Make it possible to refer to the ID column from the FORMAT expression

For example
    bcftools query test.vcf -f 'ID=%ID  ID=[ %/ID]  vs  FMT_ID=[ %ID]'

The same is now possible for CHROM, POS, REF, etc

Resolves #2337

NEWS

@@ -43,6 +43,10 @@ Changes affecting specific commands:
         bcftools query test.vcf -f '%CHROM:%POS \t [ %AD]  \t   %SUM(FMT/AD)'
         bcftools query test.vcf -f '%CHROM:%POS \t [ %AD]  \t   %SUM(INFO/AD)'
 
+    - Make it possible to refer to the ID column from the FORMAT expression (#2337)
+
+        bcftools query test.vcf -f 'ID=%ID  ID=[ %/ID]  vs  FMT_ID=[ %ID]'
+
 * bcftools roh
 
     - New visualization tool misc/roh-viz, see below

convert.c

@@ -1,6 +1,6 @@
 /*  convert.c -- functions for converting between VCF/BCF and related formats.
 
-    Copyright (C) 2013-2024 Genome Research Ltd.
+    Copyright (C) 2013-2025 Genome Research Ltd.
 
     Author: Petr Danecek <[email protected]>
 
@@ -1466,12 +1466,25 @@ static int parse_subscript(char **p)
 
 static char *parse_tag(convert_t *convert, char *p, int is_gtf)
 {
+    int is_vcf_column = p[1]=='/' ? 1 : 0;
+    if ( is_vcf_column ) p++;
+
     char *q = ++p;
     while ( *q && (isalnum(*q) || *q=='_' || *q=='.') ) q++;
     kstring_t str = {0,0,0};
     if ( q-p==0 ) error("Could not parse format string: %s\n", convert->format_str);
     kputsn(p, q-p, &str);
-    if ( is_gtf )
+    if ( is_gtf && is_vcf_column )
+    {
+        _SET_NON_FORMAT_TAGS(register_tag, str.s, convert, str.s, is_gtf)
+        else if ( !strcmp(str.s, "ALT") )
+        {
+            fmt_t *fmt = register_tag(convert, str.s, is_gtf, T_ALT);
+            fmt->subscript = parse_subscript(&q);
+        }
+        else error("Could not parse tag: %s .. %s\n", str.s,convert->format_str);
+    }
+    else if ( is_gtf )
     {
         _SET_FILTER_EXPR(convert,set_filter_expr,p,q,1)
         else if ( !strcmp(str.s, "SAMPLE") ) register_tag(convert, "SAMPLE", is_gtf, T_SAMPLE);

doc/bcftools.txt

@@ -3253,6 +3253,9 @@ Extracts fields from VCF or BCF files and outputs them in user-defined format.
     bcftools query -f '[%SAMPLE %GT %DP\n]' -i 'FMT/DP=1 || FMT/DP=2' file.vcf
     bcftools query -f '[%SAMPLE %GT %DP\n]' -i 'FMT/DP=1 |  FMT/DP=2' file.vcf
 
+    # Refer to ID column vs INFO/ID tag vs FORMAT/ID tag
+    bcftools query -f 'columnID=%ID   infoID=%INFO/ID  [fmtID=%ID ]  [columnID=%/ID]'
+
 
 [[reheader]]
 === bcftools reheader ['OPTIONS'] 'file.vcf.gz'

test/query.3.1.out

@@ -0,0 +1 @@
+1 1000 ID G A 999 FILTER 	 infoCHROM infoPOS infoID infoREF infoALT infoQUAL infoFILTER

test/query.3.2.out

@@ -0,0 +1 @@
+ fmtCHROM1 fmtCHROM2 	  fmtPOS1 fmtPOS2 	  fmtID1 fmtID2 	  fmtREF1 fmtREF2 	  fmtALT1 fmtALT2 	  fmtQUAL1 fmtQUAL2 	  fmtFILTER1 fmtFILTER2

