Fix Number in the header definition of transferred FILTER and ID tags

Resolves #2335
samtools · Jan 1, 2025 · c58d522 · c58d522
1 parent da58fb4
commit c58d522
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Showing 9 changed files with 15 additions and 11 deletions.
diff --git a/NEWS b/NEWS
@@ -12,6 +12,10 @@ Changes affecting specific commands:
     - New experimental plugin for scoring variants and assess site noisiness (allelic frequency profiles)
       from a large number of unaffected parental samples
 
+* bcftools annotate
+
+    - Fix Number in the header definition of transferred FILTER and ID tags (#2335)
+
 * bcftools convert
 
     - The command `convert --gvcf2vcf` was not filling the REF allele when BCF was output (#243)

diff --git a/test/annotate19.1.out b/test/annotate19.1.out
@@ -4,7 +4,7 @@
 ##reference=file:///lustre/scratch105/projects/g1k/ref/main_project/human_g1k_v37.fasta
 ##FILTER=<ID=ori_filter1,Description="Test">
 ##FILTER=<ID=ori_filter2,Description="Test">
-##INFO=<ID=ID,Number=1,Type=String,Description="Transferred ID column">
+##INFO=<ID=ID,Number=.,Type=String,Description="Transferred ID column">
 ##INFO=<ID=INFO_ID,Number=1,Type=String,Description="Test">
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
 1	3000001	id_id1;id_id2;info_id	C	T	.	ori_filter1;ori_filter2	ID=id_id1,id_id2;INFO_ID=info_id
diff --git a/test/annotate19.2.out b/test/annotate19.2.out
@@ -5,7 +5,7 @@
 ##FILTER=<ID=ori_filter1,Description="Test">
 ##FILTER=<ID=ori_filter2,Description="Test">
 ##FILTER=<ID=filter_filter,Description="Test">
-##INFO=<ID=FILTER,Number=1,Type=String,Description="Transferred FILTER column">
+##INFO=<ID=FILTER,Number=.,Type=String,Description="Transferred FILTER column">
 ##INFO=<ID=INFO_FILTER,Number=1,Type=String,Description="Test">
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
 1	3000001	ori_id	C	T	.	filter_filter	FILTER=filter_filter;INFO_FILTER=info_filter
diff --git a/test/annotate19.3.out b/test/annotate19.3.out
@@ -4,7 +4,7 @@
 ##reference=file:///lustre/scratch105/projects/g1k/ref/main_project/human_g1k_v37.fasta
 ##FILTER=<ID=ori_filter1,Description="Test">
 ##FILTER=<ID=ori_filter2,Description="Test">
-##INFO=<ID=FILTER,Number=1,Type=String,Description="Transferred FILTER column">
+##INFO=<ID=FILTER,Number=.,Type=String,Description="Transferred FILTER column">
 ##INFO=<ID=INFO_FILTER,Number=1,Type=String,Description="Test">
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
 1	3000001	ori_id	C	T	.	ori_filter1;ori_filter2	FILTER=filter_filter;INFO_FILTER=info_filter
diff --git a/test/annotate19.4.out b/test/annotate19.4.out
@@ -4,6 +4,6 @@
 ##reference=file:///lustre/scratch105/projects/g1k/ref/main_project/human_g1k_v37.fasta
 ##FILTER=<ID=ori_filter1,Description="Test">
 ##FILTER=<ID=ori_filter2,Description="Test">
-##INFO=<ID=FILTER,Number=1,Type=String,Description="Transferred FILTER column">
+##INFO=<ID=FILTER,Number=.,Type=String,Description="Transferred FILTER column">
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
 1	3000001	ori_id	C	T	.	ori_filter1;ori_filter2	FILTER=ori_filter1,ori_filter2
diff --git a/test/annotate19.5.out b/test/annotate19.5.out
@@ -4,6 +4,6 @@
 ##reference=file:///lustre/scratch105/projects/g1k/ref/main_project/human_g1k_v37.fasta
 ##FILTER=<ID=ori_filter1,Description="Test">
 ##FILTER=<ID=ori_filter2,Description="Test">
-##INFO=<ID=FILTER,Number=1,Type=String,Description="Transferred FILTER column">
+##INFO=<ID=FILTER,Number=.,Type=String,Description="Transferred FILTER column">
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
 1	3000001	ori_id	C	T	.	ori_filter1;ori_filter2	FILTER=filter_filter
diff --git a/test/annotate19.6.out b/test/annotate19.6.out
@@ -4,7 +4,7 @@
 ##reference=file:///lustre/scratch105/projects/g1k/ref/main_project/human_g1k_v37.fasta
 ##FILTER=<ID=ori_filter1,Description="Test">
 ##FILTER=<ID=ori_filter2,Description="Test">
-##INFO=<ID=FILTER,Number=1,Type=String,Description="Transferred FILTER column">
+##INFO=<ID=FILTER,Number=.,Type=String,Description="Transferred FILTER column">
 ##FILTER=<ID=filter_filter,Description="Test">
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
 1	3000001	ori_id	C	T	.	filter_filter	FILTER=ori_filter1,ori_filter2
diff --git a/test/annotate19.7.out b/test/annotate19.7.out
@@ -5,6 +5,6 @@
 ##FILTER=<ID=ori_filter1,Description="Test">
 ##FILTER=<ID=ori_filter2,Description="Test">
 ##FILTER=<ID=filter_filter,Description="Test">
-##INFO=<ID=FILTER,Number=1,Type=String,Description="Transferred FILTER column">
+##INFO=<ID=FILTER,Number=.,Type=String,Description="Transferred FILTER column">
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
 1	3000001	ori_id	C	T	.	filter_filter	FILTER=filter_filter
diff --git a/vcfannotate.c b/vcfannotate.c
@@ -1,6 +1,6 @@
 /*  vcfannotate.c -- Annotate and edit VCF/BCF files.
 
