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Add support for VCFv4.4 / VCFv4.5 Number= fields #1874

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Add support for VCFv4.4 / VCFv4.5 Number= fields #1874

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4e80031
Add initial support for VCFv4.4 / VCFv4.5 Number= fields
daviesrob Jan 16, 2025
7e2c0ce
Beef up bcf_hdr_check_sanity with a more complete set of Number=types.
jkbonfield Apr 17, 2025
342611f
Add more nuance for header Number=? checking.
jkbonfield Apr 17, 2025
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20 changes: 15 additions & 5 deletions htslib/vcf.h
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Original file line number Diff line number Diff line change
Expand Up @@ -65,11 +65,21 @@ extern "C" {
#define BCF_HT_STR 3
#define BCF_HT_LONG (BCF_HT_INT | 0x100) // BCF_HT_INT, but for int64_t values; VCF only!

#define BCF_VL_FIXED 0 // variable length
#define BCF_VL_VAR 1
#define BCF_VL_A 2
#define BCF_VL_G 3
#define BCF_VL_R 4
// Values for INFO / FORMAT "Number=" fields
#define BCF_VL_FIXED 0 ///< Integer defining a fixed number of items
#define BCF_VL_VAR 1 ///< Generic variable length ("Number=.")
#define BCF_VL_A 2 ///< One value per alternate allele
#define BCF_VL_G 3 ///< One value for each possible genotype
#define BCF_VL_R 4 ///< One value for each allele, including the reference

// The following was introduced in VCFv4.4 and is only valid for FORMAT header lines
#define BCF_VL_P 5 ///< One value for each allele value defined in GT

// The following were introduced in VCFv4.5 and are only valid for FORMAT header lines
#define BCF_VL_LA 6 ///< As BCF_VL_A, but only alt alleles listed in LAA are considered present
#define BCF_VL_LG 7 ///< As BCF_VL_G, but only alt alleles listed in LAA are considered present
#define BCF_VL_LR 8 ///< As BCF_VL_R, but only alt alleles listed in LAA are considered present
#define BCF_VL_M 9 ///< One value for each possible base modification for the corresponding ChEBI ID

/* === Dictionary ===

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131 changes: 113 additions & 18 deletions vcf.c
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Original file line number Diff line number Diff line change
Expand Up @@ -128,6 +128,7 @@ static inline bcf_hdr_aux_t *get_hdr_aux(const bcf_hdr_t *hdr)
//version macros
#define VCF_DEF 4002000
#define VCF44 4004000
#define VCF45 4005000

#define VCF_MAJOR_VER(x) ( (x) / 10000 / 100 )
#define VCF_MINOR_VER(x) ( ((x) % 1000000) / 1000 )
Expand Down Expand Up @@ -910,14 +911,20 @@ static int bcf_hdr_register_hrec(bcf_hdr_t *hdr, bcf_hrec_t *hrec)
}
else if ( !strcmp(hrec->keys[i], "Number") )
{
int is_fmt = hrec->type == BCF_HL_FMT;
if ( !strcmp(hrec->vals[i],"A") ) var = BCF_VL_A;
else if ( !strcmp(hrec->vals[i],"R") ) var = BCF_VL_R;
else if ( !strcmp(hrec->vals[i],"G") ) var = BCF_VL_G;
else if ( !strcmp(hrec->vals[i],".") ) var = BCF_VL_VAR;
else if ( is_fmt && !strcmp(hrec->vals[i],"P") ) var = BCF_VL_P;
else if ( is_fmt && !strcmp(hrec->vals[i],"LA") ) var = BCF_VL_LA;
else if ( is_fmt && !strcmp(hrec->vals[i],"LR") ) var = BCF_VL_LR;
else if ( is_fmt && !strcmp(hrec->vals[i],"LG") ) var = BCF_VL_LG;
else if ( is_fmt && !strcmp(hrec->vals[i],"M") ) var = BCF_VL_M;
else
{
sscanf(hrec->vals[i],"%d",&num);
var = BCF_VL_FIXED;
if (sscanf(hrec->vals[i],"%d",&num) == 1)
var = BCF_VL_FIXED;
}
if (var != BCF_VL_FIXED) num = 0xfffff;
}
Expand All @@ -928,7 +935,7 @@ static int bcf_hdr_register_hrec(bcf_hdr_t *hdr, bcf_hrec_t *hrec)
*hrec->key == 'I' ? "An" : "A", hrec->key);
type = BCF_HT_STR;
}
if (var == -1) {
if (var == UINT32_MAX) {
hts_log_warning("%s %s field has no Number defined. Assuming '.'",
*hrec->key == 'I' ? "An" : "A", hrec->key);
var = BCF_VL_VAR;
Expand Down Expand Up @@ -1226,26 +1233,114 @@ bcf_hrec_t *bcf_hdr_get_hrec(const bcf_hdr_t *hdr, int type, const char *key, co
return kh_val(d, k).hrec[type==BCF_HL_CTG?0:type];
}

