98572a57d651f8256c0d21e690f5df23fc1ce3c7
braney
Tue Jun 23 16:05:31 2026 -0700
hgTracks: show lifted (target) coordinates in quickLift bigBed mouseOvers, refs #37615
Under quickLift the bedRow used for mouseOver substitution is loaded from the
source-assembly interval, so $chrom/${chromStart}/${chromEnd} reported the
pre-lift position while the position bar showed the lifted position. Overwrite
those three coordinate fields with the lifted bed's target coordinates before
substituting, so the tooltip matches where the item is drawn. Replaces the
earlier disclaimer note that flagged the discrepancy.
diff --git src/hg/hgTracks/bigBedTrack.c src/hg/hgTracks/bigBedTrack.c
index d48d1f4519b..4431139ac4b 100644
--- src/hg/hgTracks/bigBedTrack.c
+++ src/hg/hgTracks/bigBedTrack.c
@@ -1,1157 +1,1167 @@
/* bigBed - stuff to handle loading and display of bigBed type tracks in browser.
* Mostly just links to bed code, but handles a few things itself, like the dense
* drawing code. */
/* Copyright (C) 2014 The Regents of the University of California
* See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */
#include "common.h"
#include "hash.h"
#include "linefile.h"
#include "jksql.h"
#include "hdb.h"
#include "bedCart.h"
#include "hgTracks.h"
#include "hmmstats.h"
#include "localmem.h"
#include "wigCommon.h"
#include "bbiFile.h"
#include "obscure.h"
#include "bigWig.h"
#include "bigBed.h"
#include "bigWarn.h"
#include "errCatch.h"
#include "trackHub.h"
#include "net.h"
#include "bigPsl.h"
#include "bigBedFilter.h"
#include "bigBedLabel.h"
#include "variation.h"
#include "chromAlias.h"
#include "quickLift.h"
#include "hgConfig.h"
#include "heatmap.h"
static unsigned getFieldNum(struct bbiFile *bbi, char *field)
// get field number for field name in bigBed. errAbort if field not found.
{
int fieldNum = bbFieldIndex(bbi, field);
if (fieldNum < 0)
fieldNum = defaultFieldLocation(field);
if (fieldNum < 0)
errAbort("error building filter with field %s. Field not found.", field);
return fieldNum;
}
struct bigBedFilter *bigBedMakeNumberFilter(struct cart *cart, struct bbiFile *bbi, struct trackDb *tdb, char *filter, char *defaultLimits, char *field, boolean isHighlight)
/* Make a filter/highlight on this column if the trackDb or cart wants us to. */
{
struct bigBedFilter *ret = NULL;
char *setting = trackDbSettingClosestToHome(tdb, filter);
int fieldNum = getFieldNum(bbi, field);
if (setting)
{
boolean invalid = FALSE;
double minValueTdb = 0,maxValueTdb = NO_VALUE;
double minLimit=NO_VALUE,maxLimit=NO_VALUE,min = minValueTdb,max = maxValueTdb;
colonPairToDoubles(setting,&minValueTdb,&maxValueTdb);
colonPairToDoubles(defaultLimits,&minLimit,&maxLimit);
getScoreFloatRangeFromCart(cart,tdb,FALSE,filter,&minLimit,&maxLimit,&min,&max);
if ((int)minLimit != NO_VALUE || (int)maxLimit != NO_VALUE)
{
// assume tdb default values within range!
// (don't give user errors that have no consequence)
if ((min != minValueTdb && (((int)minLimit != NO_VALUE && min < minLimit)
|| ((int)maxLimit != NO_VALUE && min > maxLimit)))
|| (max != maxValueTdb && (((int)minLimit != NO_VALUE && max < minLimit)
|| ((int)maxLimit != NO_VALUE && max > maxLimit))))
{
invalid = TRUE;
char value[64];
if ((int)max == NO_VALUE) // min only is allowed, but max only is not
safef(value, sizeof(value), "entered minimum (%g)", min);
else
safef(value, sizeof(value), "entered range (min:%g and max:%g)", min, max);
char limits[64];
if ((int)minLimit != NO_VALUE && (int)maxLimit != NO_VALUE)
safef(limits, sizeof(limits), "violates limits (%g to %g)", minLimit, maxLimit);
else if ((int)minLimit != NO_VALUE)
safef(limits, sizeof(limits), "violates lower limit (%g)", minLimit);
else //if ((int)maxLimit != NO_VALUE)
safef(limits, sizeof(limits), "violates uppper limit (%g)", maxLimit);
warn("invalid filter by %s: %s %s for track %s", field, value, limits, tdb->track);
}
}
if (invalid)
{
char filterLimitName[64];
safef(filterLimitName, sizeof(filterLimitName), "%s%s", filter, _MIN);
cartRemoveVariableClosestToHome(cart,tdb,FALSE,filterLimitName);
safef(filterLimitName, sizeof(filterLimitName), "%s%s", filter, _MAX);
cartRemoveVariableClosestToHome(cart,tdb,FALSE,filterLimitName);
}
else if (((int)min != NO_VALUE && ((int)minLimit == NO_VALUE || minLimit != min))
|| ((int)max != NO_VALUE && ((int)maxLimit == NO_VALUE || maxLimit != max)))
// Assumes min==NO_VALUE or min==minLimit is no filter
// Assumes max==NO_VALUE or max==maxLimit is no filter!
