Revert "Support dynamic variables read from a tab-delimited annotatio…

…n file"

This needs more work, didn't realize that the effect of the -c option is to
update the target VCF as well, so can't be used simply for matching. For
that, probably a new prefix will need to be introduced, but that's already
confusing as it is, for example ~ has double meaning.

This reverts commit e9bff3f. Switch to
branch bt-2151-annotate-ext to see this code.

NEWS

@@ -3,18 +3,6 @@
 
 Changes affecting specific commands:
 
-* bcftools annotate
-
-    - Support dynamic variables read from a tab-delimited annotation file (#2151)
-      For example, in the two cases below the field 'STR' from the -a file is required to match
-      the INFO/TAG in VCF. In the first example the alleles REF,ALT must match, in the second
-      example they are ignored. The option -k is required to output also records that were not
-      annotated:
-
-        bcftools annotate -a ann.tsv.gz -c CHROM,POS,REF,ALT,SCORE,STR -i'TAG={STR}' -k in.vcf
-        bcftools annotate -a ann.tsv.gz -c CHROM,POS,-,-,SCORE,STR     -i'TAG={STR}' -k in.vcf
-
-
 * bcftools consensus
 
     - Add new --regions-overlap option which allows to take into account overlapping deletions

doc/bcftools.txt

@@ -380,7 +380,6 @@ Add or remove annotations.
     To replace only existing values without modifying missing annotations, use "-TAG".
     To match the record also by ID or INFO/END, in addition to REF and ALT, use "~ID" or "~INFO/END".
     If position needs to be replaced, mark the column with the new position as "~POS".
-    Note that this works only for ID and POS, for other fields see the description of *-i* below.
     {nbsp} +
     {nbsp} +
     If the annotation file is not a VCF/BCF, all new annotations must be
@@ -424,17 +423,6 @@ Add or remove annotations.
 *-i, --include* 'EXPRESSION'::
     include only sites for which 'EXPRESSION' is true. For valid expressions see
     *<<expressions,EXPRESSIONS>>*.
-    {nbsp} +
-    {nbsp} +
-    Additionally, the command *bcftools annotate* supports expressions updated from the annotation
-    file dynamically for each record:
-----
-    # The field 'STR' from the -a file is required to match INFO/TAG in VCF. In the first example
-    # the alleles REF,ALT must match, in the second example they are ignored. The option -k is required
-    # to output also records that were not annotated
-    bcftools annotate -a annots.tsv.gz -c CHROM,POS,REF,ALT,SCORE,STR -i'TAG={STR}' -k input.vcf
-    bcftools annotate -a annots.tsv.gz -c CHROM,POS,-,-,SCORE,STR     -i'TAG={STR}' -k input.vcf
-----
 
 *-k, --keep-sites*::
     keep sites which do not pass *-i* and *-e* expressions instead of discarding them