Replace "norm --rm-dup none" with "--rm-dup exact". Resolves samtools…

…#1089

doc/bcftools.txt

@@ -1911,9 +1911,9 @@ the *<<fasta_ref,--fasta-ref>>* option is supplied.
     <http://samtools.github.io/bcftools/howtos/plugin.af-dist.html> and
     <http://samtools.github.io/bcftools/howtos/plugin.fixref.html>.)
 
-*-d, --rm-dup* 'snps'|'indels'|'both'|'all'|'none'::
-    If a record is present multiple times, output only the first instance,
-    see *--collapse* in *<<common_options,Common Options>>*.
+*-d, --rm-dup* 'snps'|'indels'|'both'|'all'|'exact'::
+    If a record is present multiple times, output only the first instance.
+    See also *--collapse* in *<<common_options,Common Options>>*.
 
 *-D, --remove-duplicates*::
     If a record is present in multiple files, output only the first instance.

test/test.pl

@@ -183,7 +183,9 @@
 test_vcf_norm($opts,in=>'norm.rmdup',out=>'norm.rmdup.3.out',args=>'-d both');
 test_vcf_norm($opts,in=>'norm.rmdup',out=>'norm.rmdup.4.out',args=>'-d all');
 test_vcf_norm($opts,in=>'norm.rmdup',out=>'norm.rmdup.5.out',args=>'-d none');
+test_vcf_norm($opts,in=>'norm.rmdup',out=>'norm.rmdup.5.out',args=>'-d exact');
 test_vcf_norm($opts,in=>'norm.rmdup.2',out=>'norm.rmdup.2.1.out',args=>'-d none');
+test_vcf_norm($opts,in=>'norm.rmdup.2',out=>'norm.rmdup.2.1.out',args=>'-d exact');
 test_vcf_norm($opts,in=>'norm.rmdup.2',out=>'norm.rmdup.2.1.out',args=>'-d indels');
 test_vcf_norm($opts,in=>'norm.rmdup.2',out=>'norm.rmdup.2.2.out',args=>'-d any');
 test_vcf_norm($opts,in=>'norm.rmdup.2',out=>'norm.rmdup.2.2.out',args=>'-d both');

vcfnorm.c

@@ -1848,7 +1848,7 @@ static void usage(void)
     fprintf(stderr, "Options:\n");
     fprintf(stderr, "    -c, --check-ref <e|w|x|s>         check REF alleles and exit (e), warn (w), exclude (x), or set (s) bad sites [e]\n");
     fprintf(stderr, "    -D, --remove-duplicates           remove duplicate lines of the same type.\n");
-    fprintf(stderr, "    -d, --rm-dup <type>               remove duplicate snps|indels|both|all|none\n");
+    fprintf(stderr, "    -d, --rm-dup <type>               remove duplicate snps|indels|both|all|exact\n");
     fprintf(stderr, "    -f, --fasta-ref <file>            reference sequence (MANDATORY)\n");
     fprintf(stderr, "    -m, --multiallelics <-|+>[type]   split multiallelics (-) or join biallelics (+), type: snps|indels|both|any [both]\n");
     fprintf(stderr, "        --no-version                  do not append version and command line to the header\n");
@@ -1915,6 +1915,7 @@ int main_vcfnorm(int argc, char *argv[])
                 else if ( !strcmp("all",optarg) ) args->rmdup = BCF_SR_PAIR_ANY;
                 else if ( !strcmp("any",optarg) ) args->rmdup = BCF_SR_PAIR_ANY;
                 else if ( !strcmp("none",optarg) ) args->rmdup = BCF_SR_PAIR_EXACT;
+                else if ( !strcmp("exact",optarg) ) args->rmdup = BCF_SR_PAIR_EXACT;
                 else error("The argument to -d not recognised: %s\n", optarg);
                 break;
             case 'm':