Merge branch 'develop' of pd3-github:samtools/bcftools into develop

pd3 · pd3 · commit dcd3658e217d · 2025-10-09T15:08:43.000+02:00
diff --git a/csq.c b/csq.c
@@ -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 )
                 {
@@ -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;
 
@@ -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);
@@ -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;
 
diff --git a/filter.c b/filter.c
@@ -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; } \
             } \
         } \
     }
diff --git a/plugins/check-sparsity.c b/plugins/check-sparsity.c
@@ -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 )
diff --git a/plugins/guess-ploidy.c b/plugins/guess-ploidy.c
@@ -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;
diff --git a/plugins/mendelian2.c b/plugins/mendelian2.c
@@ -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;
diff --git a/plugins/missing2ref.c b/plugins/missing2ref.c
@@ -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++;
diff --git a/plugins/setGT.c b/plugins/setGT.c
@@ -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
diff --git a/plugins/trio-switch-rate.c b/plugins/trio-switch-rate.c
@@ -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
diff --git a/vcfbuf.c b/vcfbuf.c
@@ -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++;
@@ -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;
@@ -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;

Original file line number	Diff line number	Diff line change
`@@ -3182,9 +3182,9 @@ int test_cds(args_t args, bcf1_t rec, vbuf_t *vbuf)`
`3182`	`3182`	`for (ismpl=0; ismpl<args->smpl->n; ismpl++)`
`3183`	`3183`	`{`
`3184`	`3184`	`int32_t gt = args->gt_arr + args->smpl->idx[ismpl]ngts;`
`3185`		`- if ( gt[0]==bcf_gt_missing ) continue;`
	`3185`	`+ if ( bcf_gt_is_missing(gt[0]) ) continue;`
`3186`	`3186`
`3187`		`- if ( ngts>1 && gt[1]!=bcf_gt_missing && gt[1]!=bcf_int32_vector_end && bcf_gt_allele(gt[0])!=bcf_gt_allele(gt[1]) )`
	`3187`	`+ 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]) )`
`3188`	`3188`	`{`
`3189`	`3189`	`if ( args->phase==PHASE_MERGE )`
`3190`	`3190`	`{`
`@@ -3206,7 +3206,7 @@ int test_cds(args_t args, bcf1_t rec, vbuf_t *vbuf)`
`3206`	`3206`
`3207`	`3207`	`for (ihap=0; ihap<ngts; ihap++)`
`3208`	`3208`	`{`
`3209`		`- if ( gt[ihap]==bcf_gt_missing \|\| gt[ihap]==bcf_int32_vector_end ) continue;`
	`3209`	`+ if ( bcf_gt_is_missing(gt[ihap]) \|\| gt[ihap]==bcf_int32_vector_end ) continue;`
`3210`	`3210`
`3211`	`3211`	`i = 2*ismpl + ihap;`
`3212`	`3212`
`@@ -3311,7 +3311,7 @@ void csq_stage(args_t args, csq_t csq, bcf1_t *rec)`
`3311`	`3311`	`int32_t gt = args->gt_arr + args->smpl->idx[i]ngt;`
`3312`	`3312`	`for (j=0; j<ngt; j++)`
`3313`	`3313`	`{`
`3314`		`- if ( gt[j]==bcf_gt_missing \|\| gt[j]==bcf_int32_vector_end ) continue;`
	`3314`	`+ if ( bcf_gt_is_missing(gt[j]) \|\| gt[j]==bcf_int32_vector_end ) continue;`
`3315`	`3315`	`int ial = bcf_gt_allele(gt[j]);`
`3316`	`3316`	`if ( !ial \|\| ial!=csq->type.vcf_ial ) continue;`
`3317`	`3317`	`csq_print_text(args, csq, args->smpl->idx[i],j+1);`
`@@ -3326,7 +3326,7 @@ void csq_stage(args_t args, csq_t csq, bcf1_t *rec)`
`3326`	`3326`	`int32_t gt = args->gt_arr + args->smpl->idx[i]ngt;`
`3327`	`3327`	`for (j=0; j<ngt; j++)`
`3328`	`3328`	`{`
`3329`		`- if ( gt[j]==bcf_gt_missing \|\| gt[j]==bcf_int32_vector_end ) continue;`
	`3329`	`+ if ( bcf_gt_is_missing(gt[j]) \|\| gt[j]==bcf_int32_vector_end ) continue;`