// Check the VCF header is correctly formatted as per the specification.
// Note the code that calls this doesn't bother to check return values and
// we have so many broken VCFs in the wild that for now we just reprt a
// warning and continue anyway. So currently this is a void function.
void bcf_hdr_check_sanity(bcf_hdr_t *hdr)
{
static int PL_warned = 0, GL_warned = 0;
int version = bcf_get_version(hdr, NULL);

if ( !PL_warned )
{
int id = bcf_hdr_id2int(hdr, BCF_DT_ID, "PL");
if ( bcf_hdr_idinfo_exists(hdr,BCF_HL_FMT,id) && bcf_hdr_id2length(hdr,BCF_HL_FMT,id)!=BCF_VL_G )
{
hts_log_warning("PL should be declared as Number=G");
PL_warned = 1;
struct tag {
char name[10];
char type_str[3];
int type;
int version;
};

struct tag info_tags[] = {
{"AD", "R", BCF_VL_R, VCF_DEF},
{"ADF", "R", BCF_VL_R, VCF_DEF},
{"ADR", "R", BCF_VL_R, VCF_DEF},
{"AC", "A", BCF_VL_A, VCF_DEF},
{"AF", "A", BCF_VL_A, VCF_DEF},
{"CIGAR", "A", BCF_VL_A, VCF_DEF},
{"AA", "1", BCF_VL_FIXED, VCF_DEF},
{"AN", "1", BCF_VL_FIXED, VCF_DEF},
{"BQ", "1", BCF_VL_FIXED, VCF_DEF},
{"DB", "0", BCF_VL_FIXED, VCF_DEF},
{"DP", "1", BCF_VL_FIXED, VCF_DEF},
{"END", "1", BCF_VL_FIXED, VCF_DEF},
{"H2", "0", BCF_VL_FIXED, VCF_DEF},
{"H3", "0", BCF_VL_FIXED, VCF_DEF},
{"SB", "4", BCF_VL_FIXED, VCF_DEF},
{"SOMATIC", "0", BCF_VL_FIXED, VCF_DEF},
{"VALIDATED", "0", BCF_VL_FIXED, VCF_DEF},
{"1000G", "0", BCF_VL_FIXED, VCF_DEF},
};
static int info_warned[sizeof(info_tags)/sizeof(*info_tags)] = {0};

