* 0.1.16-dev (r969:252)

[samtools.git] / faidx.c

diff --git a/faidx.c b/faidx.c
index 38292a13d73f33e75b12ad02baa3af2f66242bab..fd0389393d8208098a5a6ace60047b1202f37509 100644 (file)
--- a/faidx.c
+++ b/faidx.c
@@ -305,8 +305,8 @@ 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;
@@ -314,31 +314,43 @@ 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;