Ensure indirect function calls have the correct type.

faidx.c

@@ -1022,7 +1022,7 @@ const char *fai_parse_region(const faidx_t *fai, const char *s,
                              int *tid, hts_pos_t *beg, hts_pos_t *end,
                              int flags)
 {
-    return hts_parse_region(s, tid, beg, end, (hts_name2id_f)fai_name2id, (void *)fai, flags);
+    return hts_parse_region(s, tid, beg, end, fai_name2id, (void *)fai, flags);
 }
 
 void fai_set_cache_size(faidx_t *fai, int cache_size) {

header.c

@@ -1439,7 +1439,7 @@ int sam_hdr_build_from_sam_file(sam_hdr_t *hdr, htsFile* fp) {
         if (f == NULL)
             goto error;
 
-        while (line.l = 0, kgetline(&line, (kgets_func*) hgets, f) >= 0) {
+        while (line.l = 0, khgetline(&line, f) >= 0) {
             char* tab = strchr(line.s, '\t');
             size_t l_start = str.l;
             sam_hrec_type_t *h_type;

hfile.c

@@ -297,6 +297,19 @@ char *hgets(char *buffer, int size, hFILE *fp)
     return hgetln(buffer, size, fp) > 0 ? buffer : NULL;
 }
 
+// Wrap around hgets() to get the right signature for kgets_func
+static char *hgets_wrapper(char *buffer, int size, void *fp)
+{
+    return hgets(buffer, size, (hFILE *) fp);
+}
+
+int khgetline(struct kstring_t *kstr, hFILE *fp)
+{
+    if (!kstr || !fp)
+        return EOF;
+    return kgetline(kstr, hgets_wrapper, fp);
+}
+
 ssize_t hpeek(hFILE *fp, void *buffer, size_t nbytes)
 {
     size_t n = fp->end - fp->begin;

hfile_libcurl.c

@@ -517,7 +517,7 @@ static int read_auth_plain(auth_token *tok, hFILE *auth_fp) {
     kstring_t token = {0, 0, NULL};
     const char *start, *end;
 
-    if (kgetline(&line, (char * (*)(char *, int, void *)) hgets, auth_fp) < 0) goto error;
+    if (khgetline(&line, auth_fp) < 0) goto error;
     if (kputc('\0', &line) < 0) goto error;
 
     for (start = line.s; *start && isspace_c(*start); start++) {}

hfile_s3.c

@@ -249,7 +249,6 @@ static FILE *expand_tilde_open(const char *fname, const char *mode)
     return fp;
 }
 
-
 static void parse_ini(const char *fname, const char *section, ...)
 {
     kstring_t line = { 0, 0, NULL };
@@ -259,7 +258,7 @@ static void parse_ini(const char *fname, const char *section, ...)
     FILE *fp = expand_tilde_open(fname, "r");
     if (fp == NULL) return;
 
-    while (line.l = 0, kgetline(&line, (kgets_func *) fgets, fp) >= 0)
+    while (line.l = 0, kfgetline(&line, fp) >= 0)
         if (line.s[0] == '[' && (s = strchr(line.s, ']')) != NULL) {
             *s = '\0';
             active = (strcmp(&line.s[1], section) == 0);
@@ -301,7 +300,7 @@ static void parse_simple(const char *fname, kstring_t *id, kstring_t *secret)
     FILE *fp = expand_tilde_open(fname, "r");
     if (fp == NULL) return;
 
-    while (kgetline(&text, (kgets_func *) fgets, fp) >= 0)
+    while (kfgetline(&text, fp) >= 0)
         kputc(' ', &text);
     fclose(fp);
 

hts.c

@@ -2027,6 +2027,11 @@ off_t hts_utell(htsFile *fp)
         return htell(fp->fp.hfile);
 }
 
+// Wrap hgetln() with a kgets_func2 signature for kgetline2()
+static ssize_t hgetln_wrapper(char *buf, size_t len, void *vfp) {
+    return hgetln(buf, len, (hFILE *) vfp);
+}
+
 int hts_getline(htsFile *fp, int delimiter, kstring_t *str)
 {
     int ret;
@@ -2038,7 +2043,7 @@ int hts_getline(htsFile *fp, int delimiter, kstring_t *str)
     switch (fp->format.compression) {
     case no_compression:
         str->l = 0;
-        ret = kgetline2(str, (kgets_func2 *) hgetln, fp->fp.hfile);
+        ret = kgetline2(str, hgetln_wrapper, fp->fp.hfile);
         if (ret >= 0) ret = (str->l <= INT_MAX)? (int) str->l : INT_MAX;
         else if (herrno(fp->fp.hfile)) ret = -2, errno = herrno(fp->fp.hfile);
         else ret = -1;

htslib/hfile.h

@@ -211,6 +211,19 @@ kstring's `kgetline()` to read arbitrarily-long lines into a _kstring_t_.
 HTSLIB_EXPORT
 char *hgets(char *buffer, int size, hFILE *fp) HTS_RESULT_USED;
 
