static void pgSnpCodingDetail(struct vcfRecord *rec)
/* Translate rec into pgSnp (with proper chrom name) and call Belinda's
* coding effect predictor from pgSnp details. */
{
char *genePredTable = "knownGene";
if (hTableExists(database, genePredTable))
{
struct pgSnp *pgs = pgSnpFromVcfRecord(rec);
if (!sameString(rec->chrom, seqName))
// rec->chrom might be missing "chr" prefix:
pgs->chrom = seqName;
printSeqCodDisplay(database, pgs, genePredTable);
}
}
static struct pgSnp *vcfFileToPgSnp(struct vcfFile *vcff, struct trackDb *tdb)
/* Convert vcff's records to pgSnp; don't free vcff until you're done with pgSnp
* because it contains pointers into vcff's records' chrom. */
{
struct pgSnp *pgsList = NULL;
struct vcfRecord *rec;
int maxLen = 33;
int maxAlCount = 5;
for (rec = vcff->records; rec != NULL; rec = rec->next)
{
struct pgSnpVcfStartEnd *psvs = needMem(sizeof(*psvs));
psvs->vcfStart = vcfRecordTrimIndelLeftBase(rec);
psvs->vcfEnd = vcfRecordTrimAllelesRight(rec);
struct pgSnp *pgs = pgSnpFromVcfRecord(rec);
memcpy(&(psvs->pgs), pgs, sizeof(*pgs));
pgs = (struct pgSnp *)psvs; // leak mem
// Insertion sequences can be quite long; abbreviate here for display.
int len = strlen(pgs->name);
if (len > maxLen)
{
int maxAlLen = (maxLen / min(rec->alleleCount, maxAlCount)) - 1;
pgs->name[0] = '\0';
int i;
for (i = 0; i < rec->alleleCount; i++)
{
if (i > 0)
safencat(pgs->name, len+1, "/", 1);
if (i >= maxAlCount)
{
safecat(pgs->name, len+1, "...");
pgs->alleleCount = maxAlCount;
break;
}
if (strlen(rec->alleles[i]) > maxAlLen-3)
strcpy(rec->alleles[i]+maxAlLen-3, "...");
safencat(pgs->name, len+1, rec->alleles[i], maxAlLen);
}
}
slAddHead(&pgsList, pgs);
}
slReverse(&pgsList);
return pgsList;
}
