--- /dev/null
+#include "pysam.h"
+
+#include <ctype.h>
+#include <string.h>
+#include <stdlib.h>
+#include <stdio.h>
+#include <stdint.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(pysamerr, "[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(pysamerr, "[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(pysamerr, "[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(pysamerr, "[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(pysamerr, "[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(pysamerr, "[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(pysamerr, "[download_from_remote] fail to open remote file %s\n",url);
+ return NULL;
+ }
+ if ((fp = fopen(fn, "wb")) == 0) {
+ fprintf(pysamerr, "[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(pysamerr, "[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(pysamerr, "[fai_load] build FASTA index.\n");
+ fai_build(fn);
+ fp = fopen(str, "rb");
+ if (fp == 0) {
+ fprintf(pysamerr, "[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(pysamerr, "[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(pysamerr, "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