+/// Read a line from a stream and append it to a kstring
+/** @param kstr    The destination kstring
+    @param fp      The file stream
+    @return  0 on success; EOF on end of file or if an error occurred.
+    @since   1.24
+
+Reads a "\n"- or "\r\n"- terminated line from fp into kstr.
+The line read is appended without its terminator and 0 is returned;
+EOF is returned at end of file or on error.
+*/
+HTSLIB_EXPORT
+int khgetline(struct kstring_t *kstr, hFILE *fp) HTS_RESULT_USED;
+
 /// Peek at characters to be read without removing them from buffers
 /** @param fp      The file stream
     @param buffer  The buffer to which the peeked bytes will be written

htslib/kstring.h

@@ -129,6 +129,10 @@ extern "C" {
     HTSLIB_EXPORT
     int kgetline(kstring_t *s, kgets_func *fgets_fn, void *fp);
 
+    /* Convenience function to call kgetline with a FILE * */
+    HTSLIB_EXPORT
+    int kfgetline(kstring_t *s, FILE *fp);
+
     /* kgetline2() uses the supplied hgetln()-like function to read a "\n"-
      * or "\r\n"-terminated line from fp.  The line read is appended to the
      * ksring without its terminator and 0 is returned; EOF is returned at

htslib/tbx.h

@@ -58,10 +58,13 @@ extern const tbx_conf_t tbx_conf_gff, tbx_conf_bed, tbx_conf_psltbl, tbx_conf_sa
 
     #define tbx_itr_destroy(iter) hts_itr_destroy(iter)
     #define tbx_itr_queryi(tbx, tid, beg, end) hts_itr_query((tbx)->idx, (tid), (beg), (end), tbx_readrec)
-    #define tbx_itr_querys(tbx, s) hts_itr_querys((tbx)->idx, (s), (hts_name2id_f)(tbx_name2id), (tbx), hts_itr_query, tbx_readrec)
+    #define tbx_itr_querys(tbx, s) tbx_itr_querys1((tbx), (s))
     #define tbx_itr_next(htsfp, tbx, itr, r) hts_itr_next(hts_get_bgzfp(htsfp), (itr), (r), (tbx))
     #define tbx_bgzf_itr_next(bgzfp, tbx, itr, r) hts_itr_next((bgzfp), (itr), (r), (tbx))
 
+    HTSLIB_EXPORT
+    hts_itr_t *tbx_itr_querys1(tbx_t *tbx, const char *region);
+
     HTSLIB_EXPORT
     int tbx_name2id(tbx_t *tbx, const char *ss);
 

htslib/vcf.h

@@ -1318,7 +1318,11 @@ set to one of BCF_ERR* codes and must be checked before calling bcf_write().
 
     #define bcf_itr_destroy(iter) hts_itr_destroy(iter)
     #define bcf_itr_queryi(idx, tid, beg, end) hts_itr_query((idx), (tid), (beg), (end), bcf_readrec)
-    #define bcf_itr_querys(idx, hdr, s) hts_itr_querys((idx), (s), (hts_name2id_f)(bcf_hdr_name2id), (hdr), hts_itr_query, bcf_readrec)
+    #define bcf_itr_querys(idx, hdr, s) bcf_itr_querys1((idx), (hdr), (s))
+
+    HTSLIB_EXPORT
+    hts_itr_t *bcf_itr_querys1(const hts_idx_t *idx, bcf_hdr_t *hdr,
+                               const char *region);
 
     static inline int bcf_itr_next(htsFile *htsfp, hts_itr_t *itr, void *r) {
         if (htsfp->is_bgzf)

kstring.c

@@ -290,6 +290,19 @@ int kgetline(kstring_t *s, kgets_func *fgets_fn, void *fp)
 	return 0;
 }
 
+// Wrap around fgets to get the right signature for kgets_func
+static char * fgets_wrapper(char *buffer, int size, void *stream)
+{
+    return fgets(buffer, size, (FILE *) stream);
+}
+
+int kfgetline(kstring_t *s, FILE *fp)
+{
+    if (!s || !fp)
+        return EOF;
+    return kgetline(s, fgets_wrapper, fp);
+}
+
 int kgetline2(kstring_t *s, kgets_func2 *fgets_fn, void *fp)
 {
 	size_t l0 = s->l;

sam.c

@@ -414,9 +414,14 @@ int bam_hdr_write(BGZF *fp, const sam_hdr_t *h)
     return 0;
 }
 
