X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=samtools.git;a=blobdiff_plain;f=faidx.c;h=38292a13d73f33e75b12ad02baa3af2f66242bab;hp=36366c20db595ee9ffeaac4d87628dc40c3690d2;hb=9f4bebab2e0917c676ae739b2d05cb22ad6c4ed5;hpb=b27e00385f41769d03a8cca4dbd71275fc9fa906 diff --git a/faidx.c b/faidx.c index 36366c2..38292a1 100644 --- a/faidx.c +++ b/faidx.c @@ -2,6 +2,7 @@ #include #include #include +#include #include "faidx.h" #include "khash.h" @@ -14,8 +15,13 @@ 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) @@ -23,6 +29,9 @@ extern int fseeko(FILE *stream, off_t offset, int whence); #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; @@ -134,7 +143,11 @@ void fai_save(const faidx_t *fai, FILE *fp) 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 } } @@ -143,14 +156,22 @@ 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); @@ -177,15 +198,15 @@ int fai_build(const char *fn) sprintf(str, "%s.fai", fn); rz = razf_open(fn, "r"); if (rz == 0) { - fprintf(stderr, "[fai_build] fail to open the FASTA file.\n"); + 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, "w"); + fp = fopen(str, "wb"); if (fp == 0) { - fprintf(stderr, "[fai_build] fail to write FASTA index.\n"); + fprintf(stderr, "[fai_build] fail to write FASTA index %s\n",str); fai_destroy(fai); free(str); return -1; } @@ -196,6 +217,47 @@ int fai_build(const char *fn) 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; @@ -203,20 +265,36 @@ faidx_t *fai_load(const char *fn) faidx_t *fai; str = (char*)calloc(strlen(fn) + 5, 1); sprintf(str, "%s.fai", fn); - fp = fopen(str, "r"); + +#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, "r"); + 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, "r"); + + fai->rz = razf_open(fn, "rb"); free(str); if (fai->rz == 0) { fprintf(stderr, "[fai_load] fail to open FASTA file.\n"); @@ -270,7 +348,7 @@ char *fai_fetch(const faidx_t *fai, const char *str, int *len) 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) + 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; @@ -306,6 +384,40 @@ int faidx_main(int argc, char *argv[]) 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