static struct customTrack *chromGraphLoader(struct customFactory *fac,
struct hash *chromHash, struct customPp *cpp, struct customTrack *track,
boolean dbRequested)
/* Load up chromGraph data until get next track line. */
{
/* See if binary file has already been made. If so then
* no need for rest of this routine. */
struct trackDb *tdb = track->tdb;
struct hash *settings = tdb->settingsHash;
char *binaryFileName = hashFindVal(settings, "binaryFile");
if (binaryFileName != NULL)
{
if (fileExists(binaryFileName))
return track;
else
return NULL;
}
return chromGraphParser(track->genomeDb, cpp,
trackDbSettingOrDefault(tdb, "formatType", cgfFormatGuess),
trackDbSettingOrDefault(tdb, "markerType", cgfMarkerGuess),
trackDbSettingOrDefault(tdb, "columnLabels", cgfColLabelGuess),
trackDbSetting(tdb, "name"),
trackDbSetting(tdb, "description"),
tdb->settingsHash, FALSE);
}
/* Return is an array of integers, last one of value zero to indicate the
* end of the array. In case of nothing found in trackDb, return
* a NULL pointer indicating no results.
*
* If the value is 'first' then use the first span value from the table.
* Assumes that all values in the table are the same. */
int *wiggleSpanList(struct sqlConnection *conn, struct trackDb *tdb)
{
char *tdbDefault = cloneString(trackDbSettingOrDefault(tdb, SPANLIST, "NONE"));
int *ret = (int *)NULL;
if (sameWord("NONE",tdbDefault))
{
struct hashEl *hel;
/* if not found in trackDb, maybe it is in tdb->settings
* (custom tracks keep settings here)
*/
if ((tdb->settings != (char *)NULL) &&
(tdb->settingsHash != (struct hash *)NULL))
{
if ((hel = hashLookup(tdb->settingsHash, SPANLIST)) != NULL)
{
freeMem(tdbDefault);
tdbDefault = cloneString((char *)hel->val);
}
}
}
/* if we still don't have a spanList, or we got "first" for spanList,
* make up spanList by choosing the first span we find in the table */
//if (sameWord("NONE",tdbDefault) || sameWord("first",tdbDefault))
else if( sameWord("first",tdbDefault))
{
char query[1024];
snprintf(query, sizeof(query), "SELECT span FROM %s limit 1", tdb->table );
char *tmpSpan = sqlQuickString(conn, query);
AllocArray(ret,2);
ret[0] = sqlUnsigned(tmpSpan);
ret[1] = 0;
freeMem(tmpSpan);
}
else
{
/* If something found, let's parse it */
int i;
char *words[MAX_SPAN_COUNT];
int wc;
wc = chopCommas(tdbDefault,words);
AllocArray(ret,wc+1); /* + 1 for the extra zero */
for ( i = 0; i < wc; ++i )
ret[i] = sqlUnsigned(words[i]);
intSort(wc,ret);
ret[wc] = 0; /* end of list */
}
freeMem(tdbDefault);
return(ret);
} /* int *wiggleSpanList(struct trackDb *tdb) */
static int vcfHapClusterTotalHeight(struct track *tg, enum trackVisibility vis)
/* Return height of haplotype graph (2 * #samples * lineHeight);
* 2 because we're assuming diploid genomes here, no XXY, tetraploid etc. */
{
const struct vcfFile *vcff = tg->extraUiData;
if (vcff->records == NULL)
return 0;
int ploidy = sameString(chromName, "chrY") ? 1 : 2;
int simpleHeight = ploidy * vcff->genotypeCount * tg->lineHeight;
int defaultHeight = min(simpleHeight, VCF_DEFAULT_HAP_HEIGHT);
char *tdbHeight = trackDbSettingOrDefault(tg->tdb, VCF_HAP_HEIGHT_VAR, NULL);
if (isNotEmpty(tdbHeight))
defaultHeight = atoi(tdbHeight);
int cartHeight = cartOrTdbInt(cart, tg->tdb, VCF_HAP_HEIGHT_VAR, defaultHeight);
if (tg->visibility == tvSquish)
cartHeight /= 2;
int extraPixel = (getColorMode(tg->tdb) == altOnlyMode) ? 1 : 0;
int totalHeight = cartHeight + CLIP_PAD + 2*extraPixel;
tg->height = min(totalHeight, maximumTrackHeight(tg));
return tg->height;
}
static void bigBedClick(char *fileName, struct trackDb *tdb,
char *item, int start, int end, int bedSize)
/* Handle click in generic bigBed track. */
{
boolean showUrl = FALSE;
char *chrom = cartString(cart, "c");
/* Open BigWig file and get interval list. */
struct bbiFile *bbi = bigBedFileOpen(fileName);
struct lm *lm = lmInit(0);
