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();
}
void doFactorSource(struct sqlConnection *conn, struct trackDb *tdb, char *item, int start, int end)
/* Display detailed info about a cluster of TFBS peaks from other tracks. */
{
char extraWhere[256];
safef(extraWhere, sizeof extraWhere, "name='%s'", item);
int rowOffset;
struct sqlResult *sr = hRangeQuery(conn, tdb->table, seqName, start, end, extraWhere, &rowOffset);
char **row = sqlNextRow(sr);
struct factorSource *cluster = NULL;
if (row != NULL)
cluster = factorSourceLoad(row + rowOffset);
sqlFreeResult(&sr);
if (cluster == NULL)
errAbort("Error loading cluster from track %s", tdb->track);
char *sourceTable = trackDbRequiredSetting(tdb, "sourceTable");
char *factorLink = cluster->name;
char *vocab = trackDbSetting(tdb, "controlledVocabulary");
if (vocab != NULL)
{
char *file = cloneFirstWord(vocab);
factorLink = wgEncodeVocabLink(file, "term", factorLink, factorLink, factorLink, "");
}
printf("<B>Factor:</B> %s<BR>\n", factorLink);
printf("<B>Cluster Score (out of 1000):</B> %d<BR>\n", cluster->score);
printPos(cluster->chrom, cluster->chromStart, cluster->chromEnd, NULL, TRUE, item);
/* Get list of tracks we'll look through for input. */
char *inputTrackTable = trackDbRequiredSetting(tdb, "inputTrackTable");
char query[256];
sqlSafef(query, sizeof(query), "select tableName from %s where factor='%s' order by source",
inputTrackTable,
cluster->name);
/* Next do the lists of hits and misses. We have the hits from the non-zero signals in
* cluster->expScores. We need to figure out the sources actually assayed though
* some other way. We'll do this by one of two techniques. */
char *inputTableFieldDisplay = trackDbSetting(tdb, "inputTableFieldDisplay");
if (inputTableFieldDisplay != NULL)
{
struct slName *fieldList = stringToSlNames(inputTableFieldDisplay);
char *vocab = trackDbSetting(tdb, "controlledVocabulary");
/* In a new section put up list of hits. */
webNewSection("Assays for %s in Cluster", cluster->name);
webPrintLinkTableStart();
printClusterTableHeader(fieldList, TRUE, FALSE, TRUE);
printFactorSourceTableHits(cluster, conn, sourceTable,
inputTrackTable, fieldList, FALSE, vocab);
webPrintLinkTableEnd();
webNewSectionHeaderStart();
char sectionTitle[128];
safef(sectionTitle,
sizeof(sectionTitle),"Assays for %s Without Hits in Cluster", cluster->name);
jsBeginCollapsibleSectionOldStyle(cart, tdb->track, "cellNoHits", sectionTitle, FALSE);
webNewSectionHeaderEnd();
webPrintLinkTableStart();
printClusterTableHeader(fieldList, TRUE, FALSE, FALSE);
printFactorSourceTableHits(cluster, conn, sourceTable,
inputTrackTable, fieldList, TRUE, vocab);
webPrintLinkTableEnd();
jsEndCollapsibleSection();
}
else
{
errAbort("Missing required trackDb setting %s for track %s",
"inputTableFieldDisplay", tdb->track);
}
webNewSectionHeaderStart();
jsBeginCollapsibleSectionOldStyle(cart, tdb->track, "cellSources", "Cell Abbreviations", FALSE);
webNewSectionHeaderEnd();
hPrintFactorSourceAbbrevTable(conn, tdb);
jsEndCollapsibleSection();
doClusterMotifDetails(conn, tdb, cluster);
}
