Merge tag 'upstream/0.7'

[pysam.git] / tabix / index.c.pysam.c

diff --git a/tabix/index.c.pysam.c b/tabix/index.c.pysam.c
index 486e26fc1c7e6daf9ed472be9b1d3ba590963fd8..88cdc4050ffc296e34f2f91e8a0455c5b239ac4a 100644 (file)
--- a/tabix/index.c.pysam.c
+++ b/tabix/index.c.pysam.c
@@ -85,38 +85,7 @@ int ti_readline(BGZF *fp, kstring_t *str)
  * commented out above. */
 int ti_readline(BGZF *fp, kstring_t *str)
 {
-       int l, state = 0;
-       unsigned char *buf = (unsigned char*)fp->uncompressed_block;
-       str->l = 0;
-       do {
-               if (fp->block_offset >= fp->block_length) {
-                       if (bgzf_read_block(fp) != 0) { state = -2; break; }
-                       if (fp->block_length == 0) { state = -1; break; }
-               }
-               for (l = fp->block_offset; l < fp->block_length && buf[l] != '\n'; ++l);
-               if (l < fp->block_length) state = 1;
-               l -= fp->block_offset;
-               if (str->l + l + 1 >= str->m) {
-                       str->m = str->l + l + 2;
-                       kroundup32(str->m);
-                       str->s = (char*)realloc(str->s, str->m);
-               }
-               memcpy(str->s + str->l, buf + fp->block_offset, l);
-               str->l += l;
-               fp->block_offset += l + 1;
-               if (fp->block_offset >= fp->block_length) {
-#ifdef _USE_KNETFILE
-                       fp->block_address = knet_tell(fp->x.fpr);
-#else
-                       fp->block_address = ftello(fp->file);
-#endif
-                       fp->block_offset = 0;
-                       fp->block_length = 0;
-               } 
-       } while (state == 0);
-       if (str->l == 0 && state < 0) return state;
-       str->s[str->l] = 0;
-       return str->l;
+       return bgzf_getline(fp, '\n', str);
 }
 
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