isec: Notify user about frequently forgotten -w

test/test.pl

@@ -132,7 +132,7 @@ sub test_cmd
     print "$test:\n";
     print "\t$args{cmd}\n";
 
-    my ($ret,$out) = _cmd("$args{cmd} 2>&1");
+    my ($ret,$out) = _cmd("$args{cmd}");
     if ( $ret ) { failed($opts,$test); return; }
     if ( $$opts{redo_outputs} && -e "$$opts{path}/$args{out}" )
     {
@@ -282,7 +282,7 @@ sub test_vcf_isec2
     }
     my $files = join(' ',@files);
     bgzip_tabix($opts,file=>$args{tab_in},suffix=>'tab',args=>'-s 1 -b 2 -e 3');
-    test_cmd($opts,%args,cmd=>"$$opts{bin}/bcftools isec $args{args} -t $$opts{tmp}/$args{tab_in}.tab.gz $files | grep -v ^##bcftools_isec");
+    test_cmd($opts,%args,cmd=>"$$opts{bin}/bcftools isec $args{args} -t $$opts{tmp}/$args{tab_in}.tab.gz $files 2>/dev/null | grep -v ^##bcftools_isec");
 }
 sub test_vcf_query
 {

vcfisec.c

@@ -118,6 +118,8 @@ void isec_vcf(args_t *args)
         bcf_hdr_append_version(files->readers[args->iwrite].header,args->argc,args->argv,"bcftools_isec");
         bcf_hdr_write(out_fh, files->readers[args->iwrite].header);
     }
+    if ( !args->nwrite && !out_std && !args->prefix )
+        fprintf(stderr,"Note: -w option not given, printing list of sites...\n");
 
     int n;
     while ( (n=bcf_sr_next_line(files)) )
@@ -298,7 +300,6 @@ static void destroy_data(args_t *args)
 static void usage(void)
 {
 	fprintf(stderr, "About:   Create intersections, unions and complements of VCF files.\n");
-	fprintf(stderr, "         \n");
 	fprintf(stderr, "Usage:   bcftools isec [options] <A.vcf.gz> <B.vcf.gz> ...\n");
 	fprintf(stderr, "Options:\n");
 	fprintf(stderr, "    -c, --collapse <string>           treat as identical records with <snps|indels|both|all|some|none>, see man page for details [none]\n");