-    Copyright (C) 2013-2024 Genome Research Ltd.
+    Copyright (C) 2013-2025 Genome Research Ltd.
 
     Author: Petr Danecek <[email protected]>
 
@@ -2414,7 +2414,7 @@ static void init_columns(args_t *args)
                 col->hdr_key_src = strdup(ptr+2);
                 col->hdr_key_dst = strdup(str.s+5);
                 tmp.l = 0;
-                ksprintf(&tmp,"##INFO=<ID=%s,Number=1,Type=String,Description=\"Transferred FILTER column\">",col->hdr_key_dst);
+                ksprintf(&tmp,"##INFO=<ID=%s,Number=.,Type=String,Description=\"Transferred FILTER column\">",col->hdr_key_dst);
                 bcf_hdr_append(args->hdr_out, tmp.s);
                 if (bcf_hdr_sync(args->hdr_out) < 0) error_errno("[%s] Failed to update header", __func__);
                 int hdr_id = bcf_hdr_id2int(args->hdr_out, BCF_DT_ID, col->hdr_key_dst);
@@ -2672,13 +2672,13 @@ static void init_columns(args_t *args)
                     {
                         // transferring ID column into a new INFO tag
                         tmp.l = 0;
-                        ksprintf(&tmp,"##INFO=<ID=%s,Number=1,Type=String,Description=\"Transferred ID column\">",key_dst);
+                        ksprintf(&tmp,"##INFO=<ID=%s,Number=.,Type=String,Description=\"Transferred ID column\">",key_dst);
                     }
                     else if ( !strcasecmp("FILTER",key_src) && !explicit_src_info )
                     {
                         // transferring FILTER column into a new INFO tag
                         tmp.l = 0;
-                        ksprintf(&tmp,"##INFO=<ID=%s,Number=1,Type=String,Description=\"Transferred FILTER column\">",key_dst);
+                        ksprintf(&tmp,"##INFO=<ID=%s,Number=.,Type=String,Description=\"Transferred FILTER column\">",key_dst);
                     }
                     else
                     {