From 4735097b8f0e34d889e6fd347781ce60cf33ffb9 Mon Sep 17 00:00:00 2001 From: Petr Danecek Date: Wed, 2 Oct 2024 14:52:12 +0200 Subject: [PATCH] Update documentation --- NEWS | 4 ++++ doc/bcftools.txt | 5 ++--- vcfannotate.c | 2 +- vcfisec.c | 2 +- 4 files changed, 8 insertions(+), 5 deletions(-) diff --git a/NEWS b/NEWS index f7703821..872445fa 100644 --- a/NEWS +++ b/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: diff --git a/doc/bcftools.txt b/doc/bcftools.txt index 47ec59ec..ae844b4b 100644 --- a/doc/bcftools.txt +++ b/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 *<>* 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 *<>* -*--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 *<>* *-C, --complement*:: diff --git a/vcfannotate.c b/vcfannotate.c index 748e82d5..5fc0c63a 100644 --- a/vcfannotate.c +++ b/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 , see man page for details [some]\n"); + fprintf(stderr, " --pair-logic STR Matching records by , 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"); diff --git a/vcfisec.c b/vcfisec.c index 9f253254..e28a956d 100644 --- a/vcfisec.c +++ b/vcfisec.c @@ -487,7 +487,7 @@ static void usage(void) fprintf(stderr, "Usage: bcftools isec [options] [...]\n"); fprintf(stderr, "\n"); fprintf(stderr, "Options:\n"); - fprintf(stderr, " -c, --collapse STRING Treat as identical records with , see man page for details [none]\n"); + fprintf(stderr, " -c, --collapse STRING Treat as identical records with , 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");