int ivStart = start, ivEnd = end;
if (start == end)
{
// item is an insertion; expand the search range from 0 bases to 2 so we catch it:
ivStart = max(0, start-1);
ivEnd++;
}
struct bigBedInterval *bbList = bigBedIntervalQuery(bbi, chrom, ivStart, ivEnd, 0, lm);
/* Get bedSize if it's not already defined. */
if (bedSize == 0)
{
bedSize = bbi->definedFieldCount;
showUrl = TRUE;
}
char *scoreFilter = cartOrTdbString(cart, tdb, "scoreFilter", NULL);
int minScore = 0;
if (scoreFilter)
minScore = atoi(scoreFilter);
/* Find particular item in list - matching start, and item if possible. */
boolean found = FALSE;
boolean firstTime = TRUE;
struct bigBedInterval *bb;
for (bb = bbList; bb != NULL; bb = bb->next)
{
if (!(bb->start == start && bb->end == end))
continue;
if (bedSize > 3)
{
char *name = cloneFirstWordByTab(bb->rest);
boolean match = sameString(name, item);
freez(&name);
if (!match)
continue;
}
found = TRUE;
if (firstTime)
printf("<BR>\n");
int seq1Seq2Fields = 0;
// check for seq1 and seq2 in columns 7+8 (eg, pairedTagAlign)
boolean seq1Seq2 = sameOk(trackDbSetting(tdb, BASE_COLOR_USE_SEQUENCE), "seq1Seq2");
if (seq1Seq2 && bedSize == 6)
seq1Seq2Fields = 2;
char *fields[bedSize+seq1Seq2Fields];
char startBuf[16], endBuf[16];
char *rest = cloneString(bb->rest);
int bbFieldCount = bigBedIntervalToRow(bb, chrom, startBuf, endBuf, fields,
bedSize+seq1Seq2Fields);
if (bbFieldCount != bedSize+seq1Seq2Fields)
{
errAbort("Disagreement between trackDb field count (%d) and %s fieldCount (%d)",
bedSize, fileName, bbFieldCount);
}
struct bed *bed = bedLoadN(fields, bedSize);
if (bedSize >= 6 && scoreFilter && bed->score < minScore)
continue;
if (showUrl && (bedSize >= 4))
printCustomUrl(tdb, item, TRUE);
bedPrintPos(bed, bedSize, tdb);
// display seq1 and seq2
if (seq1Seq2 && bedSize+seq1Seq2Fields == 8)
printf("<table><tr><th>Sequence 1</th><th>Sequence 2</th></tr>"
"<tr><td> %s </td><td> %s </td></tr></table>", fields[6], fields[7]);
else if (isNotEmpty(rest))
{
char *restFields[256];
int restCount = chopTabs(rest, restFields);
int restBedFields = bedSize - 3;
if (restCount > restBedFields)
{
if (0 == extraFieldsPrint(tdb,NULL,restFields + restBedFields,restCount - restBedFields))
{
int i;
char label[20];
safef(label, sizeof(label), "nonBedFieldsLabel");
printf("<B>%s </B>",
trackDbSettingOrDefault(tdb, label, "Non-BED fields:"));
for (i = restBedFields; i < restCount; i++)
printf("%s%s", (i > 0 ? "\t" : ""), restFields[i]);
printf("<BR>\n");
}
}
}
if (isCustomTrack(tdb->track))
{
time_t timep = bbiUpdateTime(bbi);
printBbiUpdateTime(&timep);
}
}
if (!found)
{
printf("No item %s starting at %d\n", emptyForNull(item), start);
}
lmCleanup(&lm);
bbiFileClose(&bbi);
}
void doBamDetails(struct trackDb *tdb, char *item)
/* Show details of an alignment from a BAM file. */
{
if (item == NULL)
errAbort("doBamDetails: NULL item name");
int start = cartInt(cart, "o");
if (!tdb || !trackDbSetting(tdb, "bamSkipPrintQualScore"))
skipQualityScore = FALSE;
else
skipQualityScore = TRUE;
// TODO: libify tdb settings table_pairEndsByName, stripPrefix and pairSearchRange
knetUdcInstall();
if (udcCacheTimeout() < 300)
udcSetCacheTimeout(300);
if (sameString(item, "zoom in"))
printf("Zoom in to a region with fewer items to enable 'detail page' links for individual items.<BR>");
char varName[1024];
safef(varName, sizeof(varName), "%s_pairEndsByName", tdb->track);
boolean isPaired = cartUsualBoolean(cart, varName,
(trackDbSetting(tdb, "pairEndsByName") != NULL));
char position[512];
safef(position, sizeof(position), "%s:%d-%d", seqName, winStart, winEnd);
struct hash *pairHash = isPaired ? hashNew(0) : NULL;
struct bamTrackData btd = {start, item, pairHash};
char *fileName = hReplaceGbdb(trackDbSetting(tdb, "bigDataUrl"));
if (fileName == NULL)
{
if (isCustomTrack(tdb->table))
{