{
AllocVar(ret);
ret->fieldNum = fieldNum;
if ((int)max == NO_VALUE || ((int)maxLimit != NO_VALUE && maxLimit == max))
{
ret->comparisonType = COMPARE_MORE;
ret->value1 = min;
}
else if ((int)min == NO_VALUE || ((int)minLimit != NO_VALUE && minLimit == min))
{
ret->comparisonType = COMPARE_LESS;
ret->value1 = max;
}
else
{
ret->comparisonType = COMPARE_BETWEEN;
ret->value1 = min;
ret->value2 = max;
}
if (isHighlight)
ret->isHighlight = TRUE;
}
}
return ret;
}
struct bigBedFilter *bigBedMakeFilterText(struct cart *cart, struct bbiFile *bbi, struct trackDb *tdb, char *filterName, char *field, boolean isHighlight)
/* Add a bigBed filter using a trackDb filterText statement. */
{
struct bigBedFilter *filter;
char *setting = trackDbSettingClosestToHome(tdb, filterName);
char *value = cartUsualStringClosestToHome(cart, tdb, FALSE, filterName, setting);
if (isEmpty(value))
return NULL;
char *typeValue = getFilterType(cart, tdb, field, FILTERTEXT_WILDCARD);
AllocVar(filter);
filter->fieldNum = getFieldNum(bbi, field);
if (sameString(typeValue, FILTERTEXT_REGEXP) )
{
filter->comparisonType = COMPARE_REGEXP;
regcomp(&filter->regEx, value, REG_NOSUB);
}
else
{
filter->comparisonType = COMPARE_WILDCARD;
filter->wildCardString = cloneString(value);
}
filter->isHighlight = isHighlight;
return filter;
}
char *getHighlightType(struct cart *cart, struct trackDb *tdb, char *field, char *def)
{
char settingString[4096];
safef(settingString, sizeof settingString, "%s.%s", HIGHLIGHT_TYPE_NAME_LOW, field);
char *setting = cartOrTdbString(cart, tdb, settingString, NULL);
if (setting == NULL)
{
safef(settingString, sizeof settingString, "%s.%s", field, HIGHLIGHT_TYPE_NAME_CAP);
setting = cartOrTdbString(cart, tdb, settingString, NULL);
}
if (setting == NULL)
{
safef(settingString, sizeof settingString, "%s%s", field, HIGHLIGHT_TYPE_NAME_CAP);
setting = cartOrTdbString(cart, tdb, settingString, def);
}
return setting;
}
struct bigBedFilter *bigBedMakeFilterBy(struct cart *cart, struct bbiFile *bbi, struct trackDb *tdb, char *field, struct slName *choices, boolean isHighlight)
/* Add a bigBed filter using a trackDb filterBy statement. */
{
struct bigBedFilter *filter;
char *setting = NULL;
if (isHighlight)
setting = getHighlightType(cart, tdb, field, HIGHLIGHTBY_DEFAULT);
else
setting = getFilterType(cart, tdb, field, FILTERBY_DEFAULT);
AllocVar(filter);
filter->fieldNum = getFieldNum(bbi, field);
filter->comparisonType = COMPARE_HASH;
if (setting)
{
if (sameString(setting, FILTERBY_SINGLE_LIST)
|| sameString(setting, FILTERBY_MULTIPLE_LIST_OR)
|| sameString(setting, FILTERBY_MULTIPLE_LIST_ONLY_OR)
|| sameString(setting, HIGHLIGHTBY_SINGLE_LIST)
|| sameString(setting, HIGHLIGHTBY_MULTIPLE_LIST_OR)
|| sameString(setting, HIGHLIGHTBY_MULTIPLE_LIST_ONLY_OR))
filter->comparisonType = COMPARE_HASH_LIST_OR;
else if (sameString(setting, FILTERBY_MULTIPLE_LIST_AND)
|| sameString(setting, FILTERBY_MULTIPLE_LIST_ONLY_AND)
|| sameString(setting, HIGHLIGHTBY_MULTIPLE_LIST_AND)
|| sameString(setting, HIGHLIGHTBY_MULTIPLE_LIST_ONLY_AND))
filter->comparisonType = COMPARE_HASH_LIST_AND;
}
filter->valueHash = newHash(5);
filter->numValuesInHash = slCount(choices);
for(; choices; choices = choices->next)
hashStore(filter->valueHash, choices->name);
filter->isHighlight = isHighlight;
return filter;
}
static void addGencodeFilters(struct cart *cart, struct trackDb *tdb, struct bigBedFilter **pFilters)
/* Add GENCODE custom bigBed filters. */
{
struct bigBedFilter *filter;
char varName[64];
struct hash *hash;
/* canonical */
safef(varName, sizeof(varName), "%s.show.spliceVariants", tdb->track);
boolean option = cartUsualBoolean(cart, varName, TRUE);
if (!option)
{
AllocVar(filter);
slAddHead(pFilters, filter);
filter->fieldNum = 25;
filter->comparisonType = COMPARE_HASH_LIST_OR;
hash = newHash(5);
filter->valueHash = hash;
filter->numValuesInHash = 1;
hashStore(hash, "canonical" );
}
/* transcript class */
AllocVar(filter);
slAddHead(pFilters, filter);
filter->fieldNum = 20;
filter->comparisonType = COMPARE_HASH;
hash = newHash(5);
filter->valueHash = hash;
filter->numValuesInHash = 1;
hashStore(hash,"coding"); // coding is always included
safef(varName, sizeof(varName), "%s.show.noncoding", tdb->track);
if (cartUsualBoolean(cart, varName, TRUE))
{
filter->numValuesInHash++;
hashStore(hash,"nonCoding");
}
safef(varName, sizeof(varName), "%s.show.pseudo", tdb->track);
if (cartUsualBoolean(cart, varName, FALSE))
{
filter->numValuesInHash++;
hashStore(hash,"pseudo");
}
/* tagged sets */
safef(varName, sizeof(varName), "%s.show.set", tdb->track);
char *setString = cartUsualString(cart, varName, "basic");
if (differentString(setString, "all"))
{
AllocVar(filter);
