Improve error messages. Resolves samtools#951 and samtools#925

consensus.c

@@ -208,7 +208,7 @@ static void init_data(args_t *args)
 {
     args->files = bcf_sr_init();
     args->files->require_index = 1;
-    if ( !bcf_sr_add_reader(args->files,args->fname) ) error("Failed to open %s: %s\n", args->fname, bcf_sr_strerror(args->files->errnum));
+    if ( !bcf_sr_add_reader(args->files,args->fname) ) error("Failed to read from %s: %s\n", !strcmp("-",args->fname)?"standard input":args->fname, bcf_sr_strerror(args->files->errnum));
     args->hdr = args->files->readers[0].header;
     args->isample = -1;
     if ( args->sample )

csq.c

@@ -1365,7 +1365,7 @@ void init_data(args_t *args)
     if ( args->output_type==FT_TAB_TEXT )
     {
         args->out = args->output_fname ? fopen(args->output_fname,"w") : stdout;
-        if ( !args->out ) error("Failed to open %s: %s\n", args->output_fname,strerror(errno));
+        if ( !args->out ) error("Failed to write to %s: %s\n", !strcmp("-",args->output_fname)?"standard output":args->output_fname,strerror(errno));
 
         fprintf(args->out,"# This file was produced by: bcftools +csq(%s+htslib-%s)\n", bcftools_version(),hts_version());
         fprintf(args->out,"# The command line was:\tbcftools +%s", args->argv[0]);
@@ -4032,7 +4032,7 @@ int main_csq(int argc, char *argv[])
     if ( regions_list && bcf_sr_set_regions(args->sr, regions_list, regions_is_file)<0 )
         error("Failed to read the regions: %s\n", regions_list);
     if ( !bcf_sr_add_reader(args->sr, fname) )
-        error("Failed to open %s: %s\n", fname,bcf_sr_strerror(args->sr->errnum));
+        error("Failed to read from %s: %s\n", !strcmp("-",fname)?"standard input":fname,bcf_sr_strerror(args->sr->errnum));
     args->hdr = bcf_sr_get_header(args->sr,0);
 
     init_data(args);

plugins/mendelian.c

@@ -371,7 +371,7 @@ int run(int argc, char **argv)
     }
 
     args.sr = bcf_sr_init();
-    if ( !bcf_sr_add_reader(args.sr, fname) ) error("Failed to open %s: %s\n", fname,bcf_sr_strerror(args.sr->errnum));
+    if ( !bcf_sr_add_reader(args.sr, fname) ) error("Failed to read from %s: %s\n", !strcmp("-",fname)?"standard input":fname,bcf_sr_strerror(args.sr->errnum));
     args.hdr = bcf_sr_get_header(args.sr, 0);
     if ( args.mode!=MODE_COUNT )
     {

polysomy.c

@@ -177,7 +177,7 @@ static void init_data(args_t *args)
         if ( bcf_sr_set_targets(files, args->targets_list, args->targets_is_file, 0)<0 )
             error("Failed to read the targets: %s\n", args->targets_list);
     }
-    if ( !bcf_sr_add_reader(files, args->fname) ) error("Failed to open %s: %s\n", args->fname,bcf_sr_strerror(files->errnum));
+    if ( !bcf_sr_add_reader(files, args->fname) ) error("Failed to read from %s: %s\n", !strcmp("-",args->fname)?"standard input":args->fname,bcf_sr_strerror(files->errnum));
     bcf_hdr_t *hdr = files->readers[0].header;
     if ( !args->sample )
     {

reheader.c

@@ -676,7 +676,7 @@ int main_reheader(int argc, char *argv[])
     if ( !args->fname ) usage(args);
 
     args->fp = hts_open(args->fname,"r");
-    if ( !args->fp ) error("Failed to open: %s\n", args->fname);
+    if ( !args->fp ) error("Failed to read from %s\n", !strcmp("-",args->fname)?"standard input":args->fname);
     args->type = *hts_get_format(args->fp);
 
     if ( args->type.format==vcf )

vcfannotate.c

@@ -2625,7 +2625,7 @@ int main_vcfannotate(int argc, char *argv[])
         }
     }
     if ( bcf_sr_set_threads(args->files, args->n_threads)<0 ) error("Failed to create threads\n");
-    if ( !bcf_sr_add_reader(args->files, fname) ) error("Failed to open %s: %s\n", fname,bcf_sr_strerror(args->files->errnum));
+    if ( !bcf_sr_add_reader(args->files, fname) ) error("Failed to read from %s: %s\n", !strcmp("-",fname)?"standard input":fname,bcf_sr_strerror(args->files->errnum));
 
     static int line_errcode_warned = 0;
     init_data(args);

vcfcall.c

@@ -578,7 +578,8 @@ static void init_data(args_t *args)
             error("Failed to read the regions: %s\n", args->regions);
     }
 
