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Merged
pd3 merged 1 commit into from
Jun 16, 2026
+35 −32
Merged

Fix vcfstats.c on big-endian platforms #2569

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2 changes: 1 addition & 1 deletion Makefile
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Original file line number Diff line number Diff line change
Expand Up @@ -267,7 +267,7 @@ vcfcnv.o: vcfcnv.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_kstrin
vcfhead.o: vcfhead.c $(htslib_kstring_h) $(htslib_vcf_h) $(bcftools_h)
vcfsom.o: vcfsom.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_vcfutils_h) $(htslib_hts_os_h) $(htslib_hts_defs_h) $(bcftools_h)
vcfsort.o: vcfsort.c $(htslib_vcf_h) $(htslib_kstring_h) $(htslib_hts_os_h) $(htslib_hts_defs_h) $(htslib_bgzf_h) kheap.h $(bcftools_h)
vcfstats.o: vcfstats.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_vcfutils_h) $(htslib_faidx_h) $(bcftools_h) $(filter_h) bin.h dist.h
vcfstats.o: vcfstats.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_vcfutils_h) $(htslib_faidx_h) $(htslib_hts_endian_h) $(bcftools_h) $(filter_h) bin.h dist.h
vcfview.o: vcfview.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_vcfutils_h) $(bcftools_h) $(filter_h) $(htslib_khash_str2int_h) $(htslib_kbitset_h)
reheader.o: reheader.c $(htslib_vcf_h) $(htslib_bgzf_h) $(htslib_tbx_h) $(htslib_kseq_h) $(htslib_thread_pool_h) $(htslib_faidx_h) $(htslib_khash_str2int_h) $(bcftools_h) $(khash_str2str_h)
tabix.o: tabix.c $(htslib_bgzf_h) $(htslib_tbx_h)
Expand Down
65 changes: 34 additions & 31 deletions vcfstats.c
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Original file line number Diff line number Diff line change
Expand Up @@ -37,6 +37,7 @@ THE SOFTWARE. */
#include <htslib/synced_bcf_reader.h>
#include <htslib/vcfutils.h>
#include <htslib/faidx.h>
#include <htslib/hts_endian.h>
#include <inttypes.h>
#include "bcftools.h"
#include "filter.h"
Expand Down Expand Up @@ -899,36 +900,37 @@ static inline int get_ad(bcf1_t *line, bcf_fmt_t *ad_fmt_ptr, int ismpl, int *ia
{
int iv, ad = 0;
*ial = 0;
#define BRANCH_INT(type_t,missing,vector_end) { \
type_t *ptr = (type_t *) (ad_fmt_ptr->p + ad_fmt_ptr->size*ismpl); \
#define BRANCH_INT(type_t,convert,missing,vector_end) { \
uint8_t *x = ad_fmt_ptr->p + ad_fmt_ptr->size*ismpl; \
for (iv=1; iv<ad_fmt_ptr->n && iv<line->n_allele; iv++) \
{ \
if ( ptr[iv]==vector_end ) break; \
if ( ptr[iv]==missing ) continue; \
if ( ad < ptr[iv] ) { ad = ptr[iv]; *ial = iv; }\
type_t val = convert(&x[iv * sizeof(type_t)]); \
if ( val==vector_end ) break; \
if ( val==missing ) continue; \
if ( ad < val ) { ad = val; *ial = iv; }\
} \
}
switch (ad_fmt_ptr->type) {
case BCF_BT_INT8: BRANCH_INT(int8_t, bcf_int8_missing, bcf_int8_vector_end); break;
case BCF_BT_INT16: BRANCH_INT(int16_t, bcf_int16_missing, bcf_int16_vector_end); break;
case BCF_BT_INT32: BRANCH_INT(int32_t, bcf_int32_missing, bcf_int32_vector_end); break;
case BCF_BT_INT8: BRANCH_INT(int8_t, le_to_i8, bcf_int8_missing, bcf_int8_vector_end); break;
case BCF_BT_INT16: BRANCH_INT(int16_t, le_to_i16, bcf_int16_missing, bcf_int16_vector_end); break;
case BCF_BT_INT32: BRANCH_INT(int32_t, le_to_i32, bcf_int32_missing, bcf_int32_vector_end); break;
default: fprintf(stderr, "[E::%s] todo: %d\n", __func__, ad_fmt_ptr->type); exit(1); break;
}
#undef BRANCH_INT
return ad;
}
static inline int get_iad(bcf1_t *line, bcf_fmt_t *ad_fmt_ptr, int ismpl, int ial)
{
#define BRANCH_INT(type_t,missing,vector_end) { \
type_t *ptr = (type_t *) (ad_fmt_ptr->p + ad_fmt_ptr->size*ismpl); \
