15e8651da02e09bbd37dbb404a966ed8c7d75167
braney
  Fri Sep 4 13:32:47 2026 -0700
hgc: show the lifted alignment on a quickLifted maf track's details page

The page read the track's own file with reference coordinates and then went
looking for a reference row named for the assembly on screen.  Both kinds of maf
track failed, differently:  bigMaf aborted with "Couldn't find hg38.chr7 in maf"
out of mafFindComponent, and wigMaf drew a page with a title and nothing under
it, which is the worse of the two.

quickLiftClickMafs reads the blocks over the ranges in the other assembly, on
connections to that assembly, and maps them onto the reference, the same way the
track loader does.

refs #38249

diff --git src/hg/hgc/mafClick.c src/hg/hgc/mafClick.c
index fb20647e4dd..7c22ecaecae 100644
--- src/hg/hgc/mafClick.c
+++ src/hg/hgc/mafClick.c
@@ -1,901 +1,948 @@
 /* Handle details pages for maf tracks and axt tracks. */
 
 /* Copyright (C) 2013 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 "hgc.h"
 #include "maf.h"
 #include "obscure.h"
 #include "cheapcgi.h"
 #include "genePred.h"
 #include "botDelay.h"
 #include "hgMaf.h"
 #include "hui.h"
 #include "hCommon.h"
 #include "hubConnect.h"
 #include "trackHub.h"
 #include "chromAlias.h"
 #include "genark.h"
+#include "quickLift.h"
 
 extern boolean issueBotWarning;
 
 #define ADDEXONCAPITAL
 
 /* Javascript to help make a selection from a drop-down
  * go back to the server. */
 static char *autoSubmit = "document.gpForm.submit();";
 
 static char *splitMafSrc(char *src, char *dbOnly, int dbOnlySize, struct hash *labelHash)
 /* Split a maf component src ("db.chrom") into db (in dbOnly) and chrom
  * (return value).  If labelHash has an entry whose key is a prefix of src
  * ending at a dot, prefer that.  This handles multi-dot db names like assembly
  * hub accessions ("GCF_000009085.1.NC_002163v1").
  * Falls back to chopping at the first dot when no labelHash hit. */
 {
 safef(dbOnly, dbOnlySize, "%s", src);
 if (labelHash != NULL)
     {
     for (int i = strlen(dbOnly) - 1; i > 0; i--)
         {
         if (dbOnly[i] == '.')
             {
             dbOnly[i] = 0;
             if (hashFindVal(labelHash, dbOnly) != NULL)
                 return &dbOnly[i + 1];
             dbOnly[i] = '.';
             }
         }
     }
 return chopPrefix(dbOnly);
 }
 
 static void blueCapWrite(FILE *f, char *s, int size, char *r)
 /* Write capital letters in blue. */
 {
 boolean isBlue = FALSE;
 int i;
 for (i=0; i<size; ++i)
     {
     if (r!=NULL && s[i]==r[i])
 	fprintf(f, ".");
     else
 	{
 	char c = s[i];
 	if (isupper(c))
             {
             if (!isBlue)
                 {
                 fprintf(f, "<span style='color:#0000FF;'>");
                 isBlue = TRUE;
                 }
             }
 	else if (islower(c))
             {
             if (isBlue)
                 {
                 fprintf(f, "</span>");
                 isBlue = FALSE;
                 }
             }
 	fprintf(f, "%c", c);
 	}
     }
 
 if (isBlue)
     fprintf(f, "</span>");
 }
 
 void initSummaryLine(char *summaryLine, int size, int val)
 /* Fill summary line with stars and null terminate */
 {
 int i;
 for (i = 0; i < size; i++)
     summaryLine[i] = val;
 summaryLine[i] = 0;
 }
 
 void updateSummaryLine(char *summaryLine, char *referenceText,
                                         char *alignText, int size)
 /* Blank out columns in the summary line where this alignment
  * differs from the reference */
 {
 int i;
 for (i=0; i<size; i++)
     {
     if (alignText[i] != referenceText[i])
         summaryLine[i] = ' ';
     }
 }
 
 void mafPrettyOut(FILE *f, struct mafAli *maf, int lineSize,
                   boolean onlyDiff, int blockNo, struct hash *labelHash)
 {
 int ii, ch;
 int srcChars = 0;
 struct mafComp *mc;
 int lineStart, lineEnd;
 char *summaryLine = needMem(lineSize+1);
 char *referenceText;
 int startChars, sizeChars, srcSizeChars;
 boolean haveInserts = FALSE;
 struct mafComp *masterMc = maf->components;
 