-    if ( !bcf_sr_add_reader(args->aux.srs, args->bcf_fname) ) error("Failed to open %s: %s\n", args->bcf_fname,bcf_sr_strerror(args->aux.srs->errnum));
+    if ( !bcf_sr_add_reader(args->aux.srs, args->bcf_fname) )
+        error("Failed to read from %s: %s\n", !strcmp("-",args->bcf_fname)?"standard input":args->bcf_fname,bcf_sr_strerror(args->aux.srs->errnum));
     args->aux.hdr = bcf_sr_get_header(args->aux.srs,0);
 
     int i;

vcfcnv.c

@@ -1399,7 +1399,8 @@ int main_vcfcnv(int argc, char *argv[])
         if ( bcf_sr_set_targets(args->files, args->af_fname, 1, 3)<0 )
             error("Failed to read the targets: %s\n", args->af_fname);
     }
-    if ( !bcf_sr_add_reader(args->files, fname) ) error("Failed to open %s: %s\n", fname,bcf_sr_strerror(args->files->errnum));
+    if ( !bcf_sr_add_reader(args->files, fname) )
+        error("Failed to read from %s: %s\n", !strcmp("-",fname)?"standard input":fname,bcf_sr_strerror(args->files->errnum));
 
     init_data(args);
     while ( bcf_sr_next_line(args->files) )

vcffilter.c

@@ -539,7 +539,7 @@ int main_vcffilter(int argc, char *argv[])
         if ( bcf_sr_set_targets(args->files, args->targets_list,targets_is_file, 0)<0 )
             error("Failed to read the targets: %s\n", args->targets_list);
     }
-    if ( !bcf_sr_add_reader(args->files, fname) ) error("Failed to open %s: %s\n", fname,bcf_sr_strerror(args->files->errnum));
+    if ( !bcf_sr_add_reader(args->files, fname) ) error("Failed to read from %s: %s\n", !strcmp("-",fname)?"standard input":fname,bcf_sr_strerror(args->files->errnum));
 
     init_data(args);
     if ( bcf_hdr_write(args->out_fh, args->hdr)!=0 ) error("[%s] Error: cannot write the header to %s\n", __func__,args->output_fname);

vcfgtcheck.c

@@ -805,7 +805,8 @@ int main_vcfgtcheck(int argc, char *argv[])
     if ( regions && bcf_sr_set_regions(args->files, regions, regions_is_file)<0 ) error("Failed to read the regions: %s\n", regions);
     if ( targets && bcf_sr_set_targets(args->files, targets, targets_is_file, 0)<0 ) error("Failed to read the targets: %s\n", targets);
     if ( !bcf_sr_add_reader(args->files, fname) ) error("Failed to open %s: %s\n", fname,bcf_sr_strerror(args->files->errnum));
-    if ( args->gt_fname && !bcf_sr_add_reader(args->files, args->gt_fname) ) error("Failed to open %s: %s\n", args->gt_fname,bcf_sr_strerror(args->files->errnum));
+    if ( args->gt_fname && !bcf_sr_add_reader(args->files, args->gt_fname) )
+        error("Failed to read from %s: %s\n", !strcmp("-",args->gt_fname)?"standard input":args->gt_fname,bcf_sr_strerror(args->files->errnum));
     args->files->collapse = COLLAPSE_SNPS|COLLAPSE_INDELS;
     if ( args->plot ) args->plot = init_prefix(args->plot);
     init_data(args);