slAddHead(pFilters, filter);
filter->fieldNum = 23;
filter->comparisonType = COMPARE_HASH_LIST_OR;
hash = newHash(5);
filter->valueHash = hash;
filter->numValuesInHash = 1;
hashStore(hash, setString);
}
}
struct bigBedFilter *bigBedBuildFilters(struct cart *cart, struct bbiFile *bbi, struct trackDb *tdb)
/* Build all the numeric and filterBy filters for a bigBed */
{
struct bigBedFilter *filters = NULL, *filter;
struct trackDbFilter *tdbFilters = tdbGetTrackNumFilters(tdb);
if ((tdbFilters == NULL) && !trackDbSettingOn(tdb, "noScoreFilter") && (bbi->definedFieldCount >= 5))
{
AllocVar(filter);
slAddHead(&filters, filter);
filter->fieldNum = 4;
filter->comparisonType = COMPARE_MORE;
char buffer[2048];
safef(buffer, sizeof buffer, "%s.scoreFilter", tdb->track);
filter->value1 = cartUsualDouble(cart, buffer, 0.0);
}
for(; tdbFilters; tdbFilters = tdbFilters->next)
{
if ((filter = bigBedMakeNumberFilter(cart, bbi, tdb, tdbFilters->name, NULL, tdbFilters->fieldName, FALSE)) != NULL)
slAddHead(&filters, filter);
}
tdbFilters = tdbGetTrackTextFilters(tdb);
for(; tdbFilters; tdbFilters = tdbFilters->next)
{
if ((filter = bigBedMakeFilterText(cart, bbi, tdb, tdbFilters->name, tdbFilters->fieldName, FALSE)) != NULL)
slAddHead(&filters, filter);
}
filterBy_t *filterBySet = filterBySetGet(tdb, cart,NULL);
filterBy_t *filterBy = filterBySet;
for (;filterBy != NULL; filterBy = filterBy->next)
{
if (filterBy->slChoices && differentString(filterBy->slChoices->name, "All"))
{
if ((filter = bigBedMakeFilterBy(cart, bbi, tdb, filterBy->column, filterBy->slChoices, FALSE)) != NULL)
slAddHead(&filters, filter);
}
}
/* custom gencode filters */
boolean isGencode3 = trackDbSettingOn(tdb, "isGencode3");
if (isGencode3)
addGencodeFilters(cart, tdb, &filters);
return filters;
}
struct bigBedFilter *bigBedBuildHighlights(struct cart *cart, struct bbiFile *bbi, struct trackDb *tdb)
/* Build all the numeric and highlights for a bigBed */
{
struct bigBedFilter *highlights = NULL, *highlight;
struct trackDbFilter *tdbHighlights = tdbGetTrackNumHighlights(tdb);
for(; tdbHighlights; tdbHighlights = tdbHighlights->next)
{
if ((highlight = bigBedMakeNumberFilter(cart, bbi, tdb, tdbHighlights->name, NULL, tdbHighlights->fieldName, TRUE)) != NULL)
slAddHead(&highlights, highlight);
}
tdbHighlights = tdbGetTrackTextHighlights(tdb);
for(; tdbHighlights; tdbHighlights = tdbHighlights->next)
{
if ((highlight = bigBedMakeFilterText(cart, bbi, tdb, tdbHighlights->name, tdbHighlights->fieldName, TRUE)) != NULL)
slAddHead(&highlights, highlight);
}
filterBy_t *filterBySet = highlightBySetGet(tdb, cart,NULL);
filterBy_t *filterBy = filterBySet;
for (;filterBy != NULL; filterBy = filterBy->next)
{
if (filterBy->slChoices && differentString(filterBy->slChoices->name, "All"))
{
if ((highlight = bigBedMakeFilterBy(cart, bbi, tdb, filterBy->column, filterBy->slChoices, TRUE)) != NULL)
slAddHead(&highlights, highlight);
}
}
return highlights;
}
boolean bigBedFilterOne(struct bigBedFilter *filter, char **bedRow, struct bbiFile *bbi)
/* Return TRUE if a bedRow passes one filter or is in hgFindMatches */
{
if ((bbi->definedFieldCount > 3) && (hgFindMatches != NULL) &&
(bedRow[3] != NULL) && hashLookup(hgFindMatches, bedRow[3]) != NULL)
return TRUE;
double val = atof(bedRow[filter->fieldNum]);
switch(filter->comparisonType)
{
case COMPARE_WILDCARD:
if ( !wildMatch(filter->wildCardString, bedRow[filter->fieldNum]))
return FALSE;
break;
case COMPARE_REGEXP:
if (regexec(&filter->regEx,bedRow[filter->fieldNum], 0, NULL,0 ) != 0)
return FALSE;
break;
case COMPARE_HASH_LIST_AND:
case COMPARE_HASH_LIST_OR:
{
struct slName *values = commaSepToSlNames(bedRow[filter->fieldNum]);
unsigned found = 0;
struct hash *seenHash = newHash(3);
for(; values; values = values->next)
{
if (hashLookup(seenHash, values->name))
continue;
hashStore(seenHash, values->name);
if (hashLookup(filter->valueHash, values->name))
{
found++;
if (filter->comparisonType == COMPARE_HASH_LIST_OR)
break;
}
}
if (filter->comparisonType == COMPARE_HASH_LIST_AND)
{
if (found < filter->numValuesInHash)
return FALSE;
}
else if (!found)
return FALSE;
}
break;
case COMPARE_HASH:
if (!hashLookup(filter->valueHash, bedRow[filter->fieldNum]))
return FALSE;
break;
case COMPARE_LESS:
if (!(val <= filter->value1))
return FALSE;
break;
case COMPARE_MORE:
if (!(val >= filter->value1))
return FALSE;
break;
case COMPARE_BETWEEN:
if (!((val >= filter->value1) && (val <= filter->value2)))
return FALSE;
break;
}
return TRUE;
}
boolean bigBedFilterInterval(struct bbiFile *bbi, char **bedRow, struct bigBedFilter *filters)
/* Go through a row and filter based on filters. Return TRUE if all filters are passed. */
{
if ((bbi->definedFieldCount > 3) && (hgFindMatches != NULL) &&