 startChars = sizeChars = srcSizeChars = 0;
 
 for (mc = maf->components; mc != NULL; mc = mc->next)
     {
     /* Figure out length of source (species) field. */
     /*if (mc->size != 0)*/
 	{
 	char dbOnly[128];
 	int len;
 	char *org;
 
 	memset(dbOnly, 0, sizeof(dbOnly));
 	splitMafSrc(mc->src, dbOnly, sizeof(dbOnly), labelHash);
 
 	if ((org = hOrganism(dbOnly)) == NULL)
 	    len = strlen(dbOnly);
 	else
 	    len = strlen(org);
 	if (srcChars < len)
 	    srcChars = len;
 
 	len = digitsBaseTen(mc->start);
 	if (startChars < len)
 	    startChars = len;
 	len = digitsBaseTen(mc->size);
 	if (sizeChars < len)
 	    sizeChars = len;
 	len = digitsBaseTen(mc->srcSize);
 	if (srcSizeChars < len)
 	    srcSizeChars = len;
 
 	if (mc->text && (mc->rightStatus == MAF_INSERT_STATUS) && (masterMc->start + masterMc->size < winEnd))
 	    haveInserts = TRUE;
 
 #ifdef REVERSESTRAND
 	/* complement bases if hgTracks is on reverse strand */
 	if (mc->size && cartCgiUsualBoolean(cart, COMPLEMENT_BASES_VAR, FALSE))
 	    complement(mc->text, maf->textSize);
 #endif
 	}
     }
 /* first sequence in the alignment */
 referenceText = maf->components->text;
 
 for (lineStart = 0; lineStart < maf->textSize; lineStart = lineEnd)
     {
     int size;
     lineEnd = lineStart + lineSize;
     if (lineEnd >= maf->textSize)
         lineEnd = maf->textSize;
     size = lineEnd - lineStart;
     initSummaryLine(summaryLine, size, '*');
     for (mc = maf->components; mc != NULL; mc = mc->next)
         {
 	char dbOnly[128], *chrom;
 	int s = mc->start;
 	int e = s + mc->size;
 	char *org;
 	char *revComp = "";
 	char strand = mc->strand;
 	struct dyString *dy = dyStringNew(512);
 #ifdef REVERSESTRAND
 	if (cartCgiUsualBoolean(cart, COMPLEMENT_BASES_VAR, FALSE))
 	    strand = (strand == '+') ? '-' : '+';
 #endif
 	if (strand == '-') revComp = "&hgSeq.revComp=on";
 
 	dyStringClear(dy);
 
 	chrom = splitMafSrc(mc->src, dbOnly, sizeof(dbOnly), labelHash);
         if ((labelHash == NULL) || ((org = hashFindVal(labelHash, dbOnly)) == NULL))
             {
             if ((org = hOrganism(dbOnly)) == NULL)
                 org = dbOnly;
             }
 
 	if (mc->strand == '-')
 	    reverseIntRange(&s, &e, mc->srcSize);
 
 
 	if (mc->text != NULL)
 	    {
             if (lineStart == 0)
 		{
 		if (hDbIsActive(dbOnly))
 		    {
 		    dyStringPrintf(dy, "%s Browser %s:%d-%d %c %*dbps",hOrganism(dbOnly),chrom, s+1, e, mc->strand,sizeChars, mc->size);
 		    linkToOtherBrowserTitle(dbOnly, chrom, s, e, dy->string);
 		    dyStringClear(dy);
 		    fprintf(f, "B</A> ");
 		    }
 		else
 		    {
 		    char *hubUrl = genarkUrl(dbOnly);
 		    if (hubUrl != NULL)
 			{
 			dyStringPrintf(dy, "%s Browser %s:%d-%d %c %*dbps", org, chrom, s+1, e, mc->strand, sizeChars, mc->size);
 			fprintf(f, "<A TITLE=\"%s\" TARGET=\"_blank\" HREF=\"%s?genome=%s&hubUrl=%s&position=%s%%3A%d-%d\">B</A> ",
 				dy->string, hgTracksName(), dbOnly, cgiEncode(hubUrl), cgiEncode(chrom), s+1, e);
 			dyStringClear(dy);
 			}
 		    else
 			fprintf(f, "  ");
 		    }
 