struct tag fmt_tags[] = {
{"AD", "R", BCF_VL_R, VCF_DEF},
{"ADF", "R", BCF_VL_R, VCF_DEF},
{"ADR", "R", BCF_VL_R, VCF_DEF},
{"EC", "A", BCF_VL_A, VCF_DEF},
{"GL", "G", BCF_VL_G, VCF_DEF},
{"GP", "G", BCF_VL_G, VCF_DEF},
{"PL", "G", BCF_VL_G, VCF_DEF},
{"PP", "G", BCF_VL_G, VCF_DEF},
{"DP", "1", BCF_VL_FIXED, VCF_DEF},
{"LEN", "1", BCF_VL_FIXED, VCF_DEF},
{"FT", "1", BCF_VL_FIXED, VCF_DEF},
{"GQ", "1", BCF_VL_FIXED, VCF_DEF},
{"GT", "1", BCF_VL_FIXED, VCF_DEF},
{"HQ", "2", BCF_VL_FIXED, VCF_DEF},
{"MQ", "1", BCF_VL_FIXED, VCF_DEF},
{"PQ", "1", BCF_VL_FIXED, VCF_DEF},
{"PS", "1", BCF_VL_FIXED, VCF_DEF},
{"PSL", "P", BCF_VL_P, VCF44},
{"PSO", "P", BCF_VL_P, VCF44},
{"PSQ", "P", BCF_VL_P, VCF44},
{"LGL", "LG", BCF_VL_LG, VCF45},
{"LGP", "LG", BCF_VL_LG, VCF45},
{"LPL", "LG", BCF_VL_LG, VCF45},
{"LPP", "LP", BCF_VL_LG, VCF45},
{"LEC", "LA", BCF_VL_LA, VCF45},
{"LAD", "LR", BCF_VL_LR, VCF45},
{"LADF", "LR", BCF_VL_LR, VCF45},
{"LADR", "LR", BCF_VL_LR, VCF45},
};
static int fmt_warned[sizeof(fmt_tags)/sizeof(*fmt_tags)] = {0};

// Check INFO tag types. We shouldn't really permit ".", but it's
// commonly misused so we let it slide unless it's a new tag and the
// file format claims to be new also. We also cannot distinguish between
// Number=1 and Number=2, but we at least report the correct term if we
// get, say, Number=G in its place.
int i;
for (i = 0; i < sizeof(info_tags)/sizeof(*info_tags); i++) {
if (info_warned[i])
continue;
int id = bcf_hdr_id2int(hdr, BCF_DT_ID, info_tags[i].name);
if (bcf_hdr_idinfo_exists(hdr, BCF_HL_INFO, id) &&
bcf_hdr_id2length(hdr, BCF_HL_INFO, id) != info_tags[i].type &&
bcf_hdr_id2length(hdr, BCF_HL_INFO, id) != BCF_VL_VAR) {
hts_log_warning("%s should be declared as Number=%s",
info_tags[i].name, info_tags[i].type_str);
info_warned[i] = 1;
}
}
if ( !GL_warned )
{
int id = bcf_hdr_id2int(hdr, BCF_DT_ID, "GL");
if ( bcf_hdr_idinfo_exists(hdr,BCF_HL_FMT,id) && bcf_hdr_id2length(hdr,BCF_HL_FMT,id)!=BCF_VL_G )
{
hts_log_warning("GL should be declared as Number=G");
GL_warned = 1;

// Check FORMAT tag types.
for (i = 0; i < sizeof(fmt_tags)/sizeof(*fmt_tags); i++) {
if (fmt_warned[i])
continue;
int id = bcf_hdr_id2int(hdr, BCF_DT_ID, fmt_tags[i].name);
if (bcf_hdr_idinfo_exists(hdr, BCF_HL_FMT, id) &&
bcf_hdr_id2length(hdr, BCF_HL_FMT, id) != fmt_tags[i].type) {
// Permit "Number=." if this tag predates the vcf version it is
// defined within. This is a common tactic for callers to use
// new tags with older formats in order to avoid parsing failures
// with some software.
// We don't care for 4.3 and earlier as that's more of a wild-west
// and it's not abnormal to see incorrect usage of Number=. there.
if ((version < VCF44 &&
bcf_hdr_id2length(hdr, BCF_HL_FMT, id) != BCF_VL_VAR) ||
(version >= VCF44 && version >= fmt_tags[i].version)) {
hts_log_warning("%s should be declared as Number=%s",
fmt_tags[i].name, fmt_tags[i].type_str);
fmt_warned[i] = 1;
}
}
}
}
Expand Down