reveiw updates

htslib/synced_bcf_reader.h

@@ -1,7 +1,7 @@
 /// @file htslib/synced_bcf_reader.h
 /// Stream through multiple VCF files.
 /*
-    Copyright (C) 2012-2017, 2019-2024 Genome Research Ltd.
+    Copyright (C) 2012-2017, 2019-2025 Genome Research Ltd.
 
     Author: Petr Danecek <[email protected]>
 
@@ -243,19 +243,19 @@ int bcf_sr_add_reader(bcf_srs_t *readers, const char *fname);
  *  @readers: holder of the open readers
  *  @file_ptr: htsfile already opened
  *  @autoclose: close file along with reader or not, 1 - close, 0 - do not close
- *  @fname: file name of @file_ptr
+ *  @idxname: index file name for file in @file_ptr
  *
  *  Returns 1 if the call succeeded, or 0 on error.
  *
  *  See also the bcf_srs_t data structure for parameters controlling
  *  the reader's logic.
- *  If fname is NULL, uses file_ptr->fn for fname
- *  With fname as NULL, index file must be present in default location with
- *  default name, as file_ptr->fn doesn't contain index information
+ *  If idxname is NULL, uses file_ptr->fn to find index file.
+ *  With idxname as NULL, index file must be present along with the file with
+ *  default name
  */
 HTSLIB_EXPORT
 int bcf_sr_add_hreader(bcf_srs_t *readers, htsFile *file_ptr, int autoclose,
-    const char *fname);
+    const char *idxname);
 
 HTSLIB_EXPORT
 void bcf_sr_remove_reader(bcf_srs_t *files, int i);

synced_bcf_reader.c

@@ -1,6 +1,6 @@
 /*  synced_bcf_reader.c -- stream through multiple VCF files.
 
-    Copyright (C) 2012-2023 Genome Research Ltd.
+    Copyright (C) 2012-2023, 2025 Genome Research Ltd.
 
     Author: Petr Danecek <[email protected]>
 
@@ -253,6 +253,7 @@ int bcf_sr_add_reader(bcf_srs_t *files, const char *fname)
 {
     char fmode[5];
     int ret = 0;
+    const char *idxname = NULL;
 
     strcpy(fmode, "r");
     vcf_open_mode(fmode+1, fname, NULL);
@@ -261,13 +262,16 @@ int bcf_sr_add_reader(bcf_srs_t *files, const char *fname)
         files->errnum = open_failed;
         return 0;
     }
-    if (!(ret = bcf_sr_add_hreader(files, file_ptr, 1, fname))) {
+    //get idx name and pass to add_hreader
+    idxname = strstr(fname, HTS_IDX_DELIM);
+    idxname += idxname ? sizeof(HTS_IDX_DELIM) - 1 : 0;
+    if (!(ret = bcf_sr_add_hreader(files, file_ptr, 1, idxname))) {
         hts_close(file_ptr);    //failed, close the file
     }
     return ret;
 }
 
-int bcf_sr_add_hreader(bcf_srs_t *files, htsFile *file_ptr, int autoclose, const char *fname)
+int bcf_sr_add_hreader(bcf_srs_t *files, htsFile *file_ptr, int autoclose, const char *idxname)
 {
     aux_t *auxdata = NULL;
     if ( ! file_ptr ) {
@@ -306,7 +310,7 @@ int bcf_sr_add_hreader(bcf_srs_t *files, htsFile *file_ptr, int autoclose, const
                 return 0;
             }
 
-            reader->tbx_idx = tbx_index_load(fname ? fname : file_ptr->fn);
+            reader->tbx_idx = tbx_index_load2(file_ptr->fn, idxname);
             if ( !reader->tbx_idx )
             {
                 files->errnum = idx_load_failed;
@@ -325,7 +329,7 @@ int bcf_sr_add_hreader(bcf_srs_t *files, htsFile *file_ptr, int autoclose, const
 
             reader->header = bcf_hdr_read(reader->file);
 
-            reader->bcf_idx = bcf_index_load(fname ? fname : file_ptr->fn);
+            reader->bcf_idx = bcf_index_load2(file_ptr->fn, idxname);
             if ( !reader->bcf_idx )
             {
                 files->errnum = idx_load_failed;
@@ -378,7 +382,7 @@ int bcf_sr_add_hreader(bcf_srs_t *files, htsFile *file_ptr, int autoclose, const
         return 0;
     }
 
-    reader->fname = strdup(fname ? fname : file_ptr->fn);
+    reader->fname = strdup(file_ptr->fn);
     if ( files->apply_filters )
         reader->filter_ids = init_filters(reader->header, files->apply_filters, &reader->nfilter_ids);
 

test/test-bcf-sr.c

@@ -1,5 +1,5 @@
 /*
-    Copyright (C) 2017, 2020, 2023 Genome Research Ltd.
+    Copyright (C) 2017, 2020, 2023, 2025 Genome Research Ltd.
 
     Author: Petr Danecek <[email protected]>
 
@@ -63,6 +63,7 @@ void HTS_NORETURN usage(int exit_code)
     fprintf(stderr, "   -p, --pair <logic[+ref]>     logic: snps,indels,both,snps+ref,indels+ref,both+ref,exact,some,all\n");
     fprintf(stderr, "   -r, --regions <reg_list>     comma-separated list of regions\n");
     fprintf(stderr, "   -t, --targets <reg_list>     comma-separated list of targets\n");
+    fprintf(stderr, "   -u, --usefptr                use hfile pointer interface on reader addition\n");
     fprintf(stderr, "\n");
     exit(exit_code);
 }
@@ -240,7 +241,10 @@ int main(int argc, char *argv[])
             }
             /*with name, index can be anywhere, named as anything
               w/o name it has to be along with file with default naming*/
-            if ( !bcf_sr_add_hreader(sr, htsfp[i], 1, vcfs[i]) ) {
+
+            const char *idxname = strstr(vcfs[i], HTS_IDX_DELIM);
+            idxname += idxname ? sizeof(HTS_IDX_DELIM) - 1 : 0;
+            if ( !bcf_sr_add_hreader(sr, htsfp[i], 1, idxname) ) {
                 error("Failed to add reader %s: %s\n", vcfs[i],
                     bcf_sr_strerror(sr->errnum));
             }