80daf93864f5609f6b7695766a78edd90cac0c1d
braney
  Fri Jul 31 12:29:05 2026 -0700
quickLift: accept broadPeak tracks, and make lifted peak details right. refs #37970

Add broadPeak to the types validateOneTdb will lift; hgTracks already knew
how to load one.  Make hgc's encodePeak handler read the table out of the
source assembly and lift the items, instead of looking in the destination
assembly where the table does not exist and coming up empty.  Lift peaks with
a new quickLiftPeaks() rather than casting them to bed and calling
quickLiftBeds(), whose thickStart and thickEnd assignments land on
signalValue and pValue in struct encodePeak.

diff --git src/hg/hgTracks/encode.c src/hg/hgTracks/encode.c
index 74b869304d9..a35c45573f4 100644
--- src/hg/hgTracks/encode.c
+++ src/hg/hgTracks/encode.c
@@ -1,410 +1,410 @@
 /* encode.c - hgTracks routines that are specific to the ENCODE project */
 
 /* Copyright (C) 2012 The Regents of the University of California 
  * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */
 
 #include "common.h"
 #include "hCommon.h"
 #include "hdb.h"
 #include "hui.h"
 #include "hgTracks.h"
 #include "customTrack.h"
 #include "encode.h"
 #include "encode/encodeRna.h"
 #include "encode/encodePeak.h"
 #include "bigBedFilter.h"
 #include "quickLift.h"
 
 extern struct trackLayout tl;
 
 
 char *encodeErgeName(struct track *tg, void *item)
 /* return the actual data name, in form xx/yyyy cut off xx/ return yyyy */
 {
 char *name;
 struct linkedFeatures *lf = item;
 name = strstr(lf->name, "/");
 if (name != NULL)
     name ++;
 if (name != NULL)
     return name;
 return "unknown";
 }
 
 void encodeErgeMethods(struct track *tg)
 /* setup special methods for ENCODE dbERGE II tracks */
 {
 tg->itemName = encodeErgeName;
 }
 
 Color encodeStanfordNRSFColor(struct track *tg, void *item, struct hvGfx *hvg)
 /* color by strand */
 {
 struct bed *thisItem = item;
 int r = tg->color.r;
 int g = tg->color.g;
 int b = tg->color.b;
 
 if (thisItem->strand[0] == '-')
     {
     r = g;
     g = b;
     b = tg->color.r;
     }
 return hvGfxFindColorIx(hvg, r, g, b);
 }
 
 void encodeStanfordNRSFMethods(struct track *tg)
 /* custom methods for ENCODE Stanford NRSF data */
 {
 tg->itemColor = encodeStanfordNRSFColor;
 tg->itemNameColor = encodeStanfordNRSFColor;
 }
 
 
 
 void loadEncodeRna(struct track *tg)
 /* Load up encodeRna from database table to track items. */
 {
 bedLoadItem(tg, "encodeRna", (ItemLoader)encodeRnaLoad);
 }
 
 void freeEncodeRna(struct track *tg)
 /* Free up encodeRna items. */
 {
 encodeRnaFreeList((struct encodeRna**)&tg->items);
 }
 
 Color encodeRnaColor(struct track *tg, void *item, struct hvGfx *hvg)
 /* Return color of encodeRna track item. */
 {
 struct encodeRna *el = item;
 
 if(el->isRmasked)     return MG_BLACK;
 if(el->isTranscribed) return hvGfxFindColorIx(hvg, 0x79, 0xaa, 0x3d);
 if(el->isPrediction)  return MG_RED;
 return MG_BLUE;
 }
 
 char *encodeRnaName(struct track *tg, void *item)
 /* Return RNA gene name. */
 {
 struct encodeRna *el = item;
 char *full = el->name;
 static char abbrev[SMALLBUF];
 char *e;
 
 strcpy(abbrev, skipChr(full));
 subChar(abbrev, '_', ' ');
 abbr(abbrev, " pseudogene");
 if ((e = strstr(abbrev, "-related")) != NULL)
     strcpy(e, "-like");
 return abbrev;
 }
 
 void encodeRnaMethods(struct track *tg)
 /* Make track for rna genes . */
 {
 tg->loadItems = loadEncodeRna;
 tg->freeItems = freeEncodeRna;
 tg->itemName = encodeRnaName;
 tg->itemColor = encodeRnaColor;
 tg->itemNameColor = encodeRnaColor;
 }
 
