0564395ec363631f2ff8d295da6f6b50f873fda4
braney
  Mon Jan 24 17:01:53 2022 -0800
more chromAlias work:  some name changes and support for the new genark
chromAlias format

diff --git src/hg/hgTracks/bigWigTrack.c src/hg/hgTracks/bigWigTrack.c
index bb2a568..e6ef318 100644
--- src/hg/hgTracks/bigWigTrack.c
+++ src/hg/hgTracks/bigWigTrack.c
@@ -1,302 +1,302 @@
 /* bigWigTrack - stuff to handle loading and display of bigWig type tracks in browser.   */
 
 /* Copyright (C) 2011 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 "hgTracks.h"
 #include "localmem.h"
 #include "wigCommon.h"
 #include "bbiFile.h"
 #include "bigWig.h"
 #include "errCatch.h"
 #include "container.h"
 #include "bigWarn.h"
 #include "mathWig.h"
 #include "float.h"
 #include "hubConnect.h"
 #include "chromAlias.h"
 
 struct preDrawContainer *bigWigLoadPreDraw(struct track *tg, int seqStart, int seqEnd, int width)
 /* Do bits that load the predraw buffer tg->preDrawContainer. */
 {
 /* Just need to do this once... */
 if (tg->preDrawContainer != NULL)
     return tg->preDrawContainer;
 
 struct preDrawContainer *preDrawList = NULL;
 /* protect against temporary network error */
 struct errCatch *errCatch = errCatchNew();
 if (errCatchStart(errCatch))
     {
     /* Allocate predraw area. */
 
     /* Get summary info from bigWig */
     int summarySize = width;
     struct bbiSummaryElement *summary;
     AllocArray(summary, summarySize);
 
     struct bbiFile *bbiFile, *bbiNext;
     for(bbiFile = tg->bbiFile; bbiFile ; bbiFile = bbiNext)
 	{
 	struct preDrawContainer *pre = initPreDrawContainer(width);
 	slAddHead(&preDrawList, pre);
 
 	if (bigWigSummaryArrayExtended(bbiFile, chromName, winStart, winEnd, summarySize, summary))
 	    {
 	    /* Convert format to predraw */
 	    int i;
 	    int preDrawZero = pre->preDrawZero;
 	    struct preDrawElement *preDraw = pre->preDraw;
 	    for (i=0; i<summarySize; ++i)
 		{
 		struct preDrawElement *pe = &preDraw[i + preDrawZero];
 		struct bbiSummaryElement *be = &summary[i];
 		pe->count = be->validCount;
 		pe->min = be->minVal;
 		pe->max = be->maxVal;
 		pe->sumData = be->sumData;
 		pe->sumSquares = be->sumSquares;
 		}
 	    }
 	bbiNext = bbiFile->next;
 	bigWigFileClose(&bbiFile);
 	}
     tg->bbiFile = NULL;
     freeMem(summary);
     }
 errCatchEnd(errCatch);
 if (errCatch->gotError)
     {
     tg->networkErrMsg = cloneString(errCatch->message->string);
     }
 errCatchFree(&errCatch);
 tg->preDrawContainer = preDrawList;
 return preDrawList;
 }
 
 static void bigWigPreDrawItems(struct track *tg, int seqStart, int seqEnd,
 	struct hvGfx *hvg, int xOff, int yOff, int width,
 	MgFont *font, Color color, enum trackVisibility vis)
 {
 if (tg->networkErrMsg == NULL)
     {
     /* Call pre graphing routine. */
     wigPreDrawPredraw(tg, seqStart, seqEnd, hvg, xOff, yOff, width, font, color, vis,
 		   tg->preDrawContainer, tg->preDrawContainer->preDrawZero, tg->preDrawContainer->preDrawSize, 
 		   &tg->graphUpperLimit, &tg->graphLowerLimit);
     }
 }
 
