f577b4c8199360dac5b955dfc4ede99d57c2946f
braney
  Wed Jul 9 16:57:59 2025 -0700
ongoing work on quickLift, including displaying mismatches

diff --git src/hg/hgTracks/quickLift.c src/hg/hgTracks/quickLift.c
index fba640ce31f..9957fc410d2 100644
--- src/hg/hgTracks/quickLift.c
+++ src/hg/hgTracks/quickLift.c
@@ -1,196 +1,257 @@
 
 #include "common.h"
 #include "hgTracks.h"
 #include "chromAlias.h"
 #include "hgConfig.h"
 #include "bigChain.h"
+#include "bigLink.h"
 #include "trackHub.h"
 
 struct highRegions
 // store highlight information
 {
 struct highRegions *next;
 long chromStart;
 long chromEnd;
 long oChromStart;
 long oChromEnd;
 char strand;
 unsigned hexColor;
+char otherBase;
 };
 
 #define INSERT_COLOR     0
 #define DEL_COLOR      1
 #define DOUBLE_COLOR     2
+#define MISMATCH_COLOR     3
 
 static Color *highlightColors;
 static unsigned lengthLimit;
 
 static Color getColor(char *confVariable, char *defaultRgba)
 {
 Color color = 0xff0000ff;
 
 char *str = cloneString(cfgOptionDefault(confVariable, defaultRgba));
 char *words[10];
 if (chopCommas(str, words) != 4)
     errAbort("conf variable '%s' is expected to have a string like  r,g,b,a ", confVariable);
 
 color = MAKECOLOR_32_A(atoi(words[0]),atoi(words[1]),atoi(words[2]),atoi(words[3]));
 return color;
 }
 
 static void initializeHighlightColors()
 {
 if (highlightColors == NULL)
     {
     highlightColors = needMem(sizeof(Color) * 3);
  
     lengthLimit = atoi(cfgOptionDefault("quickLift.lengthLimit", "10000"));
 
     highlightColors[INSERT_COLOR] = getColor("quickLift.insColor","255,0,0,255");
     highlightColors[DEL_COLOR] = getColor("quickLift.delColor","0,255,0,255");
     highlightColors[DOUBLE_COLOR] = getColor("quickLift.doubleColor","0,0,255,255");
+    highlightColors[MISMATCH_COLOR] = getColor("quickLift.mismatchColor","255,0,0,255");
     }
 }
 
-struct highRegions *getQuickLiftLines(char *quickLiftFile, int seqStart, int seqEnd)
+struct highRegions *getQuickLiftLines(char *liftDb, char *quickLiftFile, int seqStart, int seqEnd)
 /* Figure out the highlight regions and cache them. */
 {
 static struct hash *highLightsHash = NULL;
 struct highRegions *hrList = NULL;
 
 initializeHighlightColors();
 if (seqEnd - seqStart > lengthLimit)
     return hrList;
 
 if (highLightsHash != NULL)
     {
     if ((hrList = (struct highRegions *)hashFindVal(highLightsHash, quickLiftFile)) != NULL)
         return hrList;
     }
 else
     {
     highLightsHash = newHash(0);
     }
 
 
-char *links = bigChainGetLinkFile(quickLiftFile);
-struct bbiFile *bbi = bigBedFileOpenAlias(links, chromAliasFindAliases);
+struct bbiFile *bbiChain = bigBedFileOpenAlias(quickLiftFile, chromAliasFindAliases);
 struct lm *lm = lmInit(0);
-struct bigBedInterval *bb, *bbList =  bigBedIntervalQuery(bbi, chromName, seqStart, seqEnd, 0, lm);
+struct bigBedInterval *bbChain, *bbChainList =  bigBedIntervalQuery(bbiChain, chromName, seqStart, seqEnd, 0, lm);
+char *links = bigChainGetLinkFile(quickLiftFile);
+struct bbiFile *bbiLink = bigBedFileOpenAlias(links, chromAliasFindAliases);
+struct bigBedInterval  *bbLink, *bbLinkList =  bigBedIntervalQuery(bbiLink, chromName, seqStart, seqEnd, 0, lm);
 