(bedRow[3] != NULL) && hashLookup(hgFindMatches, bedRow[3]) != NULL)
return TRUE;
struct bigBedFilter *filter;
for(filter = filters; filter; filter = filter->next)
if (!bigBedFilterOne(filter, bedRow, bbi))
return FALSE;
return TRUE;
}
struct bbiFile *fetchBbiForTrack(struct track *track)
/* Fetch bbiFile from track, opening it if it is not already open. */
{
struct bbiFile *bbi = track->bbiFile;
if (bbi == NULL)
{
char *fileName = NULL;
if (track->parallelLoading) // do not use mysql during parallel fetch
{
fileName = hReplaceGbdb(trackDbSetting(track->tdb, "bigDataUrl"));
if (fileName == NULL)
fileName = hReplaceGbdb(trackDbSetting(track->tdb, "bigGeneDataUrl"));
}
else
{
struct sqlConnection *conn = NULL;
if (!trackHubDatabase(database))
conn = hAllocConnTrack(database, track->tdb);
fileName = bbiNameFromSettingOrTable(track->tdb, conn, track->table);
hFreeConn(&conn);
}
#ifdef USE_GBIB_PWD
#include "gbib.c"
#endif
bbi = track->bbiFile = bigBedFileOpenAlias(fileName, chromAliasFindAliases);
}
return bbi;
}
static unsigned bigBedMaxItems()
/* Get the maximum number of items to grab from a bigBed file. Defaults to ten thousand . */
{
static boolean set = FALSE;
static unsigned maxItems = 0;
if (!set)
{
char *maxItemsStr = cfgOptionDefault("bigBedMaxItems", "10000");
maxItems = sqlUnsigned(maxItemsStr);
set = TRUE;
}
return maxItems;
}
static boolean hasOverflowedInWindow(struct track *track)
/* has it overlowed in the given track? */
{
uint resultCount = 0; // do not use -1, it messes up the compare of signed resultsCount with unsigned bigMaxItems.
char *resultCountString = trackDbSetting(track->tdb, "bigBedItemsCount");
if (resultCountString)
resultCount = sqlUnsigned(resultCountString);
return (resultCount > bigBedMaxItems());
}
static void loadBigBedSummary(struct track *track)
/* Check if summary loading needed for bigBed */
{
if (track->subtracks) // do tracks or subtracks but not parents.
{
return;
}
struct lm *lm = lmInit(0);
char *chrom = chromName;
int start = winStart;
int end = winEnd;
/* protect against temporary network error */
struct errCatch *errCatch = errCatchNew();
boolean filtering = FALSE; // for the moment assume we're not filtering
if (errCatchStart(errCatch))
{
// scan all windows for errors and overflows
boolean errorsInWindows = FALSE;
boolean overFlowedInWindows = FALSE;
struct track *thisTrack;
for(thisTrack=track->prevWindow; thisTrack; thisTrack=thisTrack->prevWindow)
{
if (hasOverflowedInWindow(thisTrack))
overFlowedInWindows = TRUE;
if (thisTrack->drawItems == bigDrawWarning)
errorsInWindows = TRUE;
}
for(thisTrack=track->nextWindow; thisTrack; thisTrack=thisTrack->nextWindow)
{
if (hasOverflowedInWindow(thisTrack))
overFlowedInWindows = TRUE;
if (thisTrack->drawItems == bigDrawWarning)
errorsInWindows = TRUE;
}
if (hasOverflowedInWindow(track))
overFlowedInWindows = TRUE;
if (!errorsInWindows && overFlowedInWindows)
{
if (filtering)
errAbort("Too many items in window to filter.Zoom in or remove filters to view track.");
else
{
struct bbiFile *bbi = fetchBbiForTrack(track);
if (bbi)
{
// use summary levels
if (track->visibility != tvDense)
{
track->limitedVis = tvFull;
track->limitWiggle = TRUE;
track->limitedVisSet = TRUE;
}
else
{
track->limitedVis = tvDense;
track->limitedVisSet = TRUE;
}
AllocArray(track->summary, insideWidth);
if (bigBedSummaryArrayExtended(bbi, chrom, start, end, insideWidth, track->summary))
{
char *denseCoverage = trackDbSettingClosestToHome(track->tdb, "denseCoverage");
if (denseCoverage != NULL)
{
double endVal = atof(denseCoverage);
if (endVal <= 0)
{
AllocVar(track->sumAll);
*track->sumAll = bbiTotalSummary(bbi);
}
}
}
else
freez(&track->summary);
}
}
}
}
errCatchEnd(errCatch);
if (errCatch->gotError)
{
track->networkErrMsg = cloneString(errCatch->message->string);
track->drawItems = bigDrawWarning;
track->totalHeight = bigWarnTotalHeight;
}
errCatchFree(&errCatch);
lmCleanup(&lm);
track->bbiFile = NULL;
}
struct bigBedInterval *bigBedSelectRangeExt(struct track *track,
char *chrom, int start, int end, struct lm *lm, int maxItems)
/* Return list of intervals in range. */
{
struct bigBedInterval *result = NULL;
/* protect against temporary network error */
struct errCatch *errCatch = errCatchNew();
if (errCatchStart(errCatch))
{
struct bbiFile *bbi = fetchBbiForTrack(track);
result = bigBedIntervalQuery(bbi, chrom, start, end, bigBedMaxItems() + 1, lm); // pass in desired limit or 0 for all.
char resultCount[32];
safef(resultCount, sizeof resultCount, "%u", slCount(result));
trackDbAddSetting(track->tdb, "bigBedItemsCount", resultCount);
if (slCount(result) > bigBedMaxItems())
{
result = NULL; // IS Having it return NULL a critical part of this?