 
 static void bigWigDrawItems(struct track *tg, int seqStart, int seqEnd,
 	struct hvGfx *hvg, int xOff, int yOff, int width,
 	MgFont *font, Color color, enum trackVisibility vis)
 {
 if (tg->networkErrMsg == NULL)
     {
     /* Call actual graphing routine. */
     wigDrawPredraw(tg, seqStart, seqEnd, hvg, xOff, yOff, width, font, color, vis,
 		   tg->preDrawContainer, tg->preDrawContainer->preDrawZero, tg->preDrawContainer->preDrawSize, 
 		   tg->graphUpperLimit, tg->graphLowerLimit);
     }
 else
     bigDrawWarning(tg, seqStart, seqEnd, hvg, xOff, yOff, width, font, color, vis);
 }
 
 static void bigWigOpenCatch(struct track *tg, char *fileName)
 /* Try to open big wig file, store error in track struct */
 {
 /* protect against temporary network error */
 struct errCatch *errCatch = errCatchNew();
 if (errCatchStart(errCatch))
     {
-    struct bbiFile *bbiFile = bigWigFileOpenAlias(fileName, chromAliasGetHash(database));
+    struct bbiFile *bbiFile = bigWigFileOpenAlias(fileName, chromAliasChromToAliasHash(database));
     slAddHead(&tg->bbiFile, bbiFile);
     }
 errCatchEnd(errCatch);
 if (errCatch->gotError)
     {
     tg->networkErrMsg = cloneString(errCatch->message->string);
     tg->drawItems = bigDrawWarning;
     if (!sameOk(parentContainerType(tg), "multiWig"))
 	tg->totalHeight = bigWarnTotalHeight;
     }
 errCatchFree(&errCatch);
 }
 
 static void dataToPixelsUp(double *data, struct preDrawContainer *pre)
 /* Up sample data into pixels. */
 {
 int preDrawZero = pre->preDrawZero;
 unsigned size = winEnd - winStart;
 double dataPerPixel = size / (double) insideWidth;
 int pixel;
 
 for (pixel=0; pixel<insideWidth; ++pixel)
     {
     struct preDrawElement *pe = &pre->preDraw[pixel + preDrawZero];
     unsigned index = pixel * dataPerPixel;
     pe->count = 1;
     pe->min = data[index];
     pe->max = data[index];
     pe->sumData = data[index] ;
     pe->sumSquares = data[index] * data[index];
     }
 }
 
 static void dataToPixelsDown(double *data, struct preDrawContainer *pre)
 /* Down sample data into pixels. */
 {
 int preDrawZero = pre->preDrawZero;
 unsigned size = winEnd - winStart;
 double dataPerPixel = size / (double) insideWidth;
 int pixel;
 
 for (pixel=0; pixel<insideWidth; ++pixel)
     {
     struct preDrawElement *pe = &pre->preDraw[pixel + preDrawZero];
     double startReal = pixel * dataPerPixel;
     double endReal = (pixel + 1) * dataPerPixel;
     unsigned startUns = startReal;
     unsigned endUns = endReal;
     double realCount, realSum, realSumSquares, max, min;
 
     realCount = realSum = realSumSquares = 0.0;
     max = -DBL_MAX;
     min = DBL_MAX;
 
     assert(startUns != endUns);
     unsigned ceilUns = ceil(startReal);
 
     if ((ceilUns != startUns) && !isnan(data[startUns]))
 	{
 	/* need a fraction of the first count */
 	double frac = (double)ceilUns - startReal;
 	realCount = frac;
 	realSum = frac * data[startUns];
 	realSumSquares = realSum * realSum;
         if (max < data[startUns])
             max = data[startUns];
         if (min > data[startUns])
             min = data[startUns];
 	startUns++;
 	}
 
     // add in all the data that are totally in this pixel
     for(; startUns < endUns; startUns++)
 	{
         if (!isnan(data[startUns]))
             {
             realCount += 1.0;
             realSum += data[startUns];
             realSumSquares += data[startUns] * data[startUns];
             if (max < data[startUns])
                 max = data[startUns];
             if (min > data[startUns])
                 min = data[startUns];
             }
 	}
 
