works

[samtools.git] / faidx.c

diff --git a/faidx.c b/faidx.c
index fd0389393d8208098a5a6ace60047b1202f37509..51c82ac1dfdcd0baf31435a0fe5f8e45c3289d0f 100644 (file)
--- a/faidx.c
+++ b/faidx.c
@@ -7,7 +7,8 @@
 #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)
@@ -64,10 +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);
@@ -119,11 +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;
@@ -340,6 +337,11 @@ char *fai_fetch(const faidx_t *fai, const char *str, int *len)
                        } else s[name_end] = ':', name_end = l;
                }
        } else iter = kh_get(s, h, str);
+       if(iter == kh_end(h)) {
+               fprintf(stderr, "[fai_fetch] Warning - Reference %s not found in FASTA file, returning empty sequence\n", str);
+               free(s);
+               return 0;
+       };
        val = kh_value(h, iter);
        // parse the interval
        if (name_end < l) {