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uses macro to check missing allele #2456

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Merged
pd3 merged 1 commit into from
Oct 9, 2025
+17 −17
Merged

uses macro to check missing allele #2456

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10 changes: 5 additions & 5 deletions csq.c
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Original file line number Diff line number Diff line change
Expand Up @@ -3182,9 +3182,9 @@ int test_cds(args_t *args, bcf1_t *rec, vbuf_t *vbuf)
for (ismpl=0; ismpl<args->smpl->n; ismpl++)
{
int32_t *gt = args->gt_arr + args->smpl->idx[ismpl]*ngts;
if ( gt[0]==bcf_gt_missing ) continue;
if ( bcf_gt_is_missing(gt[0]) ) continue;

if ( ngts>1 && gt[1]!=bcf_gt_missing && gt[1]!=bcf_int32_vector_end && bcf_gt_allele(gt[0])!=bcf_gt_allele(gt[1]) )
if ( ngts>1 && !bcf_gt_is_missing(gt[1]) && gt[1]!=bcf_int32_vector_end && bcf_gt_allele(gt[0])!=bcf_gt_allele(gt[1]) )
{
if ( args->phase==PHASE_MERGE )
{
Expand All @@ -3206,7 +3206,7 @@ int test_cds(args_t *args, bcf1_t *rec, vbuf_t *vbuf)

for (ihap=0; ihap<ngts; ihap++)
{
if ( gt[ihap]==bcf_gt_missing || gt[ihap]==bcf_int32_vector_end ) continue;
if ( bcf_gt_is_missing(gt[ihap]) || gt[ihap]==bcf_int32_vector_end ) continue;

i = 2*ismpl + ihap;

Expand Down Expand Up @@ -3311,7 +3311,7 @@ void csq_stage(args_t *args, csq_t *csq, bcf1_t *rec)
int32_t *gt = args->gt_arr + args->smpl->idx[i]*ngt;
for (j=0; j<ngt; j++)
{
if ( gt[j]==bcf_gt_missing || gt[j]==bcf_int32_vector_end ) continue;
if ( bcf_gt_is_missing(gt[j]) || gt[j]==bcf_int32_vector_end ) continue;
int ial = bcf_gt_allele(gt[j]);
if ( !ial || ial!=csq->type.vcf_ial ) continue;
csq_print_text(args, csq, args->smpl->idx[i],j+1);
Expand All @@ -3326,7 +3326,7 @@ void csq_stage(args_t *args, csq_t *csq, bcf1_t *rec)
int32_t *gt = args->gt_arr + args->smpl->idx[i]*ngt;
for (j=0; j<ngt; j++)
{
if ( gt[j]==bcf_gt_missing || gt[j]==bcf_int32_vector_end ) continue;
if ( bcf_gt_is_missing(gt[j]) || gt[j]==bcf_int32_vector_end ) continue;
int ial = bcf_gt_allele(gt[j]);
if ( !ial || ial!=csq->type.vcf_ial ) continue;

Expand Down
2 changes: 1 addition & 1 deletion filter.c
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Expand Up @@ -1397,7 +1397,7 @@ static void filters_set_nmissing(filter_t *flt, bcf1_t *line, token_t *tok)
{ \
type_t val = convert(&ptr[j * sizeof(type_t)]); \
if ( val==is_vector_end ) break; \
if ( val==bcf_gt_missing ) { nmissing++; break; } \
if ( bcf_gt_is_missing(val) ) { nmissing++; break; } \
} \
} \
}
Expand Down
2 changes: 1 addition & 1 deletion plugins/check-sparsity.c
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Expand Up @@ -206,7 +206,7 @@ static void test_region(args_t *args, char *reg)
int8_t *ptr = (int8_t*) (fmt_gt->p + args->smpl[i]*fmt_gt->size);
int ial = 0;
for (ial=0; ial<fmt_gt->n; ial++)
if ( ptr[ial]==bcf_gt_missing || ptr[ial]==bcf_int8_vector_end ) break;
if ( bcf_gt_is_missing(ptr[ial]) || ptr[ial]==bcf_int8_vector_end ) break;
if ( ial==0 ) continue; // missing
if ( ++args->nsites[i] < args->min_sites ) continue;
if ( i+1<args->nsmpl )
Expand Down
2 changes: 1 addition & 1 deletion plugins/guess-ploidy.c
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Expand Up @@ -167,7 +167,7 @@ void process_region_guess(args_t *args)
int32_t *ptr = args->arr + ismpl*ngt;
double *tmp = args->tmpf + ismpl*3;

if ( ptr[0]==bcf_gt_missing )
if ( bcf_gt_is_missing(ptr[0]) )
{
tmp[0] = -1;
continue;
Expand Down
4 changes: 2 additions & 2 deletions plugins/mendelian2.c
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Original file line number Diff line number Diff line change
Expand Up @@ -566,12 +566,12 @@ static int parse_gt(int32_t *gt, int ngt, uint64_t *a, uint64_t *b)
{
*a = *b = 0;