}
track->bbiFile = NULL;
}
errCatchEnd(errCatch);
if (errCatch->gotError)
{
track->networkErrMsg = cloneString(errCatch->message->string);
track->drawItems = bigDrawWarning;
track->totalHeight = bigWarnTotalHeight;
result = NULL;
}
errCatchFree(&errCatch);
return result;
}
char* restField(struct bigBedInterval *bb, int fieldIdx)
/* return a given field from the bb->rest field, NULL on error */
{
if (fieldIdx==0) // we don't return the first(=name) field of bigBed
return NULL;
char *rest = cloneString(bb->rest);
char *restFields[1024];
int restCount = chopTabs(rest, restFields);
char *field = NULL;
if (fieldIdx < restCount)
field = cloneString(restFields[fieldIdx]);
freeMem(rest);
return field;
}
void addHighlightToLinkedFeature(struct linkedFeatures *lf, struct bigBedFilter *highlights, struct bbiFile *bbi, char **bedRow, struct trackDb *tdb)
/* Fill out the lf->highlightColor if the cart says to highlight this item. The color will
* be the 'average' of all the highlight colors specified */
{
struct bigBedFilter *highlight;
char *cartHighlightColor = cartOrTdbString(cart, tdb, HIGHLIGHT_COLOR_CART_VAR, HIGHLIGHT_COLOR_DEFAULT);
for (highlight = highlights; highlight != NULL; highlight = highlight->next)
{
if (bigBedFilterOne(highlight, bedRow, bbi))
{
unsigned rgb = bedParseColor(cartHighlightColor);
Color color = bedColorToGfxColor(rgb);
lf->highlightColor = color;
lf->highlightMode = highlightBackground;
}
}
}
+static void quickLiftSetCoordFields(char **bedRow, struct bed *liftedBed,
+ char *startBuf, char *endBuf, int bufSize)
+/* Overwrite the chrom/chromStart/chromEnd entries (the first three bigBed fields) of bedRow
+ * with the lifted, target-assembly coordinates from liftedBed. Under quickLift bedRow is
+ * loaded from the source-assembly interval, so without this a $chrom/${chromStart}/${chromEnd}
+ * mouseOver substitution would report the pre-lift position instead of where the item is drawn. */
+{
+safef(startBuf, bufSize, "%u", liftedBed->chromStart);
+safef(endBuf, bufSize, "%u", liftedBed->chromEnd);
+bedRow[0] = liftedBed->chrom;
+bedRow[1] = startBuf;
+bedRow[2] = endBuf;
+}
+
void bigBedAddLinkedFeaturesFromExt(struct track *track,
char *chrom, int start, int end, int scoreMin, int scoreMax, boolean useItemRgb,
int fieldCount, struct linkedFeatures **pLfList, int maxItems)
/* Read in items in chrom:start-end from bigBed file named in track->bbiFileName, convert
* them to linkedFeatures, and add to head of list. */
{
struct lm *lm = lmInit(0);
struct trackDb *tdb = track->tdb;
char *mouseOverField = cartOrTdbString(cart, track->tdb, "mouseOverField", NULL);
// check if this track can merge large items, this setting must be allowed in the trackDb
// stanza for the track, but can be enabled/disabled via trackUi/right click menu so
// we also need to check the cart for the current status
int mergeCount = 0;
boolean doWindowSizeFilter = trackDbSettingOn(track->tdb, MERGESPAN_TDB_SETTING);
if (doWindowSizeFilter)
{
char hasMergedItemsSetting[256];
safef(hasMergedItemsSetting, sizeof(hasMergedItemsSetting), "%s.%s", track->track, MERGESPAN_CART_SETTING);
if (cartVarExists(cart, hasMergedItemsSetting))
doWindowSizeFilter = cartInt(cart, hasMergedItemsSetting) == 1;
else // save the cart var so javascript can offer the right toggle
cartSetInt(cart, hasMergedItemsSetting, 1);
}
/* protect against temporary network error */
struct bbiFile *bbi = NULL;
struct errCatch *errCatch = errCatchNew();
if (errCatchStart(errCatch))
{
bbi = fetchBbiForTrack(track);
}
errCatchEnd(errCatch);
if (errCatch->gotError)
{
track->networkErrMsg = cloneString(errCatch->message->string);
track->drawItems = bigDrawWarning;
track->totalHeight = bigWarnTotalHeight;
return;
}
errCatchFree(&errCatch);
fieldCount = track->bedSize;
boolean bigBedOnePath = cfgOptionBooleanDefault("bigBedOnePath", TRUE);
if (bigBedOnePath && (fieldCount == 0))
track->bedSize = fieldCount = bbi->definedFieldCount;
struct bigBedInterval *bb, *bbList;
char *quickLiftFile = cloneString(trackDbSetting(track->tdb, "quickLiftUrl"));
struct hash *chainHash = NULL;
if (quickLiftFile)
bbList = quickLiftGetIntervals(quickLiftFile, bbi, chromName, winStart, winEnd, &chainHash);
else
bbList = bigBedSelectRangeExt(track, chrom, start, end, lm, maxItems);
char *squishField = cartOrTdbString(cart, track->tdb, "squishyPackField", NULL);
int squishFieldIdx = bbExtraFieldIndex(bbi, squishField);
/* colorFields: optional alternative color scheme stored in a named extra field. */
int colorFieldIdx = 0;
char *colorFieldsSetting = trackDbSettingClosestToHome(tdb, "colorFields");
if (useItemRgb && colorFieldsSetting)
{
char *colorFieldName = cartOptionalStringClosestToHome(cart, tdb, FALSE, "colorField");
if (!isEmpty(colorFieldName))
{
colorFieldIdx = bbExtraFieldIndex(bbi, colorFieldName);
/* Append "(Coloring by: <label>)" to the track's longLabel.
