struct variant *variantFromPgSnpAnnoRow(struct annoRow *row, char *refAllele, struct lm *lm)
/* Translate pgSnp annoRow into variant (allocated by lm). */
{
struct pgSnp pgSnp;
pgSnpStaticLoad(row->data, &pgSnp);
return variantNew(pgSnp.chrom, pgSnp.chromStart, pgSnp.chromEnd, pgSnp.alleleCount,
pgSnp.name, refAllele, lm);
}
static struct variant *variantFromVcfRow(struct annoGratorGpVar *self, struct annoRow *row,
char *refAllele)
/* Translate vcf array of words into variant. */
{
char **words = row->data;
// VCF may use abbreviated refAllele, so use VCF's refAllele to detect allele->isReference
// instead of the actual refAllele that's passed in. But skip the initial extra base if
// necessary, i.e. if 1-based vcfStart is the same as row->start.
uint vcfStart = atoll(words[1]);
int offset = (vcfStart == row->start) ? 1 : 0;
char *vcfRefAllele = words[3] + offset;
char *alStr = vcfGetSlashSepAllelesFromWords(words, self->dyScratch);
unsigned alCount = chopByChar(alStr, '/', NULL, 0);
return variantNew(row->chrom, row->start, row->end, alCount, alStr, vcfRefAllele, self->lm);
}
struct variant *variantFromVcfAnnoRow(struct annoRow *row, char *refAllele, struct lm *lm,
struct dyString *dyScratch)
/* Translate vcf array of words into variant (allocated by lm, overwriting dyScratch
* as temporary scratch string). */
{
char **words = row->data;
char *alStr = vcfGetSlashSepAllelesFromWords(words, dyScratch);
// The reference allele is the first allele in alStr -- and it may be trimmed on both ends with
// respect to the raw VCF ref allele in words[3], so copy vcfRefAllele back out of alStr.
// That ensures that variantNew will get the reference allele that matches the slash-separated
// allele string.
int refLen = strlen(alStr);
char *p = strchr(alStr, '/');
if (p)
refLen = p - alStr;
char vcfRefAllele[refLen + 1];
safencpy(vcfRefAllele, sizeof(vcfRefAllele), alStr, refLen);
unsigned alCount = countChars(alStr, '/') + 1;
return variantNew(row->chrom, row->start, row->end, alCount, alStr, vcfRefAllele, lm);
}