static enum vcfInfoType typeForGtFormat(struct vcfFile *vcff, const char *key)
/* Look up the type of FORMAT component key, in the definitions from the header,
* and failing that, from the keys reserved in the spec. */
{
struct vcfInfoDef *def = vcfInfoDefForGtKey(vcff, key);
if (def == NULL)
{
vcfFileErr(vcff, "There is no FORMAT header defining \"%s\"", key);
// default to string so we can display value as-is:
return vcfInfoString;
}
return def->type;
}
static void vcfGenotypeTable(struct vcfRecord *rec, char *track, char **displayAls)
/* Put the table containing details about each genotype into a collapsible section. */
{
static struct dyString *tmp1 = NULL;
if (tmp1 == NULL)
tmp1 = dyStringNew(0);
jsBeginCollapsibleSection(cart, track, "genotypes", "Detailed genotypes", FALSE);
dyStringClear(tmp1);
dyStringAppend(tmp1, rec->format);
struct vcfFile *vcff = rec->file;
enum vcfInfoType formatTypes[256];
char *formatKeys[256];
int formatCount = chopString(tmp1->string, ":", formatKeys, ArraySize(formatKeys));
puts("<B>Genotype info key:</B><BR>");
int i;
for (i = 0; i < formatCount; i++)
{
if (sameString(formatKeys[i], vcfGtGenotype))
continue;
const struct vcfInfoDef *def = vcfInfoDefForGtKey(vcff, formatKeys[i]);
char *desc = def ? def->description : "<em>not described in VCF header</em>";
printf(" <B>%s:</B> %s<BR>\n", formatKeys[i], desc);
formatTypes[i] = def->type;
}
hTableStart();
puts("<TR><TH>Sample ID</TH><TH>Genotype</TH><TH>Phased?</TH>");
for (i = 0; i < formatCount; i++)
{
if (sameString(formatKeys[i], vcfGtGenotype))
continue;
printf("<TH>%s</TH>", formatKeys[i]);
}
puts("</TR>\n");
for (i = 0; i < vcff->genotypeCount; i++)
{
struct vcfGenotype *gt = &(rec->genotypes[i]);
char *hapA = ".", *hapB = ".";
if (gt->hapIxA >= 0)
hapA = displayAls[(unsigned char)gt->hapIxA];
if (gt->isHaploid)
hapB = "";
else if (gt->hapIxB >= 0)
hapB = displayAls[(unsigned char)gt->hapIxB];
char sep = gt->isHaploid ? ' ' : gt->isPhased ? '|' : '/';
char *phasing = gt->isHaploid ? NA : gt->isPhased ? "Y" : "n";
printf("<TR><TD>%s</TD><TD>%s%c%s</TD><TD>%s</TD>", vcff->genotypeIds[i],
hapA, sep, hapB, phasing);
int j;
for (j = 0; j < gt->infoCount; j++)
{
if (sameString(formatKeys[j], vcfGtGenotype))
continue;
printf("<TD>");
struct vcfInfoElement *el = &(gt->infoElements[j]);
int k;
for (k = 0; k < el->count; k++)
{
if (k > 0)
printf(", ");
if (el->missingData[k])
printf(".");
else
vcfPrintDatum(stdout, el->values[k], formatTypes[j]);
}
printf("</TD>");
}
puts("</TR>");
}
hTableEnd();
jsEndCollapsibleSection();
}