* Look up the human-readable label from the colorFields key=value list. */
char *label = colorFieldName;
struct slPair *pairs = slPairListFromString(colorFieldsSetting, TRUE);
if (pairs)
{
struct slPair *p = slPairFind(pairs, colorFieldName);
if (p && isNotEmpty((char *)p->val))
label = (char *)p->val;
}
char suffix[256];
safef(suffix, sizeof suffix, " (Coloring by: %s)", label);
track->longLabel = catTwoStrings(track->longLabel, suffix);
}
}
int seqTypeField = 0;
if (sameString(track->tdb->type, "bigPsl"))
{
seqTypeField = bbExtraFieldIndex(bbi, "seqType");
}
int mouseOverIdx = bbExtraFieldIndex(bbi, mouseOverField);
track->bbiFile = NULL;
struct bigBedFilter *filters = bigBedBuildFilters(cart, bbi, track->tdb) ;
struct bigBedFilter *highlights = bigBedBuildHighlights(cart, bbi, track->tdb) ;
if (compositeChildHideEmptySubtracks(cart, track->tdb, NULL, NULL))
labelTrackAsHideEmpty(track);
// mouseOvers can be built constructed via trackDb settings instead
// of embedded directly in bigBed
char *mouseOverPattern = NULL;
char **fieldNames = NULL;
if (!mouseOverIdx)
{
mouseOverPattern = cartOrTdbString(cart, track->tdb, "mouseOver", NULL);
if (mouseOverPattern)
{
AllocArray(fieldNames, bbi->fieldCount);
struct slName *field = NULL, *fields = bbFieldNames(bbi);
int i = 0;
for (field = fields; field != NULL; field = field->next)
fieldNames[i++] = field->name;
-
- // Under quickLift, $chrom/${chromStart}/${chromEnd} substitutions resolve
- // against the source assembly's row, so the tooltip will disagree with
- // the position bar. Append a note so the discrepancy isn't surprising.
- if (quickLiftFile && strstr(mouseOverPattern, "$chrom"))
- {
- char *sourceDb = trackDbSetting(track->tdb, "quickLiftDb");
- struct dyString *dy = dyStringNew(0);
- dyStringAppend(dy, mouseOverPattern);
- if (sourceDb)
- dyStringPrintf(dy, "<br><i>(coordinates from source assembly %s)</i>", sourceDb);
- else
- dyStringAppend(dy, "<br><i>(coordinates from source assembly)</i>");
- mouseOverPattern = dyStringCannibalize(&dy);
- }
}
}
// a fake item that is the union of the items that span the current window
struct linkedFeatures *spannedLf = NULL;
unsigned filtered = 0;
struct bed *bed = NULL, *bedCopy = NULL;
for (bb = bbList; bb != NULL; bb = bb->next)
{
struct linkedFeatures *lf = NULL;
+ bedCopy = NULL;
char *bedRow[bbi->fieldCount];
if (sameString(track->tdb->type, "bigPsl"))
{
// fill out bedRow to support mouseOver pattern replacements
char startBuf[16], endBuf[16];
bigBedIntervalToRow(bb, chromName, startBuf, endBuf, bedRow, ArraySize(bedRow));
char *seq, *cds;
struct psl *psl = pslFromBigPsl(chromName, bb, seqTypeField, &seq, &cds);
int sizeMul = pslIsProtein(psl) ? 3 : 1;
boolean isXeno = 0; // just affects grayIx
boolean nameGetsPos = FALSE; // we want the name to stay the name
if (sizeMul == 3)
{
// these tags are not currently supported by the drawing engine for protein psl
hashRemove(track->tdb->settingsHash, "showDiffBasesAllScales");
hashRemove(track->tdb->settingsHash, "baseColorUseSequence");
hashRemove(track->tdb->settingsHash, "baseColorDefault");
}
lf = lfFromPslx(psl, sizeMul, isXeno, nameGetsPos, track);
lf->original = psl;
if ((seq != NULL) && (lf->orientation == -1))
reverseComplement(seq, strlen(seq));
lf->extra = seq;
lf->cds = cds;
lf->useItemRgb = useItemRgb;
if ( lf->useItemRgb )
lf->filterColor = itemRgbColumn(bedRow[8]);
}
else if (sameString(tdb->type, "bigDbSnp"))
{
// bigDbSnp does not have a score field, but I want to compute the freqSourceIx from
// trackDb and settings one time instead of for each item, so I'm overloading scoreMin.
