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Add Type to INFO/FORMAT sanity check. #1967

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0f6ec20
Add type to INFO/FORMAT sanity check.
whitwham Nov 6, 2025
34946a1
Fix to warning type.
whitwham Nov 6, 2025
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159 changes: 88 additions & 71 deletions vcf.c
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Original file line number Diff line number Diff line change
Expand Up @@ -1272,104 +1272,121 @@ void bcf_hdr_check_sanity(bcf_hdr_t *hdr)

struct tag {
char name[10];
char type_str[3];
int type;
char number_str[3];
int number;
int version;
char type_str[8];
int type;
};

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},
{"MQ", "1", BCF_VL_FIXED, VCF_DEF},
{"MQ0", "1", BCF_VL_FIXED, VCF_DEF},
{"NS", "1", 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},
{"AD", "R", BCF_VL_R, VCF_DEF, "Integer", BCF_HT_INT},
{"ADF", "R", BCF_VL_R, VCF_DEF, "Integer", BCF_HT_INT},
{"ADR", "R", BCF_VL_R, VCF_DEF, "Integer", BCF_HT_INT},
{"AC", "A", BCF_VL_A, VCF_DEF, "Integer", BCF_HT_INT},
{"AF", "A", BCF_VL_A, VCF_DEF, "Float", BCF_HT_REAL},
{"CIGAR", "A", BCF_VL_A, VCF_DEF, "String", BCF_HT_STR},
{"AA", "1", BCF_VL_FIXED, VCF_DEF, "String", BCF_HT_STR},
{"AN", "1", BCF_VL_FIXED, VCF_DEF, "Integer", BCF_HT_INT},
{"BQ", "1", BCF_VL_FIXED, VCF_DEF, "Float", BCF_HT_REAL},
{"DB", "0", BCF_VL_FIXED, VCF_DEF, "Flag", BCF_HT_FLAG},
{"DP", "1", BCF_VL_FIXED, VCF_DEF, "Integer", BCF_HT_INT},
{"END", "1", BCF_VL_FIXED, VCF_DEF, "Integer", BCF_HT_INT},
{"H2", "0", BCF_VL_FIXED, VCF_DEF, "Flag", BCF_HT_FLAG},
{"H3", "0", BCF_VL_FIXED, VCF_DEF, "Flag", BCF_HT_FLAG},
{"MQ", "1", BCF_VL_FIXED, VCF_DEF, "Float", BCF_HT_REAL},
{"MQ0", "1", BCF_VL_FIXED, VCF_DEF, "Integer", BCF_HT_INT},
{"NS", "1", BCF_VL_FIXED, VCF_DEF, "Integer", BCF_HT_INT},
{"SB", "4", BCF_VL_FIXED, VCF_DEF, "Integer", BCF_HT_INT},
{"SOMATIC", "0", BCF_VL_FIXED, VCF_DEF, "Flag", BCF_HT_FLAG},
{"VALIDATED", "0", BCF_VL_FIXED, VCF_DEF, "Flag", BCF_HT_FLAG},
{"1000G", "0", BCF_VL_FIXED, VCF_DEF, "Flag", BCF_HT_FLAG},
};
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", "LG", 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},
{"AD", "R", BCF_VL_R, VCF_DEF, "Integer", BCF_HT_INT},
{"ADF", "R", BCF_VL_R, VCF_DEF, "Integer", BCF_HT_INT},
{"ADR", "R", BCF_VL_R, VCF_DEF, "Integer", BCF_HT_INT},
{"EC", "A", BCF_VL_A, VCF_DEF, "Integer", BCF_HT_INT},
{"GL", "G", BCF_VL_G, VCF_DEF, "Float", BCF_HT_REAL},
{"GP", "G", BCF_VL_G, VCF_DEF, "Float", BCF_HT_REAL},
{"PL", "G", BCF_VL_G, VCF_DEF, "Integer", BCF_HT_INT},
{"PP", "G", BCF_VL_G, VCF_DEF, "Integer", BCF_HT_INT},
{"DP", "1", BCF_VL_FIXED, VCF_DEF, "Integer", BCF_HT_INT},
{"LEN", "1", BCF_VL_FIXED, VCF_DEF, "Integer", BCF_HT_INT},
{"FT", "1", BCF_VL_FIXED, VCF_DEF, "String", BCF_HT_STR},
{"GQ", "1", BCF_VL_FIXED, VCF_DEF, "Integer", BCF_HT_INT},
{"GT", "1", BCF_VL_FIXED, VCF_DEF, "String", BCF_HT_STR},
{"HQ", "2", BCF_VL_FIXED, VCF_DEF, "Integer", BCF_HT_INT},
{"MQ", "1", BCF_VL_FIXED, VCF_DEF, "Integer", BCF_HT_INT},
{"PQ", "1", BCF_VL_FIXED, VCF_DEF, "Integer", BCF_HT_INT},
{"PS", "1", BCF_VL_FIXED, VCF_DEF, "Integer", BCF_HT_INT},
{"PSL", "P", BCF_VL_P, VCF44, "String", BCF_HT_STR},
{"PSO", "P", BCF_VL_P, VCF44, "Integer", BCF_HT_INT},
{"PSQ", "P", BCF_VL_P, VCF44, "Integer", BCF_HT_INT},
{"LGL", "LG", BCF_VL_LG, VCF45, "Integer", BCF_HT_INT},
{"LGP", "LG", BCF_VL_LG, VCF45, "Integer", BCF_HT_INT},
{"LPL", "LG", BCF_VL_LG, VCF45, "Integer", BCF_HT_INT},
{"LPP", "LG", BCF_VL_LG, VCF45, "Integer", BCF_HT_INT},
{"LEC", "LA", BCF_VL_LA, VCF45, "Integer", BCF_HT_INT},
{"LAD", "LR", BCF_VL_LR, VCF45, "Integer", BCF_HT_INT},
{"LADF", "LR", BCF_VL_LR, VCF45, "Integer", BCF_HT_INT},
{"LADR", "LR", BCF_VL_LR, VCF45, "Integer", BCF_HT_INT},
};
static int fmt_warned[sizeof(fmt_tags)/sizeof(*fmt_tags)] = {0};

// Check INFO tag types. We shouldn't really permit ".", but it's
// Check INFO tag numbers. 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.
// Also check the types.
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 (bcf_hdr_idinfo_exists(hdr, BCF_HL_INFO, id)) {
if (bcf_hdr_id2length(hdr, BCF_HL_INFO, id) != info_tags[i].number &&
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].number_str);
info_warned[i] = 1;
}

if (bcf_hdr_id2type(hdr, BCF_HL_INFO, id) != info_tags[i].type) {
hts_log_warning("%s should be declared as Type=%s",
info_tags[i].name, info_tags[i].type_str);
info_warned[i] = 1;
}
}
}

// Check FORMAT tag types.
// Check FORMAT tag numbers and 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",
if (bcf_hdr_idinfo_exists(hdr, BCF_HL_FMT, id)) {
if (bcf_hdr_id2length(hdr, BCF_HL_FMT, id) != fmt_tags[i].number) {
// 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].number_str);
fmt_warned[i] = 1;
}
}

if (bcf_hdr_id2type(hdr, BCF_HL_FMT, id) != fmt_tags[i].type) {
hts_log_warning("%s should be declared as Type=%s",
fmt_tags[i].name, fmt_tags[i].type_str);
fmt_warned[i] = 1;
}
Expand Down