 static struct linkedFeatures *lfFromEncodePeak(struct slList *item, struct trackDb *tdb,
                                         int scoreMin, int scoreMax)
 /* Translate an {encode,narrow,broad,gapped}Peak item into a linkedFeatures. */
 {
 struct encodePeak *peak = (struct encodePeak *)item;
 struct linkedFeatures *lf;
 struct simpleFeature *sfList = NULL;
 if (!peak)
     return NULL;
 AllocVar(lf);
 lf->start = peak->chromStart;
 lf->end = peak->chromEnd;
 if (peak->peak > -1)
     {
     lf->tallStart = peak->chromStart + peak->peak;
     lf->tallEnd = lf->tallStart + 1;
     }
 lf->filterColor = -1;
 lf->orientation = orientFromChar(peak->strand[0]);
 adjustBedScoreGrayLevel(tdb, (struct bed *)peak, scoreMin, scoreMax);
 lf->grayIx = grayInRange((int)peak->score, scoreMin, scoreMax);
 lf->name = cloneString(peak->name);
 if (peak->blockCount > 0)
     {
     int i;
     for (i = 0; i < peak->blockCount; i++)
 	{
 	struct simpleFeature *sf;
 	AllocVar(sf);
 	sf->start = lf->start + peak->blockStarts[i];
 	sf->end = lf->start + peak->blockStarts[i] + peak->blockSizes[i];
 	sf->grayIx = lf->grayIx;
 	slAddHead(&sfList, sf);
 	}
     slReverse(&sfList);
     }
 else
     {
     AllocVar(sfList);
     sfList->start = lf->start;
     sfList->end = lf->end;
     sfList->grayIx = lf->grayIx;
     }
 lf->components = sfList;
 return lf;
 }
 
 
 static char *encodePeakFilter(char *trackName, struct trackDb *tdb, boolean isCustom)
 {
 struct dyString *extraWhere = dyStringNew(128);
 boolean and = FALSE;
 extraWhere = dyAddFilterAsInt(cart,tdb,extraWhere,SCORE_FILTER,"0:1000","score",&and);
 extraWhere = dyAddFilterAsDouble(cart,tdb,extraWhere,SIGNAL_FILTER,NULL,"signalValue",&and);
 extraWhere = dyAddFilterAsDouble(cart,tdb,extraWhere,PVALUE_FILTER,NULL,"pValue",&and);
 extraWhere = dyAddFilterAsDouble(cart,tdb,extraWhere,QVALUE_FILTER,NULL,"qValue",&and);
 
 if (sameString(extraWhere->string, ""))
     return NULL;
 return dyStringCannibalize(&extraWhere);
 }
 
 void bigNarrowPeakLoadItems(struct track *tg)
 /* Load a set of narrowPeaks from a bigNarrowPeak file. */
 {
 struct linkedFeatures *lfList = NULL;
 enum encodePeakType pt = 0;
 int scoreMin = atoi(trackDbSettingClosestToHomeOrDefault(tg->tdb, "scoreMin", "0"));
 int scoreMax = atoi(trackDbSettingClosestToHomeOrDefault(tg->tdb, "scoreMax", "1000"));
 pt = narrowPeak;
 
 tg->customInt = pt;
 struct bbiFile *bbi =  fetchBbiForTrack(tg);
 
 struct lm *lm = lmInit(0);
 struct bigBedInterval *bb, *bbList =  bigBedIntervalQuery(bbi, chromName, winStart, winEnd, 0, lm);
 int fieldCount = 10;
 char *bedRow[fieldCount];
 char startBuf[16], endBuf[16];
 struct bigBedFilter *filters = NULL;
 struct bigBedFilter *filter;
 
 if ((filter = bigBedMakeNumberFilter(cart, bbi, tg->tdb, SCORE_FILTER, "0:1000", "score", FALSE)) != NULL)
     slAddHead(&filters, filter);
 if ((filter = bigBedMakeNumberFilter(cart, bbi, tg->tdb, SIGNAL_FILTER, NULL, "signalValue", FALSE)) != NULL)
     slAddHead(&filters, filter);
 if ((filter = bigBedMakeNumberFilter(cart, bbi, tg->tdb, PVALUE_FILTER, NULL, "pValue", FALSE)) != NULL)
     slAddHead(&filters, filter);
 if ((filter = bigBedMakeNumberFilter(cart, bbi, tg->tdb, QVALUE_FILTER, NULL, "qValue", FALSE)) != NULL)
     slAddHead(&filters, filter);
 if (compositeChildHideEmptySubtracks(cart, tg->tdb, NULL, NULL))
    labelTrackAsFiltered(tg);
 
