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Improve "not defined in the header" messages #2007

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Improve "not defined in the header" messages #2007

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14 changes: 12 additions & 2 deletions vcf.c
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Original file line number Diff line number Diff line change
Expand Up @@ -3180,6 +3180,8 @@ static int vcf_parse_format_dict2(kstring_t *s, const bcf_hdr_t *h, bcf1_t *v,
return -1;
}
hts_log_warning("FORMAT '%s' at %s:%"PRIhts_pos" is not defined in the header, assuming Type=String", t, bcf_seqname_safe(h,v), v->pos+1);
if ((v->errcode & (BCF_ERR_TAG_UNDEF|BCF_ERR_CTG_UNDEF)) == 0)
hts_log_warning("Missing headers may cause later processing to fail");
kstring_t tmp = {0,0,0};
int l;
ksprintf(&tmp, "##FORMAT=<ID=%s,Number=1,Type=String,Description=\"Dummy\">", t);
Expand Down Expand Up @@ -3788,7 +3790,10 @@ static int vcf_parse_filter(kstring_t *str, const bcf_hdr_t *h, bcf1_t *v, char
{
// Simple error recovery for FILTERs not defined in the header. It will not help when VCF header has
// been already printed, but will enable tools like vcfcheck to proceed.
hts_log_warning("FILTER '%s' is not defined in the header", t);
hts_log_warning("FILTER '%s' at %s:%"PRIhts_pos" is not defined in the header",
t, bcf_seqname_safe(h,v), v->pos+1);
if ((v->errcode & (BCF_ERR_TAG_UNDEF|BCF_ERR_CTG_UNDEF)) == 0)
hts_log_warning("Missing headers may cause later processing to fail");
kstring_t tmp = {0,0,0};
int l;
ksprintf(&tmp, "##FILTER=<ID=%s,Description=\"Dummy\">", t);
Expand Down Expand Up @@ -3847,7 +3852,10 @@ static int vcf_parse_info(kstring_t *str, const bcf_hdr_t *h, bcf1_t *v, char *p
k = kh_get(vdict, d, key);
if (k == kh_end(d) || kh_val(d, k).info[BCF_HL_INFO] == 15)
{
hts_log_warning("INFO '%s' is not defined in the header, assuming Type=String", key);
hts_log_warning("INFO '%s' at %s:%"PRIhts_pos" is not defined in the header, assuming Type=String",
key, bcf_seqname_safe(h,v), v->pos+1);
if ((v->errcode & (BCF_ERR_TAG_UNDEF|BCF_ERR_CTG_UNDEF)) == 0)
hts_log_warning("Missing headers may cause later processing to fail");
kstring_t tmp = {0,0,0};
int l;
ksprintf(&tmp, "##INFO=<ID=%s,Number=1,Type=String,Description=\"Dummy\">", key);
Expand Down Expand Up @@ -4033,6 +4041,8 @@ int vcf_parse(kstring_t *s, const bcf_hdr_t *h, bcf1_t *v)
k = kh_get(vdict, d, p);
if (k == kh_end(d)) {
hts_log_warning("Contig '%s' is not defined in the header. (Quick workaround: index the file with tabix.)", p);
if ((v->errcode & (BCF_ERR_TAG_UNDEF|BCF_ERR_CTG_UNDEF)) == 0)
hts_log_warning("Missing headers may cause later processing to fail");
v->errcode = BCF_ERR_CTG_UNDEF;
if ((k = fix_chromosome(h, d, p)) == kh_end(d)) {
hts_log_error("Could not add dummy header for contig '%s'", p);
Expand Down
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