int freqSourceIx = scoreMin;
lf = lfFromBigDbSnp(tdb, bb, filters, freqSourceIx, bbi, chainHash);
}
else
{
char startBuf[16], endBuf[16];
bigBedIntervalToRow(bb, chromName, startBuf, endBuf, bedRow, ArraySize(bedRow));
if (bigBedFilterInterval(bbi, bedRow, filters))
{
if (quickLiftFile)
{
if ((bed = quickLiftIntervalsToBed(bbi, chainHash, bb)) != NULL)
{
bedCopy = cloneBed(bed);
lf = bedMungToLinkedFeatures(&bed, tdb, fieldCount,
scoreMin, scoreMax, useItemRgb);
}
}
else
{
bed = bedLoadN(bedRow, fieldCount == 7 ? 6 : fieldCount);
bedCopy = cloneBed(bed);
lf = bedMungToLinkedFeatures(&bed, tdb, fieldCount,
scoreMin, scoreMax, useItemRgb);
}
}
if (lf && highlights)
addHighlightToLinkedFeature(lf, highlights, bbi, bedRow, track->tdb);
if (lf && squishFieldIdx)
lf->squishyPackVal = atof(restField(bb, squishFieldIdx));
if (lf && colorFieldIdx)
lf->filterColor = itemRgbColumn(restField(bb, colorFieldIdx));
if (track->visibility != tvDense && lf && doWindowSizeFilter
&& (quickLiftFile ? lf->start : bb->start) < winStart
&& (quickLiftFile ? lf->end : bb->end) > winEnd)
{
mergeCount++;
struct linkedFeatures *tmp;
if (quickLiftFile)
{
struct bed *mergeBed = cloneBed(bedCopy);
tmp = bedMungToLinkedFeatures(&mergeBed, tdb, fieldCount,
scoreMin, scoreMax, useItemRgb);
}
else
{
struct bed *bed = bedLoadN(bedRow, fieldCount);
tmp = bedMungToLinkedFeatures(&bed, tdb, fieldCount,
scoreMin, scoreMax, useItemRgb);
}
if (spannedLf)
{
if (tmp->start < spannedLf->start)
spannedLf->start = tmp->start;
if (tmp->end > spannedLf->end)
spannedLf->end = tmp->end;
if (fieldCount > 9) // average the colors in the merged item
{
// Not sure how averaging alphas in the merged item would work; probably better
// to ignore it.
struct rgbColor itemColor = colorIxToRgb(lf->filterColor);
struct rgbColor currColor = colorIxToRgb(spannedLf->filterColor);
int r = currColor.r + round((itemColor.r - currColor.r) / mergeCount);
int g = currColor.g + round((itemColor.g - currColor.g) / mergeCount);
int b = currColor.b + round((itemColor.b - currColor.b) / mergeCount);
spannedLf->filterColor = MAKECOLOR_32(r,g,b);
}
}
else
{
// setting the label here protects against the case when only one item would
// have been merged. When this happens we warn in the track longLabel that
// nothing happened and essentially make the spanned item be what the actual
// item would be. If multiple items are merged then the labels and mouseOvers
// will get fixed up later
tmp->label = bigBedMakeLabel(track->tdb, track->labelColumns, bb, chromName);
if (mouseOverIdx > 0)
tmp->mouseOver = restField(bb, mouseOverIdx);
else if (mouseOverPattern)
+ {
+ char qStartBuf[16], qEndBuf[16];
+ if (quickLiftFile && bedCopy)
+ quickLiftSetCoordFields(bedRow, bedCopy, qStartBuf, qEndBuf, sizeof qStartBuf);
tmp->mouseOver = replaceFieldInPattern(mouseOverPattern, bbi->fieldCount, fieldNames, bedRow);
+ }
slAddHead(&spannedLf, tmp);
}
continue; // lf will be NULL, but these items aren't "filtered", they're merged
}
}
if (lf == NULL)
{
filtered++;
continue;
}
if (lf->label == NULL)
lf->label = bigBedMakeLabel(track->tdb, track->labelColumns, bb, chromName);
if (startsWith("bigGenePred", track->tdb->type) || startsWith("genePred", track->tdb->type))
{
// bedRow[5] has original strand in it, bedCopy has new strand. If they're different we want to reverse exonFrames
boolean changedStrand = FALSE;
if (quickLiftFile)
{
if (*bedRow[5] != *bedCopy->strand)
changedStrand = TRUE;
}
lf->original = genePredFromBedBigGenePred(chromName, bedCopy, bb, changedStrand);
}
if (startsWith("bigBed", track->tdb->type))
{
// Clone bb so that we'll have access the to extra fields contents. This is used in
// alternate display modes for bigBeds (so far just "heatmap", but more are likely to come).