 unsigned filtered = 0;
 for (bb = bbList; bb != NULL; bb = bb->next)
     {
     bigBedIntervalToRow(bb, chromName, startBuf, endBuf, bedRow, ArraySize(bedRow));
     if (bigBedFilterInterval(bbi, bedRow, filters))
         {
         struct encodePeak *peak = encodePeakGeneralLoad(bedRow, pt);
         struct linkedFeatures *lf = lfFromEncodePeak((struct slList *)peak, tg->tdb, scoreMin, scoreMax);
 
         if (lf)
             slAddHead(&lfList, lf);
         else 
             filtered++;
         }
     else
         filtered++;
     }
 if (filtered)
    labelTrackAsFilteredNumber(tg, filtered);
 
 slReverse(&lfList);
 slSort(&lfList, linkedFeaturesCmp);
 tg->items = lfList;
 }
 
 static void encodePeakLoadItemsBoth(struct track *tg, struct customTrack *ct)
 /* Load up an encodePeak table from the regular database or the customTrash one. */
 {
 char *db, *table;
 struct sqlConnection *conn;
 struct sqlResult *sr = NULL;
 char **row;
 char *filterConstraints = NULL;
 int rowOffset;
 struct linkedFeatures *lfList = NULL;
 enum encodePeakType pt = 0;
 int scoreMin = atoi(trackDbSettingClosestToHomeOrDefault(tg->tdb, "scoreMin", "0"));
 int scoreMax = atoi(trackDbSettingClosestToHomeOrDefault(tg->tdb, "scoreMax", "1000"));
 char *liftDb = cloneString(trackDbSetting(tg->tdb, "quickLiftDb"));
 if (ct)
     {
     db = CUSTOM_TRASH;
     table = ct->dbTableName;
     }
 else
     {
 
     db = database;
     if (liftDb != NULL)
         db = liftDb;
     table = tg->tdb->table;
     }
 conn = hAllocConn(db);
 pt = encodePeakInferTypeFromTable(db, table, tg->tdb->type);
 tg->customInt = pt;
 filterConstraints = encodePeakFilter(tg->tdb->track, tg->tdb, (ct!=NULL));
 if (liftDb == NULL)
     {
     sr = hRangeQuery(conn, table, chromName, winStart, winEnd, filterConstraints, &rowOffset);
     while ((row = sqlNextRow(sr)) != NULL)
         {
         struct encodePeak *peak = encodePeakGeneralLoad(row + rowOffset, pt);
         struct linkedFeatures *lf = lfFromEncodePeak((struct slList *)peak, tg->tdb, scoreMin, scoreMax);
 
         if (lf)
             slAddHead(&lfList, lf);
         }
     sqlFreeResult(&sr);
     }
 else
     {
     struct hash *chainHash = newHash(12);
     char *quickLiftFile = cloneString(trackDbSetting(tg->tdb, "quickLiftUrl"));
 
     ItemLoader2 loader;
     switch(pt)
     {
     case narrowPeak:
         loader = (ItemLoader2)narrowPeakLoad;
         break;
     case broadPeak:
         loader = (ItemLoader2)broadPeakLoad;
         break;
     case gappedPeak:
         loader = (ItemLoader2)gappedPeakLoad;
         break;
     case encodePeak:
         loader =  (ItemLoader2)encodePeakLoad;
         break;
     default:
         errAbort("bad value for peak type %d\n", pt);
         break;
     }
 
     struct encodePeak *peakList = (struct encodePeak *)quickLiftSql(conn, quickLiftFile, table, chromName, winStart, winEnd,  NULL, NULL, (ItemLoader2)loader, 0, chainHash);
-    struct encodePeak *liftedPeaks = (struct encodePeak *)quickLiftBeds((struct bed *)peakList, chainHash, FALSE);
+    struct encodePeak *liftedPeaks = quickLiftPeaks(peakList, chainHash);
 
