bcftools.1 and samtools.1 were merged in upstream release 0.1.17.

[samtools.git] / faidx.c

diff --git a/faidx.c b/faidx.c
index 811bdf8858ff9ef18479fb644981ad4780bf7a8d..f0798fccc8057a5e33fdb04afaae1af084badbc9 100644 (file)
--- a/faidx.c
+++ b/faidx.c
@@ -2,11 +2,13 @@
 #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;
+       int32_t line_len, line_blen;
+       int64_t len;
        uint64_t offset;
 } faidx1_t;
 KHASH_MAP_INIT_STR(s, faidx1_t)
@@ -63,10 +65,11 @@ faidx_t *fai_build_core(RAZF *rz)
 {
        char c, *name;
        int l_name, m_name, ret;
-       int len, line_len, line_blen, state;
+       int line_len, line_blen, state;
        int l1, l2;
        faidx_t *idx;
        uint64_t offset;
+       int64_t len;
 
        idx = (faidx_t*)calloc(1, sizeof(faidx_t));
        idx->hash = kh_init(s);
@@ -118,11 +121,6 @@ faidx_t *fai_build_core(RAZF *rz)
                                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;
@@ -197,7 +195,7 @@ 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 %s\n",str);
+               fprintf(stderr, "[fai_build] fail to open the FASTA file %s\n",fn);
                free(str);
                return -1;
        }
@@ -304,8 +302,8 @@ faidx_t *fai_load(const char *fn)
 
 char *fai_fetch(const faidx_t *fai, const char *str, int *len)
 {
-       char *s, *p, c;
-       int i, l, k;
+       char *s, c;
+       int i, l, k, name_end;
        khiter_t iter;
        faidx1_t val;
        khash_t(s) *h;
@@ -313,31 +311,43 @@ char *fai_fetch(const faidx_t *fai, const char *str, int *len)
 
        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;
-       }
+       name_end = l = strlen(str);
+       s = (char*)malloc(l+1);
+       // remove space
+       for (i = k = 0; i < l; ++i)
+               if (!isspace(str[i])) s[k++] = str[i];
+       s[k] = 0; l = k;
+       // determine the sequence name
+       for (i = l - 1; i >= 0; --i) if (s[i] == ':') break; // look for colon from the end
+       if (i >= 0) name_end = i;
+       if (name_end < l) { // check if this is really the end
+               int n_hyphen = 0;
+               for (i = name_end + 1; i < l; ++i) {
+                       if (s[i] == '-') ++n_hyphen;
+                       else if (!isdigit(s[i]) && s[i] != ',') break;
+               }
+               if (i < l || n_hyphen > 1) name_end = l; // malformated region string; then take str as the name
+               s[name_end] = 0;
+               iter = kh_get(s, h, s);
+               if (iter == kh_end(h)) { // cannot find the sequence name
+                       iter = kh_get(s, h, str); // try str as the name
+                       if (iter == kh_end(h)) {
+                               *len = 0;
+                       free(s); return 0;
+                       } else s[name_end] = ':', name_end = l;
+               }
+       } else iter = kh_get(s, h, str);
        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;
+       // parse the interval
+       if (name_end < l) {
+               for (i = k = name_end + 1; i < l; ++i)
+                       if (s[i] != ',') s[k++] = s[i];
+               s[k] = 0;
+               beg = atoi(s + name_end + 1);
+               for (i = name_end + 1; i != k; ++i) if (s[i] == '-') break;
+               end = i < k? atoi(s + i + 1) : val.len;
+               if (beg > 0) --beg;
+       } else beg = 0, end = val.len;
        if (beg >= val.len) beg = val.len;
        if (end >= val.len) end = val.len;
        if (beg > end) beg = end;