norm: set --old-rec-tag and count REF-only trims as realigned

NEWS

@@ -88,6 +88,9 @@ Changes affecting specific commands:
     - Fix incorrect allele mappings and associated annotations when atomizing (`-a`)
       multiallelic records after a compound variant (#2607)
 
+    - When trimming the REF of reference-only records (ALT='.'), set the
+      `--old-rec-tag` annotation and count the record as realigned (#2391)
+
 * bcftools +prune
 
     - Fix a serious bug in estimating AF from genotypes when --AF-tag is not given.

test/norm.trim-ref.fa

@@ -0,0 +1,2 @@
+>1
+ACGTACGTACGGTTTTAGCATCGATCGATCAGCTAGCTAGCATCGACTAGCATCAGCTA

test/norm.trim-ref.out

@@ -0,0 +1,8 @@
+##fileformat=VCFv4.2
+##FILTER=<ID=PASS,Description="All filters passed">
+##reference=norm.trim-ref.fa
+##contig=<ID=1,length=59>
+##INFO=<ID=XX,Number=1,Type=String,Description="Original variant. Format: CHR|POS|REF|ALT|USED_ALT_IDX">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
+1	2	.	C	.	.	.	.
+1	12	.	G	.	.	.	XX=1|12|GTTTT|

test/norm.trim-ref.vcf

@@ -0,0 +1,6 @@
+##fileformat=VCFv4.2
+##reference=norm.trim-ref.fa
+##contig=<ID=1,length=59>
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
+1	2	.	C	.	.	.	.
+1	12	.	GTTTT	.	.	.	.

test/test.pl

@@ -358,6 +358,7 @@
 run_test(\&test_vcf_norm,$opts,in=>'norm.iupac.2',fai=>'norm.iupac.2',out=>'norm.iupac.2.1.out',args=>'-c sc --old-rec-tag XX');
 run_test(\&test_vcf_norm,$opts,in=>'norm.3',fai=>'norm.3',out=>'norm.3.out',args=>'-c s --old-rec-tag XX');
 run_test(\&test_vcf_norm,$opts,in=>'norm.3',fai=>'norm.3',out=>'norm.3.2.out',args=>q[-c s -i'alt="N"' --old-rec-tag XX]);
+run_test(\&test_vcf_norm,$opts,in=>'norm.trim-ref',fai=>'norm.trim-ref',out=>'norm.trim-ref.out',args=>'--old-rec-tag XX');
 run_test(\&test_vcf_norm,$opts,in=>'atomize.split.1',out=>'atomize.split.1.0.out',args=>['-a --old-rec-tag OLD_REC','-m -any --force']);
 run_test(\&test_vcf_norm,$opts,in=>'atomize.split.1',out=>'atomize.split.1.1.out',args=>['-m -any --old-rec-tag OLD_REC --force','-a']);
 run_test(\&test_vcf_norm,$opts,in=>'atomize.split.1',out=>'atomize.split.1.1.out',args=>'-m -any --old-rec-tag OLD_REC --force -a');

vcfnorm.c

@@ -762,6 +762,8 @@ static int realign(args_t *args, bcf1_t *line)
         {
             line->d.allele[0][1] = 0;
             bcf_update_alleles(args->out_hdr,line,(const char**)line->d.allele,line->n_allele);
+            old_rec_tag_set(args, line, 0);
+            args->nchanged++;
         }
         return ERR_OK;
     }