Update documentation

Author: pd3

NEWS

@@ -1,5 +1,9 @@
 ## Release a.b
 
+Changes affecting the whole of bcftools, or multiple commands:
+
+* Add support for matching lines by ID (#1739)
+
 
 Changes affecting specific commands:
 

doc/bcftools.txt

@@ -163,7 +163,6 @@ specific commands to see if they apply.
 
         'id';;
             only records with identical ID column are compatible.
-            Supported by *<<merge,bcftools merge>>* only.
 
 *-f, --apply-filters* 'LIST'::
     Skip sites where FILTER column does not contain any of the strings listed
@@ -501,7 +500,7 @@ Add or remove annotations.
 *-O, --output-type* 'b'|'u'|'z'|'v'[0-9]::
     see *<<common_options,Common Options>>*
 
-*--pair-logic* 'snps'|'indels'|'both'|'all'|'some'|'exact'::
+*--pair-logic* 'snps'|'indels'|'both'|'all'|'some'|'exact'|'id'::
     Controls how to match records from the annotation file to the target VCF.
     Effective only when *-a* is a VCF or BCF. The option replaces the former
     uninuitive *--collapse*.
@@ -1919,7 +1918,7 @@ on the options, the program can output records from one (or more) files
 which have (or do not have) corresponding records with the same position
 in the other files.
 
-*-c, --collapse* 'snps'|'indels'|'both'|'all'|'some'|'none'::
+*-c, --collapse* 'snps'|'indels'|'both'|'all'|'some'|'none'|'id'::
     see *<<common_options,Common Options>>*
 
 *-C, --complement*::

vcfannotate.c

@@ -3658,7 +3658,7 @@ static void usage(args_t *args)
     fprintf(stderr, "       --no-version                Do not append version and command line to the header\n");
     fprintf(stderr, "   -o, --output FILE               Write output to a file [standard output]\n");
     fprintf(stderr, "   -O, --output-type u|b|v|z[0-9]  u/b: un/compressed BCF, v/z: un/compressed VCF, 0-9: compression level [v]\n");
-    fprintf(stderr, "       --pair-logic STR            Matching records by <snps|indels|both|all|some|exact>, see man page for details [some]\n");
+    fprintf(stderr, "       --pair-logic STR            Matching records by <snps|indels|both|all|some|exact|id>, see man page for details [some]\n");
     fprintf(stderr, "   -r, --regions REGION            Restrict to comma-separated list of regions\n");
     fprintf(stderr, "   -R, --regions-file FILE         Restrict to regions listed in FILE\n");
     fprintf(stderr, "       --regions-overlap 0|1|2     Include if POS in the region (0), record overlaps (1), variant overlaps (2) [1]\n");

vcfisec.c

@@ -487,7 +487,7 @@ static void usage(void)
     fprintf(stderr, "Usage:   bcftools isec [options] <A.vcf.gz> <B.vcf.gz> [...]\n");
     fprintf(stderr, "\n");
     fprintf(stderr, "Options:\n");
-    fprintf(stderr, "    -c, --collapse STRING          Treat as identical records with <snps|indels|both|all|some|none>, see man page for details [none]\n");
+    fprintf(stderr, "    -c, --collapse STRING          Treat as identical records with <snps|indels|both|all|some|none|id>, see man page for details [none]\n");
     fprintf(stderr, "    -C, --complement               Output positions present only in the first file but missing in the others\n");
     fprintf(stderr, "    -e, --exclude EXPR             Exclude sites for which the expression is true\n");
     fprintf(stderr, "    -f, --apply-filters LIST       Require at least one of the listed FILTER strings (e.g. \"PASS,.\")\n");