-char *bedRow[5];
+char *chainRow[1024];
+char *linkRow[1024];
 char startBuf[16], endBuf[16];
+int chainCount = 0;
+
+for (bbChain = bbChainList; bbChain != NULL; bbChain = bbChain->next)
+    {
+    bigBedIntervalToRow(bbChain, chromName, startBuf, endBuf, chainRow, ArraySize(chainRow));
+    struct bigChain *bc = bigChainLoad(chainRow);
 
     int previousTEnd = -1;
     int previousQEnd = -1;
-for (bb = bbList; bb != NULL; bb = bb->next)
+    int linkCount = 0;
+    for (bbLink = bbLinkList; bbLink != NULL; bbLink = bbLink->next)
         {
-    bigBedIntervalToRow(bb, chromName, startBuf, endBuf, bedRow, ArraySize(bedRow));
-    int tStart = atoi(bedRow[1]);
-    int tEnd = atoi(bedRow[2]);
-    int qStart = atoi(bedRow[4]);
+        bigBedIntervalToRow(bbLink, chromName, startBuf, endBuf, linkRow, ArraySize(linkRow));
+        struct bigLink *bl = bigLinkLoad(linkRow);
+
+        if (!sameString(bl->name, bc->name))
+            continue;
+
+        int tStart = bl->chromStart;
+        int tEnd = bl->chromEnd;
+        int qStart = bl->qStart;
         int qEnd = qStart + (tEnd - tStart);
         struct highRegions *hr;
         if ((previousTEnd != -1) && (previousTEnd == tStart))
             {
             AllocVar(hr);
             slAddHead(&hrList, hr);
-        hr->strand = 
+        //    hr->strand = 
             hr->chromStart = previousTEnd;
             hr->chromEnd = tStart;
             hr->oChromStart = previousQEnd;
             hr->oChromEnd = qStart;
             hr->hexColor = highlightColors[DEL_COLOR];
             }
         if ( (previousQEnd != -1) && (previousQEnd == qStart))
             {
             AllocVar(hr);
             slAddHead(&hrList, hr);
             hr->chromStart = previousTEnd;
             hr->chromEnd = tStart;
             hr->oChromStart = previousQEnd;
             hr->oChromEnd = qStart;
             hr->hexColor = highlightColors[INSERT_COLOR];
             }
         if ( ((previousQEnd != -1) && (previousQEnd != qStart)) 
              && ((previousTEnd != -1) && (previousTEnd != tStart)))
             {
             AllocVar(hr);
             slAddHead(&hrList, hr);
             hr->chromStart = previousTEnd;
             hr->chromEnd = tStart;
             hr->oChromStart = previousQEnd;
             hr->oChromEnd = qStart;
             hr->hexColor = highlightColors[DOUBLE_COLOR];
             }
         previousQEnd = qEnd;
         previousTEnd = tEnd;
+
+        // crop the chain block if it's bigger than the window
+        int tMin, tMax;
+        int qMin, qMax;
+        tMin = bl->chromStart;
+        tMax = bl->chromEnd;
+        qMin = bl->qStart;
+        if (seqStart > bl->chromStart) 
+            {
+            tMin = seqStart;
+            qMin = qStart + (seqStart - bl->chromStart);
+            }
+        if (seqEnd < bl->chromEnd) 
+            {
+            tMax = seqEnd;
+            }
+        qMax = qMin + (tMax - tMin);
+
+        struct dnaSeq *tSeq = hDnaFromSeq(database, chromName, tMin, tMax, dnaUpper);
+        struct dnaSeq *qSeq = hDnaFromSeq(liftDb, bc->qName, qMin, qMax, dnaUpper);
+
+        unsigned tAddr = tMin;
+        unsigned qAddr = qMin;
+        int count = 0;
+        for(; tAddr < tEnd; tAddr++, qAddr++, count++)
+            {
+            if (tSeq->dna[count] != qSeq->dna[count])
+                {
+                AllocVar(hr);
+                slAddHead(&hrList, hr);
+                hr->chromStart = tAddr;
+                hr->chromEnd = tAddr + 1;
+                hr->oChromStart = qAddr;
+                hr->oChromEnd = qAddr + 1;
+                hr->otherBase = qSeq->dna[count];
+                hr->hexColor = highlightColors[MISMATCH_COLOR];
+                }
+            }
+        }
     }
 