struct bigBedInterval *bbCopy = CloneVar(bb);
if (bbCopy->rest)
bbCopy->rest = cloneMem(bbCopy->rest, strlen(bbCopy->rest)+1);
bbCopy->next = NULL;
lf->original = bbCopy;
}
if (lf->mouseOver == NULL)
{
if (mouseOverIdx > 0)
lf->mouseOver = restField(bb, mouseOverIdx);
else if (mouseOverPattern)
+ {
+ char qStartBuf[16], qEndBuf[16];
+ if (quickLiftFile && bedCopy)
+ quickLiftSetCoordFields(bedRow, bedCopy, qStartBuf, qEndBuf, sizeof qStartBuf);
lf->mouseOver = replaceFieldInPattern(mouseOverPattern, bbi->fieldCount, fieldNames, bedRow);
}
+ }
slAddHead(pLfList, lf);
}
if (filtered)
labelTrackAsFilteredNumber(track, filtered);
if (doWindowSizeFilter)
// add the number of merged items to the track longLabel
{
char labelBuf[256];
if (mergeCount > 1)
safef(labelBuf, sizeof(labelBuf), " (Merged %d items)", mergeCount);
else
safef(labelBuf, sizeof(labelBuf), " (No Items Merged in window)");
track->longLabel = catTwoStrings(track->longLabel, labelBuf);
}
if (spannedLf)
{
// if two or more items were merged together, fix up the label of the special merged item,
// otherwise the label and mouseOver will be the normal bed one
char itemLabelBuf[256], mouseOver[256];
if (mergeCount > 1)
{
safef(itemLabelBuf, sizeof(itemLabelBuf), "Merged %d items", mergeCount);
safef(mouseOver, sizeof(mouseOver), "Merged %d items. Click to expand or right-click and select 'show merged items'", mergeCount);
spannedLf->label = cloneString(itemLabelBuf);
spannedLf->name = "mergedItem"; // always, for correct hgc clicks
spannedLf->mouseOver = cloneString(mouseOver);
}
slAddHead(pLfList, spannedLf);
}
lmCleanup(&lm);
if (!trackDbSettingClosestToHomeOn(track->tdb, "linkIdInName"))
track->itemName = bigLfItemName;
bbiFileClose(&bbi);
}
boolean canDrawBigBedDense(struct track *tg)
/* Return TRUE if conditions are such that can do the fast bigBed dense data fetch and
* draw. */
{
return tg->isBigBed;
}
void bigBedDrawDense(struct track *tg, int seqStart, int seqEnd,
struct hvGfx *hvg, int xOff, int yOff, int width,
MgFont *font, Color color)
/* Use big-bed summary data to quickly draw bigBed. */
{
struct bbiSummaryElement *summary = tg->summary;
if (summary)
{
char *denseCoverage = trackDbSettingClosestToHome(tg->tdb, "denseCoverage");
if (denseCoverage != NULL)
{
double startVal = 0, endVal = atof(denseCoverage);
if (endVal <= 0)
{
struct bbiSummaryElement sumAll = *tg->sumAll;
double mean = sumAll.sumData/sumAll.validCount;
double std = calcStdFromSums(sumAll.sumData, sumAll.sumSquares, sumAll.validCount);
rangeFromMinMaxMeanStd(0, sumAll.maxVal, mean, std, &startVal, &endVal);
}
int x;
for (x=0; x<width; ++x)
{
if (summary[x].validCount > 0)
{
Color color = shadesOfGray[grayInRange(summary[x].maxVal, startVal, endVal)];
hvGfxBox(hvg, x+xOff, yOff, 1, tg->heightPer, color);
}
}
}
else
{
int x;
for (x=0; x<width; ++x)
{
if (summary[x].validCount > 0)
{
hvGfxBox(hvg, x+xOff, yOff, 1, tg->heightPer, color);
}
}
}
}
maybeDrawQuickLiftLines(tg, seqStart, seqEnd, hvg, xOff, yOff, width, font, color, tvDense);
freez(&tg->summary);
}
char *bigBedItemName(struct track *tg, void *item)
// return label for simple beds
{
struct bed *bed = (struct bed *)item;
return bed->label;
}
char *bigLfItemName(struct track *tg, void *item)
// return label for linked features
{
struct linkedFeatures *lf = (struct linkedFeatures *)item;
return lf->label;
}
#ifdef NOTNOW
static int getFieldCount(struct track *track)
// return the definedFieldCount of the passed track with is assumed to be a bigBed
{
struct bbiFile *bbi = NULL;
struct errCatch *errCatch = errCatchNew();
if (errCatchStart(errCatch))
{
bbi = fetchBbiForTrack(track);
}
errCatchEnd(errCatch);
if (bbi)
return bbi->definedFieldCount;
return 3; // if we can't get the bbi, use the minimum
}
#endif
void commonBigBedMethods(struct track *track, struct trackDb *tdb,
int wordCount, char *words[])
/* Set up common bigBed methods used by several track types that depend on the bigBed format. */
{
boolean bigBedOnePath = cfgOptionBooleanDefault("bigBedOnePath", TRUE);
if (bigBedOnePath)
{
track->isBigBed = TRUE;
linkedFeaturesMethods(track);
track->extraUiData = newBedUiData(track->track);
track->loadItems = loadGappedBed;
if (wordCount > 1)
track->bedSize = atoi(words[1]);
if (trackDbSetting(tdb, "colorByStrand"))
{
Color lfItemColorByStrand(struct track *tg, void *item, struct hvGfx *hvg);
track->itemColor = lfItemColorByStrand;
}
}
else
{
char *newWords[wordCount];
int ii;
for(ii=0; ii < wordCount; ii++)
newWords[ii] = words[ii];
#ifdef NOTNOW
// let's help the user out and get the definedFieldCount if they didn't specify it on the type line
if (!tdbIsSuper(track->tdb) && (track->tdb->subtracks == NULL) && (wordCount == 1) && sameString(words[0], "bigBed"))
{
int fieldCount = getFieldCount(track);
if (fieldCount > 3)
{
char buffer[1024];
safef(buffer, sizeof buffer, "%d", fieldCount);
newWords[1] = cloneString(buffer);
wordCount = 2;
}
}
#endif
complexBedMethods(track, tdb, TRUE, wordCount, newWords);
}
track->loadSummary = loadBigBedSummary;
}
void bigBedMethods(struct track *track, struct trackDb *tdb,
int wordCount, char *words[])
/* Set up bigBed methods for tracks that are type bigBed. */
{
commonBigBedMethods(track, tdb, wordCount, words);
if (sameWordOk(trackDbSetting(tdb, "style"), "heatmap"))
{
// Might want to check here if required heatmap settings/fields are in place,
// maybe some combo of row count and labels.
heatmapMethods(track);
}
}