vcfnorm.c

@@ -1990,7 +1990,7 @@ int main_vcfnorm(int argc, char *argv[])
     }
 
     if ( bcf_sr_set_threads(args->files, args->n_threads)<0 ) error("Failed to create threads\n");
-    if ( !bcf_sr_add_reader(args->files, fname) ) error("Failed to open %s: %s\n", fname,bcf_sr_strerror(args->files->errnum));
+    if ( !bcf_sr_add_reader(args->files, fname) ) error("Failed to read from %s: %s\n", !strcmp("-",fname)?"standard input":fname,bcf_sr_strerror(args->files->errnum));
     if ( args->mrows_op&MROWS_SPLIT && args->rmdup ) error("Cannot combine -D and -m-\n");
     init_data(args);
     normalize_vcf(args);

vcfplugin.c

@@ -624,7 +624,7 @@ int main_plugin(int argc, char *argv[])
             error("Failed to read the targets: %s\n", args->targets_list);
         args->files->collapse |= COLLAPSE_SOME;
     }
-    if ( !bcf_sr_add_reader(args->files, fname) ) error("Failed to open %s: %s\n", fname,bcf_sr_strerror(args->files->errnum));
+    if ( !bcf_sr_add_reader(args->files, fname) ) error("Failed to read from %s: %s\n", !strcmp("-",fname)?"standard input":fname,bcf_sr_strerror(args->files->errnum));
 
     init_data(args);
     while ( bcf_sr_next_line(args->files) )

vcfquery.c

@@ -323,7 +323,7 @@ int main_vcfquery(int argc, char *argv[])
     {
         if ( !fname ) error("Missing the VCF file name\n");
         args->files = bcf_sr_init();
-        if ( !bcf_sr_add_reader(args->files, fname) ) error("Failed to open %s: %s\n", fname,bcf_sr_strerror(args->files->errnum));
+        if ( !bcf_sr_add_reader(args->files, fname) ) error("Failed to read from %s: %s\n", !strcmp("-",fname)?"standard input":fname,bcf_sr_strerror(args->files->errnum));
         list_columns(args);
         bcf_sr_destroy(args->files);
         free(args);
@@ -352,7 +352,7 @@ int main_vcfquery(int argc, char *argv[])
         }
         while ( fname )
         {
-            if ( !bcf_sr_add_reader(args->files, fname) ) error("Failed to open %s: %s\n", fname,bcf_sr_strerror(args->files->errnum));
+            if ( !bcf_sr_add_reader(args->files, fname) ) error("Failed to read from %s: %s\n", !strcmp("-",fname)?"standard input":fname,bcf_sr_strerror(args->files->errnum));
             fname = ++optind < argc ? argv[optind] : NULL;
         }
         init_data(args);

vcfroh.c

@@ -1234,7 +1234,7 @@ int main_vcfroh(int argc, char *argv[])
     }
     if ( args->n_threads && bcf_sr_set_threads(args->files, args->n_threads)<0)
         error("Failed to create threads\n");
-    if ( !bcf_sr_add_reader(args->files, fname) ) error("Failed to open %s: %s\n", fname,bcf_sr_strerror(args->files->errnum));
+    if ( !bcf_sr_add_reader(args->files, fname) ) error("Failed to read from %s: %s\n", !strcmp("-",fname)?"standard input":fname,bcf_sr_strerror(args->files->errnum));
 
     init_data(args);
     while ( bcf_sr_next_line(args->files) )

vcfstats.c

@@ -1716,7 +1716,7 @@ int main_vcfstats(int argc, char *argv[])
     while (fname)
     {
         if ( !bcf_sr_add_reader(args->files, fname) )
-            error("Failed to open %s: %s\n", fname,bcf_sr_strerror(args->files->errnum));
+            error("Failed to read from %s: %s\n", !strcmp("-",fname)?"standard input":fname,bcf_sr_strerror(args->files->errnum));
         fname = ++optind < argc ? argv[optind] : NULL;
     }
 

vcfview.c

@@ -740,7 +740,7 @@ int main_vcfview(int argc, char *argv[])
     }
 
     if ( bcf_sr_set_threads(args->files, args->n_threads)<0 ) error("Failed to create threads\n");
-    if ( !bcf_sr_add_reader(args->files, fname) ) error("Failed to open %s: %s\n", fname,bcf_sr_strerror(args->files->errnum));
+    if ( !bcf_sr_add_reader(args->files, fname) ) error("Failed to read from %s: %s\n", !strcmp("-",fname)?"standard input":fname,bcf_sr_strerror(args->files->errnum));
 
     init_data(args);
     bcf_hdr_t *out_hdr = args->hnull ? args->hnull : (args->hsub ? args->hsub : args->hdr);