示例#1
0
void bcf_sr_destroy(bcf_srs_t *files)
{
    int i;
    for (i=0; i<files->nreaders; i++)
        bcf_sr_destroy1(&files->readers[i]);
    free(files->has_line);
    free(files->readers);
    for (i=0; i<files->n_smpl; i++) free(files->samples[i]);
    free(files->samples);
    if (files->targets) bcf_sr_regions_destroy(files->targets);
    if (files->regions) bcf_sr_regions_destroy(files->regions);
    if ( files->tmps.m ) free(files->tmps.s);
    free(files);
}
示例#2
0
void destroy(void)
{
    bcf_sr_regions_destroy(exons);
}
示例#3
0
int bcf_sr_regions_next(bcf_sr_regions_t *reg)
{
    if ( reg->iseq<0 ) return -1;
    reg->start = reg->end = -1;
    reg->nals = 0;

    // using in-memory regions
    if ( reg->regs )
    {
        while ( reg->iseq < reg->nseqs )
        {
            reg->regs[reg->iseq].creg++;
            if ( reg->regs[reg->iseq].creg < reg->regs[reg->iseq].nregs ) break;
            reg->iseq++;
        }
        if ( reg->iseq >= reg->nseqs ) { reg->iseq = -1; return -1; } // no more regions left
        region1_t *creg = &reg->regs[reg->iseq].regs[reg->regs[reg->iseq].creg];
        reg->start = creg->start;
        reg->end   = creg->end;
        return 0;
    }

    // reading from tabix
    char *chr, *chr_end;
    int ichr = 0, ifrom = 1, ito = 2, is_bed = 0, from, to;
    if ( reg->tbx )
    {
        ichr   = reg->tbx->conf.sc-1;
        ifrom  = reg->tbx->conf.bc-1;
        ito    = reg->tbx->conf.ec-1;
        if ( ito<0 ) ito = ifrom;
        is_bed = reg->tbx->conf.preset==TBX_UCSC ? 1 : 0;
    }

    int ret = 0;
    while ( !ret )
    {
        if ( reg->itr )
        {
            // tabix index present, reading a chromosome block
            ret = tbx_itr_next(reg->file, reg->tbx, reg->itr, &reg->line);
            if ( ret<0 ) { reg->iseq = -1; return -1; }
        }
        else
        {
            if ( reg->is_bin )
            {
                // Waited for seek which never came. Reopen in text mode and stream
                // through the regions, otherwise hts_getline would fail
                hts_close(reg->file);
                reg->file = hts_open(reg->fname, "r");
                if ( !reg->file )
                {
                    fprintf(stderr,"[%s:%d %s] Could not open file: %s\n", __FILE__,__LINE__,__FUNCTION__,reg->fname);
                    reg->file = NULL;
                    bcf_sr_regions_destroy(reg);
                    return -1;
                }
                reg->is_bin = 0;
            }

            // tabix index absent, reading the whole file
            ret = hts_getline(reg->file, KS_SEP_LINE, &reg->line);
            if ( ret<0 ) { reg->iseq = -1; return -1; }
        }
        ret = _regions_parse_line(reg->line.s, ichr,ifrom,ito, &chr,&chr_end,&from,&to);
        if ( ret<0 )
        {
            fprintf(stderr,"[%s:%d] Could not parse the file %s, using the columns %d,%d,%d\n", __FILE__,__LINE__,reg->fname,ichr+1,ifrom+1,ito+1);
            return -1;
        }
    }
    if ( is_bed ) from++;

    *chr_end = 0;
    if ( khash_str2int_get(reg->seq_hash, chr, &reg->iseq)<0 )
    {
        fprintf(stderr,"Broken tabix index? The sequence \"%s\" not in dictionary [%s]\n", chr,reg->line.s);
        exit(1);
    }
    *chr_end = '\t';

    reg->start = from - 1;
    reg->end   = to - 1;
    return 0;
}