Use hts_get_format() rather than direct access to htsFile internals

dlaehnemann · Nov 3, 2014 · c415df1 · c415df1
1 parent 3d5d3d9
commit c415df1
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Showing 3 changed files with 5 additions and 5 deletions.
diff --git a/reheader.c b/reheader.c
@@ -48,7 +48,7 @@ args_t;
 static void init_data(args_t *args)
 {
     htsFile *fp = hts_open(args->fname,"r");
-    args->type = fp->type;
+    args->type = *hts_get_format(fp);
     hts_close(fp);
 }
 

diff --git a/vcfannotate.c b/vcfannotate.c
@@ -1419,7 +1419,7 @@ int main_vcfannotate(int argc, char *argv[])
     if ( args->targets_fname )
     {
         htsFile *fp = hts_open(args->targets_fname,"r"); 
-        htsFormat type = fp->type;
+        htsFormat type = *hts_get_format(fp);
         hts_close(fp);
 
         if ( type.format==vcf || type.format==bcf )

diff --git a/vcfindex.c b/vcfindex.c
@@ -70,12 +70,12 @@ int vcf_index_stats(char *fname, int stats)
     bcf_hdr_t *hdr = bcf_hdr_read(fp);
     if ( !hdr ) { fprintf(stderr,"Could not read the header: %s\n", fname); return 1; }
 
-    if ( fp->type.format==vcf )
+    if ( hts_get_format(fp)->format==vcf )
     {
         tbx = tbx_index_load(fname);
         if ( !tbx ) { fprintf(stderr,"Could not load TBI index: %s\n", fname); return 1; }
     }
-    else if ( fp->type.format==bcf )
+    else if ( hts_get_format(fp)->format==bcf )
     {
         idx = bcf_index_load(fname);
         if ( !idx ) { fprintf(stderr,"Could not load CSI index: %s\n", fname); return 1; }
@@ -178,7 +178,7 @@ int main_vcfindex(int argc, char *argv[])
     if (stats) return vcf_index_stats(fname, stats);
 
     htsFile *fp = hts_open(fname,"r"); 
-    htsFormat type = fp->type;
+    htsFormat type = *hts_get_format(fp);
     hts_close(fp);
 
     if ( (type.format!=bcf && type.format!=vcf) || type.compression!=bgzf )