Exemplo n.º 1
0
int bcf_sr_set_targets(bcf_srs_t *readers, const char *targets, int is_file, int alleles)
{
    assert( !readers->targets );
    readers->targets = bcf_sr_regions_init(targets,is_file,0,1,-2);
    if ( !readers->targets ) return -1;
    readers->targets_als = alleles;
    return 0;
}
Exemplo n.º 2
0
int bcf_sr_set_regions(bcf_srs_t *readers, const char *regions, int is_file)
{
    assert( !readers->regions );
    if ( readers->nreaders )
    {
        fprintf(stderr,"[%s:%d %s] Error: bcf_sr_set_regions() must be called before bcf_sr_add_reader()\n", __FILE__,__LINE__,__FUNCTION__);
        return -1;
    }
    readers->regions = bcf_sr_regions_init(regions,is_file,0,1,-2);
    if ( !readers->regions ) return -1;
    readers->explicit_regs = 1;
    readers->require_index = 1;
    return 0;
}
Exemplo n.º 3
0
int init(int argc, char **argv, bcf_hdr_t *in, bcf_hdr_t *out)
{
    int c;
    char *fname = NULL;

    static struct option loptions[] =
    {
        {"exons",1,0,'e'},
        {0,0,0,0}
    };
    while ((c = getopt_long(argc, argv, "e:?h",loptions,NULL)) >= 0)
    {
        switch (c) 
        {
            case 'e': fname = optarg; break;
            case 'h':
            case '?':
            default: fprintf(stderr,"%s", usage()); exit(1); break;
        }
    }
    if ( !fname )
    {
        fprintf(stderr,"Missing the -e option.\n");
        return -1;
    }

    in_hdr = in;
    out_hdr = out;

    int ret = bcf_hdr_append(out_hdr,"##INFO=<ID=OOF,Number=A,Type=Integer,Description=\"Frameshift Indels: out-of-frame (1), in-frame (0), not-applicable (-1 or missing)\">");
    if ( ret!=0 )
    {
        fprintf(stderr,"Error updating the header\n");
        return -1;
    }

    exons = bcf_sr_regions_init(fname,1,0,1,2);
    if ( !exons )
    {
        fprintf(stderr,"Error occurred while reading (was the file compressed with bgzip?): %s\n", fname);
        return -1;
    }

    return 0;
}
Exemplo n.º 4
0
int init(const char *opts, bcf_hdr_t *in, bcf_hdr_t *out)
{
    in_hdr = in;
    out_hdr = out;

    int ret = bcf_hdr_append(out_hdr,"##INFO=<ID=OOF,Number=A,Type=Integer,Description=\"Frameshift Indels: out-of-frame (1), in-frame (0), not-applicable (-1 or missing)\">");
    if ( ret!=0 )
    {
        fprintf(stderr,"Error updating the header\n");
        return -1;
    }

    char *fname = config_get_string(opts,"exons");
    if ( !fname )
    {
        fprintf(stderr,"No exons given, please run as \"bcftools annotate -p frameshifts:exons=path/to/file.tab.gz\".\n");
        return -1;
    }

    wordexp_t wexp;
    wordexp(fname, &wexp, 0);
    if ( !wexp.we_wordc )
    {
        fprintf(stderr,"No such file: %s\n", fname);
        return -1;
    }
    free(fname);
    fname = wexp.we_wordv[0];

    exons = bcf_sr_regions_init(fname,1,0,1,2);
    if ( !exons )
    {
        fprintf(stderr,"Error occurred while reading (was the file compressed with bgzip?): %s\n", fname);
        return -1;
    }

    wordfree(&wexp);
    return 0;
}