if ( gt[0]==bcf_gt_missing || gt[0]==bcf_int32_vector_end ) return 0;
if ( bcf_gt_is_missing(gt[0]) || gt[0]==bcf_int32_vector_end ) return 0;
*a |= 1<<bcf_gt_allele(gt[0]);

if ( ngt==1 || gt[1]==bcf_int32_vector_end ) return 1;

if ( gt[1]==bcf_gt_missing ) return 0;
if ( bcf_gt_is_missing(gt[1]) ) return 0;
*b |= 1<<bcf_gt_allele(gt[1]);

return 2;
Expand Down
2 changes: 1 addition & 1 deletion plugins/missing2ref.c
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Original file line number Diff line number Diff line change
Expand Up @@ -121,7 +121,7 @@ bcf1_t *process(bcf1_t *rec)
// replace gts
for (i=0; i<ngts; i++)
{
if ( gts[i]==bcf_gt_missing )
if ( bcf_gt_is_missing(gts[i]) )
{
gts[i] = new_gt;
changed++;
Expand Down
2 changes: 1 addition & 1 deletion plugins/setGT.c
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Expand Up @@ -403,7 +403,7 @@ static inline int set_gt_custom(args_t *args, int32_t *ptr, int ngts, int nals)
{
if ( args->custom.gt[i]==MINOR_ALLELE ) new_allele = args->custom.m_allele;
else if ( args->custom.gt[i]==MAJOR_ALLELE ) new_allele = args->custom.M_allele;
else if ( args->custom.gt[i]==X_VAF_ALLELE ) new_allele = args->custom.x_vaf_allele==bcf_gt_missing ? nals : bcf_gt_allele(args->custom.x_vaf_allele);
else if ( args->custom.gt[i]==X_VAF_ALLELE ) new_allele = bcf_gt_is_missing(args->custom.x_vaf_allele) ? nals : bcf_gt_allele(args->custom.x_vaf_allele);
else if ( args->custom.gt[i]==MISSING_ALLELE ) new_allele = nals; // this is to trigger the `new_allele = bcf_gt_missing` branch below
else new_allele = args->custom.gt[i];
if ( new_allele >= nals ) // cannot set, the requested index is bigger than there are alleles in ALT
Expand Down
4 changes: 2 additions & 2 deletions plugins/trio-switch-rate.c
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Expand Up @@ -182,8 +182,8 @@ int parse_genotype(gt_t *gt, int32_t *ptr);

inline int parse_genotype(gt_t *gt, int32_t *ptr)
{
if ( ptr[0]==bcf_gt_missing ) return 0;
if ( ptr[1]==bcf_gt_missing ) return 0;
if ( bcf_gt_is_missing(ptr[0]) ) return 0;
if ( bcf_gt_is_missing(ptr[1]) ) return 0;
if ( ptr[1]==bcf_int32_vector_end ) return 0;
gt->phased = bcf_gt_is_phased(ptr[1]) ? 1 : 0;
gt->a = bcf_gt_allele(ptr[0]); if ( gt->a > 1 ) return 0; // consider only the first two alleles at biallelic sites
Expand Down
6 changes: 3 additions & 3 deletions vcfbuf.c
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Expand Up @@ -842,7 +842,7 @@ static double _estimate_af(int8_t *ptr, int size, int nvals, int nsamples)
{
for (j=0; j<nvals; j++)
{
if ( ptr[j]==bcf_gt_missing ) break;
if ( bcf_gt_is_missing(ptr[j]) ) break;
if ( ptr[j]==bcf_int8_vector_end ) break;
if ( bcf_gt_allele(ptr[j]) ) nalt++;
else nref++;
Expand Down Expand Up @@ -911,7 +911,7 @@ static int _calc_r2_ld(vcfbuf_t *buf, bcf1_t *arec, bcf1_t *brec, vcfbuf_ld_t *l
for (j=0; j<afmt->n; j++)
{
if ( aptr[j]==bcf_int8_vector_end ) break;
if ( aptr[j]==bcf_gt_missing )
if ( bcf_gt_is_missing(aptr[j]) )
{
if ( !buf->ld.rand_missing ) break;
if ( hts_drand48() >= aaf ) adsg += 1;
Expand All @@ -922,7 +922,7 @@ static int _calc_r2_ld(vcfbuf_t *buf, bcf1_t *arec, bcf1_t *brec, vcfbuf_ld_t *l
for (j=0; j<bfmt->n; j++)
{
if ( bptr[j]==bcf_int8_vector_end ) break;
if ( bptr[j]==bcf_gt_missing )
if ( bcf_gt_is_missing(bptr[j]) )
{
if ( !buf->ld.rand_missing ) break;
if ( hts_drand48() >= baf ) bdsg += 1;
Expand Down
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