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);
}
void destroy(void)
{
bcf_sr_regions_destroy(exons);
}
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 = ®->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, ®->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, ®->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, ®->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;
}