 hashAdd(highLightsHash, quickLiftFile, hrList);
 
 return hrList;
 }
 
 static void drawTri(struct hvGfx *hvg, int x1, int x2, int y, Color color)
 /* Draw traingle. */
 {
 struct gfxPoly *poly = gfxPolyNew();
 int half = (x2 - x1) / 2;
 
 gfxPolyAddPoint(poly, x1, y);
 gfxPolyAddPoint(poly, x1+half, y+2*half);
 gfxPolyAddPoint(poly, x2, y);
 hvGfxDrawPoly(hvg, poly, color, TRUE);
 gfxPolyFree(&poly);
 }
 
 void maybeDrawQuickLiftLines( struct track *tg, int seqStart, int seqEnd,
                       struct hvGfx *hvg, int xOff, int yOff, int width,
                       MgFont *font, Color color, enum trackVisibility vis)
 /* Draw the indel regions in quickLifted tracks as a highlight. */
 {
 char *quickLiftFile = cloneString(trackDbSetting(tg->tdb, "quickLiftUrl"));
 if (quickLiftFile == NULL)
     return;
 
 boolean drawTriangle = FALSE;
 if (startsWith("quickLiftChain", trackHubSkipHubName(tg->track)))
     drawTriangle = TRUE;
-struct highRegions *regions = getQuickLiftLines(quickLiftFile, seqStart, seqEnd);
+char *liftDb = trackDbSetting(tg->tdb, "quickLiftDb");
+struct highRegions *regions = getQuickLiftLines(liftDb, quickLiftFile, seqStart, seqEnd);
 struct highRegions *hr = regions;
 
 int fontHeight = mgFontLineHeight(tl.font);
 int height = tg->height;
 if (!drawTriangle && isCenterLabelIncluded(tg))
     {
     height += fontHeight;
     yOff -= fontHeight;
     }
 
 for(; hr; hr = hr->next)
     {
     unsigned int hexColor = hr->hexColor;
     double scale = scaleForWindow(width, seqStart, seqEnd);
     int x1 = xOff + scale * (hr->chromStart - seqStart);
     int w =  scale * (hr->chromEnd - hr->chromStart);
     if (w == 0) 
         w = 1;
     hvGfxSetClip(hvg, xOff, yOff, width, height);  // we're drawing in the center label at the moment
     if (drawTriangle)
         {
         drawTri(hvg, x1 + w/2 - fontHeight/2, x1 + w/2 + fontHeight/2 , yOff, hexColor);
         }
     else
         hvGfxBox(hvg, x1, yOff, w, height, hexColor);
 
     char mouseOver[4096];
 
-    if (hr->chromStart == hr->chromEnd)
+    if (hr->otherBase != 0)
+        safef(mouseOver, sizeof mouseOver, "mismatch %c", hr->otherBase);
+    else if (hr->chromStart == hr->chromEnd)
         safef(mouseOver, sizeof mouseOver, "deletion %ldbp", hr->oChromStart - hr->oChromStart);
     else
         safef(mouseOver, sizeof mouseOver, "insertion %ldbp", hr->oChromEnd - hr->oChromStart);
     mapBoxHc(hvg, seqStart, seqEnd, x1, yOff, width, height, tg->track, "insert", mouseOver);
 
     }
 }