`3330`	`3330`	`int ial = bcf_gt_allele(gt[j]);`
`3331`	`3331`	`if ( !ial \|\| ial!=csq->type.vcf_ial ) continue;`
`3332`	`3332`
Original file line number	Diff line number	Diff line change
`@@ -1397,7 +1397,7 @@ static void filters_set_nmissing(filter_t flt, bcf1_t line, token_t *tok)`
`1397`	`1397`	`{ \`
`1398`	`1398`	`type_t val = convert(&ptr[j * sizeof(type_t)]); \`
`1399`	`1399`	`if ( val==is_vector_end ) break; \`
`1400`		`- if ( val==bcf_gt_missing ) { nmissing++; break; } \`
	`1400`	`+ if ( bcf_gt_is_missing(val) ) { nmissing++; break; } \`
`1401`	`1401`	`} \`
`1402`	`1402`	`} \`
`1403`	`1403`	`}`
Original file line number	Diff line number	Diff line change
`@@ -167,7 +167,7 @@ void process_region_guess(args_t *args)`
`167`	`167`	`int32_t ptr = args->arr + ismplngt;`
`168`	`168`	`double tmp = args->tmpf + ismpl3;`
`169`	`169`
`170`		`- if ( ptr[0]==bcf_gt_missing )`
	`170`	`+ if ( bcf_gt_is_missing(ptr[0]) )`
`171`	`171`	`{`
`172`	`172`	`tmp[0] = -1;`
`173`	`173`	`continue;`
Original file line number	Diff line number	Diff line change
`@@ -121,7 +121,7 @@ bcf1_t process(bcf1_t rec)`
`121`	`121`	`// replace gts`
`122`	`122`	`for (i=0; i<ngts; i++)`
`123`	`123`	`{`
`124`		`- if ( gts[i]==bcf_gt_missing )`
	`124`	`+ if ( bcf_gt_is_missing(gts[i]) )`
`125`	`125`	`{`
`126`	`126`	`gts[i] = new_gt;`
`127`	`127`	`changed++;`
Original file line number	Diff line number	Diff line change
`@@ -403,7 +403,7 @@ static inline int set_gt_custom(args_t args, int32_t ptr, int ngts, int nals)`
`403`	`403`	`{`
`404`	`404`	`if ( args->custom.gt[i]==MINOR_ALLELE ) new_allele = args->custom.m_allele;`
`405`	`405`	`else if ( args->custom.gt[i]==MAJOR_ALLELE ) new_allele = args->custom.M_allele;`
`406`		`- 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);`
	`406`	`+ 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);`
`407`	`407`	else if ( args->custom.gt[i]==MISSING_ALLELE ) new_allele = nals; // this is to trigger the `new_allele = bcf_gt_missing` branch below
`408`	`408`	`else new_allele = args->custom.gt[i];`
`409`	`409`	`if ( new_allele >= nals ) // cannot set, the requested index is bigger than there are alleles in ALT`
Original file line number	Diff line number	Diff line change
`@@ -842,7 +842,7 @@ static double _estimate_af(int8_t *ptr, int size, int nvals, int nsamples)`
`842`	`842`	`{`
`843`	`843`	`for (j=0; j<nvals; j++)`
`844`	`844`	`{`
`845`		`- if ( ptr[j]==bcf_gt_missing ) break;`
	`845`	`+ if ( bcf_gt_is_missing(ptr[j]) ) break;`
`846`	`846`	`if ( ptr[j]==bcf_int8_vector_end ) break;`
`847`	`847`	`if ( bcf_gt_allele(ptr[j]) ) nalt++;`
`848`	`848`	`else nref++;`
`@@ -911,7 +911,7 @@ static int _calc_r2_ld(vcfbuf_t buf, bcf1_t arec, bcf1_t brec, vcfbuf_ld_t l`
`911`	`911`	`for (j=0; j<afmt->n; j++)`
`912`	`912`	`{`
`913`	`913`	`if ( aptr[j]==bcf_int8_vector_end ) break;`
`914`		`- if ( aptr[j]==bcf_gt_missing )`
	`914`	`+ if ( bcf_gt_is_missing(aptr[j]) )`
`915`	`915`	`{`
`916`	`916`	`if ( !buf->ld.rand_missing ) break;`
`917`	`917`	`if ( hts_drand48() >= aaf ) adsg += 1;`
`@@ -922,7 +922,7 @@ static int _calc_r2_ld(vcfbuf_t buf, bcf1_t arec, bcf1_t brec, vcfbuf_ld_t l`
`922`	`922`	`for (j=0; j<bfmt->n; j++)`
`923`	`923`	`{`
`924`	`924`	`if ( bptr[j]==bcf_int8_vector_end ) break;`
`925`		`- if ( bptr[j]==bcf_gt_missing )`
	`925`	`+ if ( bcf_gt_is_missing(bptr[j]) )`
`926`	`926`	`{`
`927`	`927`	`if ( !buf->ld.rand_missing ) break;`
`928`	`928`	`if ( hts_drand48() >= baf ) bdsg += 1;`