Make the -t ./x mode select both phased and unphased genotypes,

as advertised by the usage page.

Fixes #1844

Author: pd3

NEWS

@@ -105,6 +105,9 @@ Changes affecting specific commands:
 
     - Add new `--new-gt X` option (#1800)
 
+    - Fix a bug where `-t ./x` mode was advertised as selecting both phased and unphased
+      half-missing genotypes, but was in fact selecting only unphased genotypes (#1844)
+
 * bcftools +split-vep
 
     - New options `-g, --gene-list` and `--gene-list-fields` which allow to prioritize
@@ -119,7 +122,7 @@ Changes affecting specific commands:
 
 * bcftools +tag2tag
 
-    - Revamp of the plugin to allo wider range of tag conversions, specifically all combinations
+    - Revamp of the plugin to allow wider range of tag conversions, specifically all combinations
       from FORMAT/GL,PL,GP to FORMAT/GL,PL,GP,GT
 
 * bcftools +trio-dnm2

plugins/setGT.c

@@ -1,6 +1,6 @@
 /*  plugins/setGT.c -- set gentoypes to given values
 
-    Copyright (C) 2015-2022 Genome Research Ltd.
+    Copyright (C) 2015-2023 Genome Research Ltd.
 
     Author: Petr Danecek <[email protected]>
 
@@ -570,7 +570,7 @@ bcf1_t *process(bcf1_t *rec)
             {
                 if ( ptr[j]==bcf_int32_vector_end ) break;
                 ploidy++;
-                if ( ptr[j]==bcf_gt_missing ) nmiss++;
+                if ( bcf_gt_is_missing(ptr[j]) ) nmiss++;
             }
 
             int do_set = 0;

test/setGT.6.1.out

@@ -0,0 +1,7 @@
+##fileformat=VCFv4.2
+##FILTER=<ID=PASS,Description="All filters passed">
+##contig=<ID=1,assembly=b37,length=249250621>
+##reference=file:ref.fa
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	A	B	C	D
+1	1890	.	A	G	.	.	.	GT	./.	./.	1/1	1|1

test/setGT.6.vcf

@@ -0,0 +1,6 @@
+##fileformat=VCFv4.2
+##contig=<ID=1,assembly=b37,length=249250621>
+##reference=file:ref.fa
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	A	B	C	D
+1	1890	.	A	G	.	.	.	GT	1/.	1|.	1/1	1|1

test/test.pl

@@ -522,6 +522,8 @@
 run_test(\&test_vcf_plugin,$opts,in=>'setGT.4',out=>'setGT.4.1.out',cmd=>'+setGT --no-version',args=>q[-- -t q -n . -e 'FMT/DP>90']);
 run_test(\&test_vcf_plugin,$opts,in=>'setGT.4',out=>'setGT.4.2.out',cmd=>'+setGT --no-version',args=>q[-- -t q -n . -e 'FMT/DP>100']);
 run_test(\&test_vcf_plugin,$opts,in=>'setGT.5',out=>'setGT.5.1.out',cmd=>'+setGT --no-version',args=>q[-- -t a -n X]);
+run_test(\&test_vcf_plugin,$opts,in=>'setGT.6',out=>'setGT.6.1.out',cmd=>'+setGT --no-version',args=>q[-- -t ./x -n .]);
+run_test(\&test_vcf_plugin,$opts,in=>'setGT.6',out=>'setGT.6.1.out',cmd=>'+setGT --no-version',args=>q[-- -t . -n .]);
 run_test(\&test_vcf_plugin,$opts,in=>'plugin1',out=>'fill-AN-AC.out',cmd=>'+fill-AN-AC --no-version');
 run_test(\&test_vcf_plugin,$opts,in=>'dosage',out=>'dosage.1.out',cmd=>'+dosage',args=>'-- -t PL');
 run_test(\&test_vcf_plugin,$opts,in=>'dosage',out=>'dosage.2.out',cmd=>'+dosage',args=>'-- -t GL');