forked from samtools/bcftools
-
Notifications
You must be signed in to change notification settings - Fork 0
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Updated usage strings to correspond to actual commands
- Loading branch information
Showing
11 changed files
with
499 additions
and
43 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,121 @@ | ||
| #include <stdio.h> | ||
| #include <unistd.h> | ||
| #include <getopt.h> | ||
| #include <ctype.h> | ||
| #include <string.h> | ||
| #include <errno.h> | ||
| #include <sys/stat.h> | ||
| #include <sys/types.h> | ||
| #include <math.h> | ||
| #include <htslib/vcf.h> | ||
| #include <htslib/synced_bcf_reader.h> | ||
| #include "bcftools.h" | ||
|
|
||
| typedef struct _args_t | ||
| { | ||
| bcf_srs_t *files; | ||
| bcf_hdr_t *hdr; | ||
| htsFile *out_fh; | ||
| int output_type; | ||
| bcf_sr_regions_t *tgts; | ||
|
|
||
| char **argv, *targets_fname, *regions_fname; | ||
| int argc; | ||
| } | ||
| args_t; | ||
|
|
||
| static void init_data(args_t *args) | ||
| { | ||
| args->hdr = args->files->readers[0].header; | ||
|
|
||
| // bcf_hdr_append(args->hdr,"##INFO=<ID=AC,Number=A,Type=Integer,Description=\"Allele count in genotypes\">"); | ||
| bcf_hdr_append_version(args->hdr, args->argc, args->argv, "bcftools_annotate"); | ||
| bcf_hdr_fmt_text(args->hdr); | ||
|
|
||
| args->out_fh = hts_open("-",hts_bcf_wmode(args->output_type)); | ||
|
|
||
| args->tgts = bcf_sr_regions_init(args->targets_fname); | ||
| } | ||
|
|
||
| static void destroy_data(args_t *args) | ||
| { | ||
| bcf_sr_regions_destroy(args->tgts); | ||
| } | ||
|
|
||
| static void annotate(args_t *args, bcf1_t *line) | ||
| { | ||
| } | ||
|
|
||
| static void usage(args_t *args) | ||
| { | ||
| fprintf(stderr, "\n"); | ||
| fprintf(stderr, "About: Annotate and edit VCF/BCF files.\n"); | ||
| fprintf(stderr, "Usage: bcftools annotate [OPTIONS] <in.bcf>|<in.vcf>|<in.vcf.gz>|-\n"); | ||
| fprintf(stderr, "Options:\n"); | ||
| fprintf(stderr, " -a, --annotations <file> tabix-indexed file with annotations: CHR\tPOS[\tVALUE]+\n"); | ||
| fprintf(stderr, " -o, --output-type <b|u|z|v> b: compressed BCF, u: uncompressed BCF, z: compressed VCF, v: uncompressed VCF [v]\n"); | ||
| fprintf(stderr, " -r, --regions <reg|file> same as -t but index-jumps rather than streams to a region (requires indexed VCF/BCF)\n"); | ||
| fprintf(stderr, "\n"); | ||
| fprintf(stderr, "\n"); | ||
| exit(1); | ||
| } | ||
|
|
||
| int main_vcfannotate(int argc, char *argv[]) | ||
| { | ||
| int c; | ||
| args_t *args = (args_t*) calloc(1,sizeof(args_t)); | ||
| args->argc = argc; args->argv = argv; | ||
| args->files = bcf_sr_init(); | ||
| args->output_type = FT_VCF; | ||
|
|
||
| error("not finished yet, sorry\n"); | ||
|
|
||
| static struct option loptions[] = | ||
| { | ||
| {"output-type",1,0,'o'}, | ||
| {"annotations",1,0,'a'}, | ||
| {"regions",1,0,'r'}, | ||
| {0,0,0,0} | ||
| }; | ||
| while ((c = getopt_long(argc, argv, "h?o:r:a:",loptions,NULL)) >= 0) { | ||
| switch (c) { | ||
| case 'o': | ||
| switch (optarg[0]) { | ||
| case 'b': args->output_type = FT_BCF_GZ; break; | ||
| case 'u': args->output_type = FT_BCF; break; | ||
| case 'z': args->output_type = FT_VCF_GZ; break; | ||
| case 'v': args->output_type = FT_VCF; break; | ||
| default: error("The output type \"%s\" not recognised\n", optarg); | ||
| }; | ||
| break; | ||
| case 'a': args->targets_fname = optarg; break; | ||
| case 'r': args->regions_fname = optarg; break; | ||
| case 'h': | ||
| case '?': usage(args); break; | ||
| default: error("Unknown argument: %s\n", optarg); | ||
| } | ||
| } | ||
|
|
||
| if ( argc<optind+1 ) usage(args); | ||
| if ( args->regions_fname ) | ||
| { | ||
| if ( bcf_sr_set_regions(args->files, args->regions_fname)<0 ) | ||
| error("Failed to read the regions: %s\n", args->regions_fname); | ||
| } | ||
| if ( !args->targets_fname ) error("Missing the -a option\n"); | ||
| if ( !bcf_sr_add_reader(args->files, argv[optind]) ) error("Failed to open or the file not indexed: %s\n", argv[optind]); | ||
|
|
||
| init_data(args); | ||
| bcf_hdr_write(args->out_fh, args->hdr); | ||
| while ( bcf_sr_next_line(args->files) ) | ||
| { | ||
| bcf1_t *line = args->files->readers[0].buffer[0]; | ||
| annotate(args, line); | ||
| bcf_write1(args->out_fh, args->hdr, line); | ||
| } | ||
| hts_close(args->out_fh); | ||
| destroy_data(args); | ||
| bcf_sr_destroy(args->files); | ||
| free(args); | ||
| return 0; | ||
| } |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Oops, something went wrong.