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Fix filter engine: OOB write, undefined shift, wrong fallbacks, debug output #2523

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Merged
pd3 merged 1 commit into from
Mar 28, 2026
+10 −11
Merged

Fix filter engine: OOB write, undefined shift, wrong fallbacks, debug output #2523

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17 changes: 8 additions & 9 deletions filter.c
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Original file line number Diff line number Diff line change
Expand Up @@ -458,7 +458,7 @@ static int filters_cache_genotypes(filter_t *flt, bcf1_t *line)
flt->cached_GT.nbuf = 0;
return -1;
}
flt->cached_GT.mask[i] |= 1<<allele;
flt->cached_GT.mask[i] |= 1ULL<<allele;
}
}
return 0;
Expand Down Expand Up @@ -1001,7 +1001,7 @@ static void filters_set_format_int(filter_t *flt, bcf1_t *line, token_t *tok)
int k, j = 0;
for (k=0; k<nsrc1; k++) // source values are AD[0..nsrc1]
{
if ( !(flt->cached_GT.mask[i] & (1<<k)) ) continue;
if ( !(flt->cached_GT.mask[i] & (1ULL<<k)) ) continue;
dst[j++] = src[k];
}
if ( !j ) { bcf_double_set_missing(dst[j]); j++; }
Expand Down Expand Up @@ -1086,7 +1086,7 @@ static void filters_set_format_float(filter_t *flt, bcf1_t *line, token_t *tok)
int k, j = 0;
for (k=0; k<nsrc1; k++) // source values are AF[0..nsrc1]
{
if ( !(flt->cached_GT.mask[i] & (1<<k)) ) continue;
if ( !(flt->cached_GT.mask[i] & (1ULL<<k)) ) continue;
if ( bcf_float_is_missing(src[k]) )
bcf_double_set_missing(dst[j]);
else if ( bcf_float_is_vector_end(src[k]) )
Expand Down Expand Up @@ -1167,7 +1167,7 @@ static void filters_set_format_string(filter_t *flt, bcf1_t *line, token_t *tok)
}
else if ( tok->idx == -3 ) // given by GT index, e.g. AD[:GT]
{
if ( flt->cached_GT.mask[i] & (1<<idx) ) keep = 1;
if ( flt->cached_GT.mask[i] & (1ULL<<idx) ) keep = 1;
}
else // given as a list, e.g. AD[:0,3]
{
Expand Down Expand Up @@ -1753,7 +1753,7 @@ static int func_median(filter_t *flt, bcf1_t *line, token_t *rtok, token_t **sta
static int func_smpl_median(filter_t *flt, bcf1_t *line, token_t *rtok, token_t **stack, int nstack)
{
token_t *tok = stack[nstack - 1];
if ( !tok->nsamples ) return func_avg(flt,line,rtok,stack,nstack);
if ( !tok->nsamples ) return func_median(flt,line,rtok,stack,nstack);
rtok->nsamples = tok->nsamples;
rtok->nvalues = tok->nsamples;
rtok->nval1 = 1;
Expand Down Expand Up @@ -1831,7 +1831,7 @@ static int func_stddev(filter_t *flt, bcf1_t *line, token_t *rtok, token_t **sta
static int func_smpl_stddev(filter_t *flt, bcf1_t *line, token_t *rtok, token_t **stack, int nstack)
{
token_t *tok = stack[nstack - 1];
if ( !tok->nsamples ) return func_avg(flt,line,rtok,stack,nstack);
if ( !tok->nsamples ) return func_stddev(flt,line,rtok,stack,nstack);
rtok->nsamples = tok->nsamples;
rtok->nvalues = tok->nsamples;
rtok->nval1 = 1;
Expand Down Expand Up @@ -1903,7 +1903,7 @@ static int func_sum(filter_t *flt, bcf1_t *line, token_t *rtok, token_t **stack,
static int func_smpl_sum(filter_t *flt, bcf1_t *line, token_t *rtok, token_t **stack, int nstack)
{
token_t *tok = stack[nstack - 1];
if ( !tok->nsamples ) return func_avg(flt,line,rtok,stack,nstack);
if ( !tok->nsamples ) return func_sum(flt,line,rtok,stack,nstack);
rtok->nsamples = tok->nsamples;
rtok->nvalues = tok->nsamples;
rtok->nval1 = 1;
Expand Down Expand Up @@ -2006,7 +2006,7 @@ static int func_count(filter_t *flt, bcf1_t *line, token_t *rtok, token_t **stac
static int func_smpl_count(filter_t *flt, bcf1_t *line, token_t *rtok, token_t **stack, int nstack)
{
token_t *tok = stack[nstack - 1];
if ( !tok->nsamples ) return func_max(flt,line,rtok,stack,nstack);
if ( !tok->nsamples ) return func_count(flt,line,rtok,stack,nstack);
rtok->nsamples = tok->nsamples;
rtok->nvalues = tok->nsamples;
rtok->nval1 = 1;
Expand Down Expand Up @@ -2888,7 +2888,6 @@ static void cmp_vector_strings(token_t *atok, token_t *btok, token_t *rtok)
{
token_t *tok = atok->regex ? btok : atok;
rtok->pass_site = _regex_vector_strings(regex, tok->str_value.s, tok->str_value.l, logic, missing_logic);
fprintf(stderr,"pass=%d [%s]\n",rtok->pass_site,tok->str_value.s);
}
return;
}
Expand Down
4 changes: 2 additions & 2 deletions vcffilter.c
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Original file line number Diff line number Diff line change
Expand Up @@ -420,14 +420,14 @@ static void set_genotypes(args_t *args, bcf1_t *line, int pass_site)
if ( args->set_gts==SET_GTS_MISSING && !bcf_gt_is_missing(gts[j]) )
{
int ial = bcf_gt_allele(gts[j]);
if ( has_ac && ial>0 && ial<=line->n_allele ) args->tmp_ac[ ial-1 ]--;
if ( has_ac && ial>0 && ial<line->n_allele ) args->tmp_ac[ ial-1 ]--;
an--;
}
else if ( args->set_gts==SET_GTS_REF )
{
int ial = bcf_gt_allele(gts[j]);
if ( bcf_gt_is_missing(gts[j]) ) an++;
else if ( has_ac && ial>0 && ial<=line->n_allele ) args->tmp_ac[ ial-1 ]--;
else if ( has_ac && ial>0 && ial<line->n_allele ) args->tmp_ac[ ial-1 ]--;
}
gts[j] = new_gt;
}
Expand Down