+// Wrap around bam_name2id() to get the right signature for hts_name2id_f
+static int bam_name2id_wrapper(void *vhdr, const char *ref) {
+    return bam_name2id((sam_hdr_t *) vhdr, ref);
+}
+
 const char *sam_parse_region(sam_hdr_t *h, const char *s, int *tid,
                              hts_pos_t *beg, hts_pos_t *end, int flags) {
-    return hts_parse_region(s, tid, beg, end, (hts_name2id_f)bam_name2id, h, flags);
+    return hts_parse_region(s, tid, beg, end, bam_name2id_wrapper, h, flags);
 }
 
 /*************************
@@ -1755,7 +1760,7 @@ static int cram_name2id(void *fdv, const char *ref)
 hts_itr_t *sam_itr_querys(const hts_idx_t *idx, sam_hdr_t *hdr, const char *region)
 {
     const hts_cram_idx_t *cidx = (const hts_cram_idx_t *) idx;
-    return hts_itr_querys(idx, region, (hts_name2id_f)(bam_name2id), hdr,
+    return hts_itr_querys(idx, region, bam_name2id_wrapper, hdr,
                           cidx->fmt == HTS_FMT_CRAI ? cram_itr_query : hts_itr_query,
                           sam_readrec);
 }
@@ -1777,10 +1782,10 @@ hts_itr_t *sam_itr_regarray(const hts_idx_t *idx, sam_hdr_t *hdr, char **regarra
         itr = hts_itr_regions(idx, r_list, r_count, cram_name2id, cidx->cram,
                    hts_itr_multi_cram, cram_readrec, cram_pseek, cram_ptell);
     } else {
-        r_list = hts_reglist_create(regarray, regcount, &r_count, hdr, (hts_name2id_f)(bam_name2id));
+        r_list = hts_reglist_create(regarray, regcount, &r_count, hdr, bam_name2id_wrapper);
         if (!r_list)
             return NULL;
-        itr = hts_itr_regions(idx, r_list, r_count, (hts_name2id_f)(bam_name2id), hdr,
+        itr = hts_itr_regions(idx, r_list, r_count, bam_name2id_wrapper, hdr,
                    hts_itr_multi_bam, sam_readrec, bam_pseek, bam_ptell);
     }
 
@@ -1801,7 +1806,7 @@ hts_itr_t *sam_itr_regions(const hts_idx_t *idx, sam_hdr_t *hdr, hts_reglist_t *
         return hts_itr_regions(idx, reglist, regcount, cram_name2id, cidx->cram,
                    hts_itr_multi_cram, cram_readrec, cram_pseek, cram_ptell);
     else
-        return hts_itr_regions(idx, reglist, regcount, (hts_name2id_f)(bam_name2id), hdr,
+        return hts_itr_regions(idx, reglist, regcount, bam_name2id_wrapper, hdr,
                    hts_itr_multi_bam, sam_readrec, bam_pseek, bam_ptell);
 }
 

tbx.c

@@ -640,3 +640,14 @@ const char **tbx_seqnames(tbx_t *tbx, int *n)
     return names;
 }
 
+// Wrap around tbx_name2id() to get the right signature for hts_name2id_f
+static int tbx_name2id_wrapper(void *vhdr, const char *ref)
+{
+    return tbx_name2id((tbx_t *) vhdr, ref);
+}
+
+hts_itr_t *tbx_itr_querys1(tbx_t *tbx, const char *region)
+{
+    return hts_itr_querys(tbx->idx, region, tbx_name2id_wrapper, tbx,
+                          hts_itr_query, tbx_readrec);
+}

vcf.c

@@ -2618,7 +2618,7 @@ bcf_hdr_t *vcf_hdr_read(htsFile *fp)
                 hts_log_error("Couldn't open \"%s\"", fp->fn_aux);
                 goto error;
             }
-            while (tmp.l = 0, kgetline(&tmp, (kgets_func *) hgets, f) >= 0) {
+            while (tmp.l = 0, khgetline(&tmp, f) >= 0) {
                 char *tab = strchr(tmp.s, '\t');
                 if (tab == NULL) continue;
                 e |= (kputs("##contig=<ID=", &txt) < 0);
@@ -4823,6 +4823,18 @@ int bcf_idx_save(htsFile *fp) {
     return sam_idx_save(fp);
 }
 
+// Wrap around bcf_hdr_name2id() to get the right signature for hts_name2id_f
+static int bcf_hdr_name2id_wrapper(void *vhdr, const char *ref) {
+    return bcf_hdr_name2id((bcf_hdr_t *) vhdr, ref);
+}
+
+hts_itr_t *bcf_itr_querys1(const hts_idx_t *idx, bcf_hdr_t *hdr,
+                           const char *region) {
+    return hts_itr_querys(idx, region, bcf_hdr_name2id_wrapper, hdr,
+                          hts_itr_query, bcf_readrec);
+}
+
+
 /*****************
  *** Utilities ***
  *****************/