Adjust position
- iter = kh_get(s, fai->hash, c_name);
- if(iter == kh_end(fai->hash)) return 0;
- val = kh_value(fai->hash, iter);
- if(p_end_i < p_beg_i) p_beg_i = p_end_i;
- if(p_beg_i < 0) p_beg_i = 0;
- else if(val.len <= p_beg_i) p_beg_i = val.len - 1;
- if(p_end_i < 0) p_end_i = 0;
- else if(val.len <= p_end_i) p_end_i = val.len - 1;
-
- // Now retrieve the sequence
- l = 0;
- seq = (char*)malloc(p_end_i - p_beg_i + 2);
- razf_seek(fai->rz, val.offset + p_beg_i / val.line_blen * val.line_len + p_beg_i % val.line_blen, SEEK_SET);
- while (razf_read(fai->rz, &c, 1) == 1 && l < p_end_i - p_beg_i + 1)
- if (isgraph(c)) seq[l++] = c;
- seq[l] = '\0';
- *len = l;
- return seq;
-}
-
-#ifdef FAIDX_MAIN
-int main(int argc, char *argv[]) { return faidx_main(argc, argv); }
-#endif
projects / pysam.git / blobdiff