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@vasudeva8
vasudeva8 committed Jan 7, 2025
1 parent 6a0fb00 commit 3f89c0a
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128 changes: 6 additions & 122 deletions htslib/vcf.h
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Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,7 @@
/// High-level VCF/BCF variant calling file operations.
/*
Copyright (C) 2012, 2013 Broad Institute.
Copyright (C) 2012-2020, 2022-2023 Genome Research Ltd.
Copyright (C) 2012-2020, 2022-2025 Genome Research Ltd.
Author: Heng Li <[email protected]>
Expand Down Expand Up @@ -1501,63 +1501,9 @@ static inline int bcf_float_is_vector_end(float f)
return u.i==bcf_float_vector_end ? 1 : 0;
}

typedef enum bcf_version {v41 = 1, v42, v43, v44} bcf_version;
/**
* bcf_get_version - get the version as bcf_version enumeration
* @param hdr - bcf header, to get version
* @param ipver - pointer to return version
* Returns 0 on success and -1 on failure
*/
static inline int bcf_get_version(const bcf_hdr_t *hdr, bcf_version *ver)
{
const char *version = NULL;

if (!hdr || !ver) {
return -1;
}

version = bcf_hdr_get_version(hdr);
if (!strcmp("VCFv4.1", version)) {
*ver = v41;
} else if (!strcmp("VCFv4.2", version)) {
*ver = v42;
} else if (!strcmp("VCFv4.3", version)) {
*ver = v43;
} else {
*ver = v44;
}
return 0;
}

static inline int bcf_format_gt(bcf_fmt_t *fmt, int isample, kstring_t *str)
{
uint32_t e = 0;
#define BRANCH(type_t, convert, missing, vector_end) { \
uint8_t *ptr = fmt->p + isample*fmt->size; \
int i; \
for (i=0; i<fmt->n; i++, ptr += sizeof(type_t)) \
{ \
type_t val = convert(ptr); \
if ( val == vector_end ) break; \
if ( i ) e |= kputc("/|"[val&1], str) < 0; \
if ( !(val>>1) ) e |= kputc('.', str) < 0; \
else e |= kputw((val>>1) - 1, str) < 0; \
} \
if (i == 0) e |= kputc('.', str) < 0; \
}
switch (fmt->type) {
case BCF_BT_INT8: BRANCH(int8_t, le_to_i8, bcf_int8_missing, bcf_int8_vector_end); break;
case BCF_BT_INT16: BRANCH(int16_t, le_to_i16, bcf_int16_missing, bcf_int16_vector_end); break;
case BCF_BT_INT32: BRANCH(int32_t, le_to_i32, bcf_int32_missing, bcf_int32_vector_end); break;
case BCF_BT_NULL: e |= kputc('.', str) < 0; break;
default: hts_log_error("Unexpected type %d", fmt->type); return -2;
}
#undef BRANCH
return e == 0 ? 0 : -1;
}

/**
* bcf_format_gt1 - formats GT information on a string
* bcf_format_gt_v2 - formats GT information on a string
* @param hdr - bcf header, to get version
* @param fmt - pointer to bcf format data
* @param isample - position of interested sample in data
Expand All @@ -1569,73 +1515,11 @@ static inline int bcf_format_gt(bcf_fmt_t *fmt, int isample, kstring_t *str)
* Explicit / prefixed phasing for 1st allele is used only when it is a must to
* correctly express phasing.
*/
static inline int bcf_format_gt1(const bcf_hdr_t *hdr, bcf_fmt_t *fmt, int isample, kstring_t *str)
HTSLIB_EXPORT int bcf_format_gt_v2(const bcf_hdr_t *hdr, bcf_fmt_t *fmt, int isample, kstring_t *str);

static inline int bcf_format_gt(bcf_fmt_t *fmt, int isample, kstring_t *str)
{
uint32_t e = 0;
bcf_version ver = v42;
int ploidy = 1, anyunphased = 0;
int32_t val0 = 0;
kstring_t tmp1 = KS_INITIALIZE, tmp2 = KS_INITIALIZE;

if (bcf_get_version(hdr, &ver)) {
hts_log_error("Failed to get version information");
return -1;
}
#define BRANCH(type_t, convert, missing, vector_end) { \
uint8_t *ptr = fmt->p + isample*fmt->size; \
int i; \
for (i=0; i<fmt->n; i++, ptr += sizeof(type_t)) \
{ \
type_t val = convert(ptr); \
if ( val == vector_end ) break; \
if (!i) { val0 = val; } \
if (i) { \
e |= kputc("/|"[val & 1], &tmp1) < 0; \
anyunphased |= !(val & 1); \
} \
if (!(val >> 1)) e |= kputc('.', &tmp1) < 0; \
else e |= kputw((val >> 1) - 1, &tmp1) < 0; \
} \
if (i == 0) e |= kputc('.', &tmp1) < 0; \
ploidy = i; \
}
switch (fmt->type) {
case BCF_BT_INT8: BRANCH(int8_t, le_to_i8, bcf_int8_missing, bcf_int8_vector_end); break;
case BCF_BT_INT16: BRANCH(int16_t, le_to_i16, bcf_int16_missing, bcf_int16_vector_end); break;
case BCF_BT_INT32: BRANCH(int32_t, le_to_i32, bcf_int32_missing, bcf_int32_vector_end); break;
case BCF_BT_NULL: e |= kputc('.', &tmp1) < 0; break;
default: hts_log_error("Unexpected type %d", fmt->type); return -2;
}
#undef BRANCH

if (ver >= v44) { //output which supports prefixed phasing
/* update 1st allele's phasing if required and append rest to it.
use prefixed phasing only when it is a must. i.e. without which the
inferred value will be incorrect */
if (val0 & 1) {
/* 1st one is phased, if ploidy is > 1 and an unphased allele exists
need to specify explicitly */
e |= (ploidy > 1 && anyunphased) ?
(kputc('|', &tmp2) < 0) :
(ploidy <= 1 && !((val0 >> 1)) ? //|. needs explicit o/p
(kputc('|', &tmp2) < 0) :
0);
} else {
/* 1st allele is unphased, if ploidy is = 1 or allele is '.' or
ploidy > 1 and no other unphased allele exist, need to specify
explicitly */
e |= ((ploidy <= 1 && val0 != 0) || (ploidy > 1 && !anyunphased)) ?
(kputc('/', &tmp2) < 0) :
0;
}
e |= kputsn(tmp1.s, tmp1.l, &tmp2) < 0; //append rest with updated one
ks_free(&tmp1);
tmp1 = tmp2;
}
//updated v44 string or <v44 without any update
e |= kputsn(tmp1.s, tmp1.l, str) < 0;
ks_free(&tmp1);
return e == 0 ? 0 : -1;
return bcf_format_gt_v2(NULL, fmt, isample, str);
}

static inline int bcf_enc_size(kstring_t *s, int size, int type)
Expand Down
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