errAbort("bamLoadItemsCore: can't find bigDataUrl for custom track %s", tdb->track);
}
else
{
struct sqlConnection *conn = hAllocConnTrack(database, tdb);
fileName = hReplaceGbdb(bamFileNameFromTable(conn, tdb->table, seqName));
hFreeConn(&conn);
}
}
char *indexName = hReplaceGbdb(trackDbSetting(tdb, "bigDataIndex"));
char *cacheDir = cfgOption("cramRef");
char *refUrl = trackDbSetting(tdb, "refUrl");
bamAndIndexFetchPlus(fileName, indexName, position, oneBam, &btd, NULL, refUrl, cacheDir);
if (isPaired)
{
char *setting = trackDbSettingOrDefault(tdb, "pairSearchRange", "20000");
int pairSearchRange = atoi(setting);
if (pairSearchRange > 0 && hashNumEntries(pairHash) > 0)
{
// Repeat the search for item in a larger window:
struct hash *newPairHash = hashNew(0);
btd.pairHash = newPairHash;
safef(position, sizeof(position), "%s:%d-%d", seqName,
max(0, winStart-pairSearchRange), winEnd+pairSearchRange);
bamFetch(fileName, position, oneBam, &btd, NULL);
}
struct hashEl *hel;
struct hashCookie cookie = hashFirst(btd.pairHash);
while ((hel = hashNext(&cookie)) != NULL)
{
bam1_t *bam = hel->val;
const bam1_core_t *core = &bam->core;
if (! (core->flag & BAM_FMUNMAP))
printf("<B>Note: </B>unable to find paired end for %s "
"within +-%d bases of viewing window %s<BR>\n",
item, pairSearchRange, addCommasToPos(database, cartString(cart, "position")));
else
printf("<B>Paired read name:</B> %s<BR>\n", item);
singleBamDetails(bam);
}
}
}
void doExpRatio(struct trackDb *tdb, char *item, struct customTrack *ct)
/* Generic expression ratio deatils using microarrayGroups.ra file */
/* and not the expRecord tables. */
{
char *expScale = trackDbRequiredSetting(tdb, "expScale");
char *expStep = trackDbRequiredSetting(tdb, "expStep");
double maxScore = atof(expScale);
double stepSize = atof(expStep);
struct bed *bedList;
char *itemName = cgiUsualString("i2","none");
char *expName = (item == NULL) ? itemName : item;
char *tdbSetting = trackDbSettingOrDefault(tdb, "expColor", "redGreen");
char *colorVal = NULL;
enum expColorType colorScheme;
char colorVarName[256];
safef(colorVarName, sizeof(colorVarName), "%s.color", tdb->track);
colorVal = cartUsualString(cart, colorVarName, tdbSetting);
colorScheme = getExpColorType(colorVal);
if (sameWord(tdb->grp, "cancerGenomics"))
{
/* set global flag */
isCancerGenomicsTrack = TRUE;
}
if (!ct)
{
genericHeader(tdb, itemName);
bedList = loadMsBed(tdb, tdb->table, seqName, winStart, winEnd);
}
else if (ct->dbTrack)
{
genericHeader(tdb, itemName);
printCustomUrl(tdb, itemName, TRUE);
bedList = ctLoadMultScoresBedDb(ct, seqName, winStart, winEnd);
}
else
bedList = bedFilterListInRange(ct->bedList, NULL, seqName, winStart, winEnd);
if (bedList == NULL)
printf("<b>No Expression Data in this Range.</b>\n");
else if (expName && sameString(expName, "zoomInMore"))
printf("<b>Too much data to display in detail in this range.</b>\n");
else
{
struct microarrayGroups *groupings = NULL;
struct maGrouping *combineGroup;
struct hash *erHash = newHash(6);
int i;
if (!ct)
{
groupings = maGetTrackGroupings(database, tdb);
combineGroup = maCombineGroupingFromCart(groupings, cart, tdb->track);
}
else
combineGroup = maGetGroupingFromCt(ct);
maBedClumpGivenGrouping(bedList, combineGroup);
for (i = 0; i < combineGroup->numGroups; i++)
{
/* make stupid exprecord hash.perhaps eventually this won't be needed */
char id[16];
struct expRecord *er = basicExpRecord(combineGroup->names[i], i, 2);
safef(id, sizeof(id), "%d", i);
hashAdd(erHash, id, er);
}
puts("<h2></h2><p>\n");
msBedPrintTable(bedList, erHash, itemName, expName, -1*maxScore, maxScore,
stepSize, 2, msBedDefaultPrintHeader, msBedExpressionPrintRow,
printExprssnColorKey, getColorForExprBed, colorScheme);
hashTraverseEls(erHash, erHashElFree);
hashFree(&erHash);
microarrayGroupsFree(&groupings);
}
puts("<h2></h2><p>\n");
bedFreeList(&bedList);
}
