Add chunked hFILE input scheme

hfile.c

@@ -1111,6 +1111,7 @@ static int init_add_plugin(void *obj, int (*init)(struct hFILE_plugin *),
 static int load_hfile_plugins(void)
 {
     static const struct hFILE_scheme_handler
+        chunked = { hopen_chunked_manifest, hfile_always_local, "built-in", 80 },
         data = { hopen_mem, hfile_always_local, "built-in", 80 },
         file = { hopen_fd_fileuri, hfile_always_local, "built-in", 80 },
         preload = { hopen_preload, is_preload_url_remote, "built-in", 80 };
@@ -1119,6 +1120,7 @@ static int load_hfile_plugins(void)
     if (schemes == NULL)
         return -1;
 
+    hfile_add_scheme_handler("chunked", &chunked);
     hfile_add_scheme_handler("data", &data);
     hfile_add_scheme_handler("file", &file);
     hfile_add_scheme_handler("preload", &preload);

hfile_internal.h

@@ -57,6 +57,10 @@ struct BGZF;
  */
 struct hFILE *bgzf_hfile(struct BGZF *fp);
 
+/* Opens chunked: manifests as seekable logical files. */
+struct hFILE *hopen_chunked_manifest(const char *url, const char *mode)
+    HTS_RESULT_USED;
+
 /*!
   @abstract Closes all hFILE plugins that have been loaded
 */

hts.c

@@ -2827,11 +2827,17 @@ static int idx_save_core(const hts_idx_t *idx, BGZF *fp, int fmt)
 int hts_idx_save(const hts_idx_t *idx, const char *fn, int fmt)
 {
     int ret, save;
+    const char *fn_local;
+
     if (idx == NULL || fn == NULL) { errno = EINVAL; return -1; }
-    char *fnidx = (char*)calloc(1, strlen(fn) + 5);
+
+    fn_local = strncmp(fn, "chunked:", 8) == 0 && !hisremote(fn + 8)
+        ? fn + 8 : fn;
+
+    char *fnidx = (char*)calloc(1, strlen(fn_local) + 5);
     if (fnidx == NULL) return -1;
 
-    strcpy(fnidx, fn);
+    strcpy(fnidx, fn_local);
     switch (fmt) {
     case HTS_FMT_BAI: strcat(fnidx, ".bai"); break;
     case HTS_FMT_CSI: strcat(fnidx, ".csi"); break;
@@ -4776,8 +4782,9 @@ int hts_idx_check_local(const char *fn, int fmt, char **fnidx) {
                 break;
             }
     } else {
+        if (strncmp(fn, "chunked:", 8) == 0 && !hisremote(fn + 8)) fn_tmp = fn + 8;
         // Borrowed from hopen_fd_fileuri()
-        if (strncmp(fn, "file://localhost/", 17) == 0) fn_tmp = fn + 16;
+        else if (strncmp(fn, "file://localhost/", 17) == 0) fn_tmp = fn + 16;
         else if (strncmp(fn, "file:///", 8) == 0) fn_tmp = fn + 7;
         else fn_tmp = fn;
 #if defined(_WIN32) || defined(__MSYS__)

htslib/hfile.h

@@ -69,6 +69,10 @@ The usual `fopen(3)` _mode_ letters are supported: one of
 `r` (read), `w` (write), `a` (append), optionally followed by any of
 `+` (update), `e` (close on `exec(2)`), `x` (create exclusively),
 `:` (indicates scheme-specific variable arguments follow).
+
+The built-in `chunked:` scheme opens a read-only manifest containing one
+chunk filename per line and presents the chunks as one seekable logical file.
+Blank lines and lines beginning with `#` are ignored.
 */
 HTSLIB_EXPORT
 hFILE *hopen(const char *filename, const char *mode, ...) HTS_RESULT_USED;