Improve support for very long input lines (> 2Gbyte)

bgzf.c

@@ -2298,7 +2298,7 @@ int bgzf_getline(BGZF *fp, int delim, kstring_t *str)
     fp->uncompressed_address += str->l + 1;
     if ( delim=='\n' && str->l>0 && str->s[str->l-1]=='\r' ) str->l--;
     str->s[str->l] = 0;
-    return str->l;
+    return str->l <= INT_MAX ? (int) str->l : INT_MAX;
 }
 
 void bgzf_index_destroy(BGZF *fp)

htslib/bgzf.h

@@ -303,7 +303,8 @@ typedef struct BGZF BGZF;
      * @param fp     BGZF file handler
      * @param delim  delimiter
      * @param str    string to write to; must be initialized
-     * @return       length of the string; -1 on end-of-file; <= -2 on error
+     * @return       length of the string (capped at INT_MAX);
+     *               -1 on end-of-file; <= -2 on error
      */
     HTSLIB_EXPORT
     int bgzf_getline(BGZF *fp, int delim, struct kstring_t *str);

tbx.c

@@ -91,9 +91,10 @@ int tbx_name2id(tbx_t *tbx, const char *ss)
     return get_tid(tbx, ss, 0);
 }
 
-int tbx_parse1(const tbx_conf_t *conf, int len, char *line, tbx_intv_t *intv)
+int tbx_parse1(const tbx_conf_t *conf, size_t len, char *line, tbx_intv_t *intv)
 {
-    int i, b = 0, id = 1;
+    size_t i, b = 0;
+    int id = 1;
     char *s;
     intv->ss = intv->se = 0; intv->beg = intv->end = -1;
     for (i = 0; i <= len; ++i) {

vcf.c

@@ -3437,7 +3437,7 @@ int vcf_write_line(htsFile *fp, kstring_t *line)
 
 int vcf_write(htsFile *fp, const bcf_hdr_t *h, bcf1_t *v)
 {
-    int ret;
+    ssize_t ret;
     fp->line.l = 0;
     if (vcf_format1(h, v, &fp->line) != 0)
         return -1;