     for(; liftedPeaks; liftedPeaks = liftedPeaks->next)
         {
         struct linkedFeatures *lf = lfFromEncodePeak((struct slList *)liftedPeaks, tg->tdb, scoreMin, scoreMax);
 
         if (lf)
             slAddHead(&lfList, lf);
         }
     }
 hFreeConn(&conn);
 slReverse(&lfList);
 slSort(&lfList, linkedFeaturesCmp);
 tg->items = lfList;
 }
 
 static void encodePeakLoadItemsNormal(struct track *tg)
 /* Load the encodePeak table form the database. */
 {
 encodePeakLoadItemsBoth(tg, NULL);
 }
 
 static void encodePeakLoadItemsCt(struct track *tg)
 /* Load the encodePeak table form the customTrash database. */
 {
 struct customTrack *ct = tg->customPt;
 encodePeakLoadItemsBoth(tg, ct);
 }
 
 static void encodePeakDrawAt(struct track *tg, void *item,
         struct hvGfx *hvg, int xOff, int y, double scale,
         MgFont *font, Color color, enum trackVisibility vis)
 /* Draw the peak from the linkedFeature.  Currently this doesn't draw any */
 /* sorta shading based on the signalValue/pValue. */
 {
 struct linkedFeatures *lf = item;
 int heightPer = tg->heightPer;
 int shortOff = heightPer/4;
 int shortHeight = heightPer - 2*shortOff;
 char *exonArrows = trackDbSettingClosestToHomeOrDefault(tg->tdb, "exonArrows", "off");
 boolean drawArrows = FALSE;
 if ((exonArrows != NULL) && sameString(exonArrows, "on"))
     drawArrows = TRUE;
 Color rangeColor = shadesOfGray[lf->grayIx];
 Color peakColor = (tg->ixColor != blackIndex()) ? tg->ixColor : getOrangeColor();
 if (drawArrows || lf->tallStart == 0)
     {
     shortOff = 0;
     shortHeight = heightPer;
     }
 if (lf->components)
     {
     struct simpleFeature *sf;
     drawScaledBox(hvg, lf->start, lf->end, scale, xOff, y+(heightPer/2), 1, rangeColor);
     for (sf = lf->components; sf != NULL; sf = sf->next)
 	{
         drawScaledBox(hvg, sf->start, sf->end, scale, xOff, y+shortOff,
                       shortHeight, rangeColor);
 	if (drawArrows)
 	    {
 	    int x1 = round((double)(sf->start-winStart)*scale) + xOff;
 	    int x2 = round((double)(sf->end-winStart)*scale) + xOff;
 	    int w = x2-x1;
             if (w < 1)
                 w = 1;
 
             clippedBarbs(hvg, x1, y + heightPer/2, w, 
                     tl.barbHeight, tl.barbSpacing, lf->orientation,
                     MG_WHITE, FALSE);
             }
 	}
     }
 else
     drawScaledBox(hvg, lf->start, lf->end, scale, xOff, y+shortOff,
 		  shortHeight, rangeColor);
 if ((lf->tallEnd > 0) && (lf->tallStart < lf->end))
     drawScaledBox(hvg, lf->tallStart, lf->tallEnd, scale, xOff, y,
 		  heightPer, peakColor);
 }
 
 char *encodePeakItemName(struct track *tg, void *item)
 /* Get rid of the '.' names */
 {
 struct linkedFeatures *lf = item;
 if (lf->name && sameString(lf->name, "."))
     return "";
 else
     return lf->name;
 }
 
 void encodePeakMethods(struct track *tg)
 /* Methods for ENCODE peak track uses mostly linkedFeatures. */
 {
 linkedFeaturesMethods(tg);
 tg->loadItems = encodePeakLoadItemsNormal;
 tg->drawItemAt = encodePeakDrawAt;
 tg->nextPrevItem = linkedFeaturesLabelNextPrevItem;
 tg->itemName = encodePeakItemName;
 tg->mapItemName = encodePeakItemName;
 tg->canPack = TRUE;
 }
 
 void encodePeakMethodsCt(struct track *tg)
 /* Methods for ENCODE peak track uses mostly linkedFeatures. */
 {
 encodePeakMethods(tg);
 tg->loadItems = encodePeakLoadItemsCt;
 }