if ( ptr[ial]==vector_end ) return 0; \
if ( ptr[ial]==missing ) return 0; \
return ptr[ial]; \
#define BRANCH_INT(type_t,convert,missing,vector_end) { \
type_t val = convert(ad_fmt_ptr->p + ad_fmt_ptr->size*ismpl + ial*sizeof(type_t)); \
if ( val==vector_end ) return 0; \
if ( val==missing ) return 0; \
return val; \
}
switch (ad_fmt_ptr->type) {
case BCF_BT_INT8: BRANCH_INT(int8_t, bcf_int8_missing, bcf_int8_vector_end); break;
case BCF_BT_INT16: BRANCH_INT(int16_t, bcf_int16_missing, bcf_int16_vector_end); break;
case BCF_BT_INT32: BRANCH_INT(int32_t, bcf_int32_missing, bcf_int32_vector_end); break;
case BCF_BT_INT8: BRANCH_INT(int8_t, le_to_i8, bcf_int8_missing, bcf_int8_vector_end); break;
case BCF_BT_INT16: BRANCH_INT(int16_t, le_to_i16, bcf_int16_missing, bcf_int16_vector_end); break;
case BCF_BT_INT32: BRANCH_INT(int32_t, le_to_i32, bcf_int32_missing, bcf_int32_vector_end); break;
default: fprintf(stderr, "[E::%s] todo: %d\n", __func__, ad_fmt_ptr->type); exit(1); break;
}
#undef BRANCH_INT
Expand Down Expand Up @@ -957,36 +959,37 @@ static inline int calc_sample_depth(args_t *args, int ismpl, bcf_fmt_t *ad_fmt_p
{
if ( dp_fmt_ptr )
{
#define BRANCH_INT(type_t,missing,vector_end) { \
type_t *ptr = (type_t *) (dp_fmt_ptr->p + dp_fmt_ptr->size*ismpl); \
if ( *ptr==missing || *ptr==vector_end ) return -1; \
return *ptr; \
#define BRANCH_INT(type_t,convert,missing,vector_end) { \
type_t val = convert(dp_fmt_ptr->p + dp_fmt_ptr->size*ismpl); \
if ( val==missing || val==vector_end ) return -1; \
return val; \
}
switch (dp_fmt_ptr->type) {
case BCF_BT_INT8: BRANCH_INT(int8_t, bcf_int8_missing, bcf_int8_vector_end); break;
case BCF_BT_INT16: BRANCH_INT(int16_t, bcf_int16_missing, bcf_int16_vector_end); break;
case BCF_BT_INT32: BRANCH_INT(int32_t, bcf_int32_missing, bcf_int32_vector_end); break;
case BCF_BT_INT8: BRANCH_INT(int8_t, le_to_i8, bcf_int8_missing, bcf_int8_vector_end); break;
case BCF_BT_INT16: BRANCH_INT(int16_t, le_to_i16, bcf_int16_missing, bcf_int16_vector_end); break;
case BCF_BT_INT32: BRANCH_INT(int32_t, le_to_i32, bcf_int32_missing, bcf_int32_vector_end); break;
default: fprintf(stderr, "[E::%s] todo: %d\n", __func__, dp_fmt_ptr->type); exit(1); break;
}
#undef BRANCH_INT
}
if ( ad_fmt_ptr )
{
int iv, dp = 0, has_value = 0;
#define BRANCH_INT(type_t,missing,vector_end) { \
type_t *ptr = (type_t *) (ad_fmt_ptr->p + ad_fmt_ptr->size*ismpl); \
#define BRANCH_INT(type_t,convert,missing,vector_end) { \
uint8_t *x = ad_fmt_ptr->p + ad_fmt_ptr->size*ismpl; \
for (iv=0; iv<ad_fmt_ptr->n; iv++) \
{ \
if ( ptr[iv]==vector_end ) break; \
if ( ptr[iv]==missing ) continue; \
type_t val = convert(&x[iv * sizeof(type_t)]); \
if ( val==vector_end ) break; \
if ( val==missing ) continue; \
has_value = 1; \
dp += ptr[iv]; \
dp += val; \
} \
}
switch (ad_fmt_ptr->type) {
case BCF_BT_INT8: BRANCH_INT(int8_t, bcf_int8_missing, bcf_int8_vector_end); break;
case BCF_BT_INT16: BRANCH_INT(int16_t, bcf_int16_missing, bcf_int16_vector_end); break;
case BCF_BT_INT32: BRANCH_INT(int32_t, bcf_int32_missing, bcf_int32_vector_end); break;
case BCF_BT_INT8: BRANCH_INT(int8_t, le_to_i8, bcf_int8_missing, bcf_int8_vector_end); break;
case BCF_BT_INT16: BRANCH_INT(int16_t, le_to_i16, bcf_int16_missing, bcf_int16_vector_end); break;
case BCF_BT_INT32: BRANCH_INT(int32_t, le_to_i32, bcf_int32_missing, bcf_int32_vector_end); break;
default: fprintf(stderr, "[E::%s] todo: %d\n", __func__, ad_fmt_ptr->type); exit(1); break;
}
#undef BRANCH_INT
Expand Down
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