Imported Upstream version 0.5

[pysam.git] / samtools / faidx.c.pysam.c

diff --git a/samtools/faidx.c.pysam.c b/samtools/faidx.c.pysam.c
index 376629ead6701fc4bebdec4337c10abbed1da06b..526a9c0022ff477807e6475b2910c2497f4caf36 100644 (file)
--- a/samtools/faidx.c.pysam.c
+++ b/samtools/faidx.c.pysam.c
@@ -9,8 +9,7 @@
 #include "khash.h"
 
 typedef struct {
-       int32_t line_len, line_blen;
-       int64_t len;
+       uint64_t len:32, line_len:16, line_blen:16;
        uint64_t offset;
 } faidx1_t;
 KHASH_MAP_INIT_STR(s, faidx1_t)
@@ -67,11 +66,10 @@ faidx_t *fai_build_core(RAZF *rz)
 {
        char c, *name;
        int l_name, m_name, ret;
-       int line_len, line_blen, state;
+       int len, 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);
@@ -123,6 +121,11 @@ faidx_t *fai_build_core(RAZF *rz)
                                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;
@@ -304,8 +307,8 @@ faidx_t *fai_load(const char *fn)
 
 char *fai_fetch(const faidx_t *fai, const char *str, int *len)
 {
-       char *s, c;
-       int i, l, k, name_end;
+       char *s, *p, c;
+       int i, l, k;
        khiter_t iter;
        faidx1_t val;
        khash_t(s) *h;
@@ -313,43 +316,31 @@ char *fai_fetch(const faidx_t *fai, const char *str, int *len)
 
        beg = end = -1;
        h = fai->hash;
-       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);
+       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);
-       // 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 (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;