test/query.3.3.out

@@ -0,0 +1 @@
+ 1 1 	  1000 1000 	  ID ID 	  G G 	  A A 	  999 999 	  FILTER FILTER

test/query.3.vcf

@@ -0,0 +1,20 @@
+##fileformat=VCFv4.2
+##reference=file:///lustre/scratch105/projects/g1k/ref/main_project/human_g1k_v37.fasta
+##contig=<ID=1,assembly=b37,length=249250621>
+##FILTER=<ID=FILTER,Description="">
+##INFO=<ID=CHROM,Number=.,Type=String,Description="">
+##INFO=<ID=POS,Number=.,Type=String,Description="">
+##INFO=<ID=ID,Number=.,Type=String,Description="">
+##INFO=<ID=REF,Number=.,Type=String,Description="">
+##INFO=<ID=ALT,Number=.,Type=String,Description="">
+##INFO=<ID=QUAL,Number=.,Type=String,Description="">
+##INFO=<ID=FILTER,Number=.,Type=String,Description="">
+##FORMAT=<ID=CHROM,Number=.,Type=String,Description="">
+##FORMAT=<ID=POS,Number=.,Type=String,Description="">
+##FORMAT=<ID=ID,Number=.,Type=String,Description="">
+##FORMAT=<ID=REF,Number=.,Type=String,Description="">
+##FORMAT=<ID=ALT,Number=.,Type=String,Description="">
+##FORMAT=<ID=QUAL,Number=.,Type=String,Description="">
+##FORMAT=<ID=FILTER,Number=.,Type=String,Description="">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	a	b
+1	1000	ID	G	A	999	FILTER	CHROM=infoCHROM;POS=infoPOS;ID=infoID;REF=infoREF;ALT=infoALT;QUAL=infoQUAL;FILTER=infoFILTER	CHROM:POS:ID:REF:ALT:QUAL:FILTER	fmtCHROM1:fmtPOS1:fmtID1:fmtREF1:fmtALT1:fmtQUAL1:fmtFILTER1	fmtCHROM2:fmtPOS2:fmtID2:fmtREF2:fmtALT2:fmtQUAL2:fmtFILTER2

test/test.pl

@@ -115,6 +115,9 @@
 run_test(\&test_vcf_merge,$opts,in=>['merge.gvcf.5.a','merge.gvcf.5.b'],out=>'merge.gvcf.5.1.out',args=>'--gvcf - --merge none');
 run_test(\&test_vcf_merge,$opts,in=>['merge.gvcf.11.a','merge.gvcf.11.b','merge.gvcf.11.c'],out=>'merge.gvcf.11.1.out',args=>'--gvcf -');
 # run_test(\&test_vcf_merge_big,$opts,in=>'merge_big.1',out=>'merge_big.1.1',nsmpl=>79000,nfiles=>79,nalts=>486,args=>'');   # commented out for speed
+run_test(\&test_vcf_query,$opts,in=>'query.3',out=>'query.3.1.out',args=>q[-f '%CHROM %POS %ID %REF %ALT %QUAL %FILTER \\t %INFO/CHROM %INFO/POS %INFO/ID %INFO/REF %INFO/ALT %INFO/QUAL %INFO/FILTER']);
+run_test(\&test_vcf_query,$opts,in=>'query.3',out=>'query.3.2.out',args=>q[-f '[ %CHROM] \\t [ %POS] \\t [ %ID] \\t [ %REF] \\t [ %ALT] \\t [ %QUAL] \\t [ %FILTER]']);
+run_test(\&test_vcf_query,$opts,in=>'query.3',out=>'query.3.3.out',args=>q[-f '[ %/CHROM] \\t [ %/POS] \\t [ %/ID] \\t [ %/REF] \\t [ %/ALT] \\t [ %/QUAL] \\t [ %/FILTER]']);
 run_test(\&test_vcf_query,$opts,in=>'query.filter.14',out=>'query.filter.14.1.out',args=>q[-f '%CHROM:%POS [ %SAMPLE %GT]']);
 run_test(\&test_vcf_query,$opts,in=>'query.filter.14',out=>'query.filter.14.2.out',args=>q[-f '%CHROM:%POS [ %SAMPLE %GT]' -i'GT="."']);
 run_test(\&test_vcf_query,$opts,in=>'query.filter.14',out=>'query.filter.14.3.out',args=>q[-f '%CHROM:%POS [ %SAMPLE %GT]' -i'GT="0|1"']);