     // add any fraction of the count that's only partially in this pixel
     double lastFrac = endReal - endUns;
     double lastSum = lastFrac * data[endUns];
     if ((lastFrac > 0.0) && (endUns < size) && !isnan(data[endUns]))
 	{
 	if (max < data[endUns])
 	    max = data[endUns];
 	if (min > data[endUns])
 	    min = data[endUns];
 	realCount += lastFrac;
 	realSum += lastSum;
 	realSumSquares += lastSum * lastSum;
 	}
 
     pe->count = normalizeCount(pe, realCount, min, max, realSum, realSumSquares);
     }
 }
 
 static void dataToPixels(double *data, struct preDrawContainer *pre)
 /* Sample data into pixels. */
 {
 unsigned size = winEnd - winStart;
 double dataPerPixel = size / (double) insideWidth;
 
 if (dataPerPixel <= 1.0)
     dataToPixelsUp(data, pre);
 else
     dataToPixelsDown(data, pre);
 }
 
 static void mathWigLoadItems(struct track *tg)
 /* Fill up tg->items with bedGraphItems derived from a bigWig file */
 {
 char *missingSetting;
 boolean missingIsZero = TRUE;
 if ((missingSetting = cartOrTdbString(cart, tg->tdb, "missingMethod", NULL)) != NULL)
     {
     missingIsZero = differentString(missingSetting, "missing");
     }
 char *equation = cloneString(trackDbSetting(tg->tdb, "mathDataUrl"));
 
 struct preDrawContainer *pre = tg->preDrawContainer = initPreDrawContainer(insideWidth);
 double *data;
 data = mathWigGetValues(database, equation, chromName, winStart, winEnd, missingIsZero);
 dataToPixels(data, pre);
 
 free(data);
 }
 
 static void bigWigLoadItems(struct track *tg)
 /* Fill up tg->items with bedGraphItems derived from a bigWig file */
 {
 char *extTableString = trackDbSetting(tg->tdb, "extTable");
 
 if (tg->bbiFile == NULL)
     {
     /* Figure out bigWig file name. */
     if (isHubTrack(database) || tg->parallelLoading) // do not use mysql during parallel-fetch or if assembly hub
 	{
 	char *fileName = cloneString(trackDbSetting(tg->tdb, "bigDataUrl"));
 	bigWigOpenCatch(tg, fileName);
 	}
     else
 	{
 	struct sqlConnection *conn = hAllocConnTrack(database, tg->tdb);
 	char *fileName = bbiNameFromSettingOrTable(tg->tdb, conn, tg->table);
 	bigWigOpenCatch(tg, fileName);
 	// if there's an extra table, read this one in too
 	if (extTableString != NULL)
 	    {
 	    fileName = bbiNameFromSettingOrTable(tg->tdb, conn, extTableString);
 	    bigWigOpenCatch(tg, fileName);
 	    }
 	hFreeConn(&conn);
 	}
     }
 bigWigLoadPreDraw(tg, winStart, winEnd, insideWidth);
 }
 
 void mathWigMethods(struct track *track, struct trackDb *tdb, 
 	int wordCount, char *words[])
 /* Set up bigWig methods. */
 {
 bigWigMethods(track, tdb, wordCount, words);
 track->loadItems = mathWigLoadItems;
 }
 
 void bigWigMethods(struct track *track, struct trackDb *tdb, 
 	int wordCount, char *words[])
 /* Set up bigWig methods. */
 {
 bedGraphMethods(track, tdb, wordCount, words);
 track->loadItems = bigWigLoadItems;
 track->preDrawItems = bigWigPreDrawItems;
 track->preDrawMultiRegion = wigMultiRegionGraphLimits;
 track->drawItems = bigWigDrawItems;
 track->loadPreDraw = bigWigLoadPreDraw;
 }