                 if (hDbExists(dbOnly))
                     {
                     dyStringPrintf(dy, "Get %s DNA %s:%d-%d %c %*dbps",hOrganism(dbOnly),chrom, s+1, e, mc->strand,sizeChars, mc->size);
                     printf("<A TITLE=\"%s\" TARGET=\"_blank\" HREF=\"%s?o=%d&g=getDna&i=%s&c=%s&l=%d&r=%d&db=%s%s\">D</A> ",  dy->string,hgcName(),
                        s, cgiEncode(chrom),
                        chrom, s, e, dbOnly, revComp);
                     }
                 else
                     fprintf(f, "  ");
                 }
             else
                 {
                 fprintf(f, "    ");
                 }
 
             dyStringClear(dy);
             dyStringPrintf(dy, "%s:%d-%d %c %*dbps",chrom, s+1, e, mc->strand,sizeChars, mc->size);
             fprintf(f, "<A TITLE=\"%s\"> %*s </A> ", dy->string, srcChars, org);
 
             updateSummaryLine(summaryLine, referenceText + lineStart, mc->text + lineStart, size);
             blueCapWrite(f, mc->text + lineStart, size,
 			 (onlyDiff && mc != maf->components) ? referenceText + lineStart : NULL);
 	    fprintf(f, "\n");
 	    }
 	else
 	    {
 	    if (((mc->leftStatus == MAF_CONTIG_STATUS) && (mc->rightStatus == MAF_CONTIG_STATUS) )
 	    || ((mc->leftStatus == MAF_TANDEM_STATUS) && (mc->rightStatus == MAF_TANDEM_STATUS) )
 	    || ((mc->leftStatus == MAF_INSERT_STATUS) && (mc->rightStatus == MAF_INSERT_STATUS) )
 	    || ((mc->leftStatus == MAF_MISSING_STATUS) && (mc->rightStatus == MAF_MISSING_STATUS) ))
 		{
                 if (lineStart == 0)
 		    {
 		    int s = mc->start;
 		    int e = s + mc->rightLen;
 		    struct dyString *dy = dyStringNew(512);
 
 		    if (mc->strand == '-')
 			reverseIntRange(&s, &e, mc->srcSize);
 
 		    if ( hDbIsActive(dbOnly))
 			{
 			dyStringPrintf(dy, "%s Browser %s:%d-%d %c %d bps Unaligned",hOrganism(dbOnly),chrom, s+1, e, mc->strand, e-s);
 			linkToOtherBrowserTitle(dbOnly, chrom, s, e, dy->string);
 
 			fprintf(f,"B</A> ");
 			dyStringClear(dy);
 			}
 		    else
 			{
 			char *hubUrl = genarkUrl(dbOnly);
 			if (hubUrl != NULL)
 			    {
 			    dyStringPrintf(dy, "%s Browser %s:%d-%d %c %d bps Unaligned", org, chrom, s+1, e, mc->strand, e-s);
 			    fprintf(f, "<A TITLE=\"%s\" TARGET=\"_blank\" HREF=\"%s?genome=%s&hubUrl=%s&position=%s%%3A%d-%d\">B</A> ",
 				    dy->string, hgTracksName(), dbOnly, cgiEncode(hubUrl), cgiEncode(chrom), s+1, e);
 			    dyStringClear(dy);
 			    }
 			else
 			    fprintf(f,"  ");
 			}
 
                     if (hDbExists(dbOnly))
                         {
                         dyStringPrintf(dy, "Get %s DNA %s:%d-%d %c %d bps Unaligned",hOrganism(dbOnly),chrom, s+1, e, mc->strand, e-s);
 
                         printf("<A TITLE=\"%s\" TARGET=\"_blank\" HREF=\"%s?o=%d&g=getDna&i=%s&c=%s&l=%d&r=%d&db=%s%s\">D</A>  ", dy->string,  hgcName(),
                            s, cgiEncode(chrom),
                            chrom, s, e, dbOnly,revComp);
                         }
                     else
                         fprintf(f, "  ");
                     }
                 else
 		    fprintf(f, "     ");
 		initSummaryLine(summaryLine, size, ' ');
 		dyStringClear(dy);
 		dyStringPrintf(dy, "%s:%d-%d %c %*dbps",chrom, s+1, e, mc->strand,sizeChars, mc->size);
 		fprintf(f, "<A TITLE=\"%s\">%*s</A>  ", dy->string, srcChars, org);
 		ch = '-';
 		switch(mc->rightStatus)
 		    {
 		    case MAF_INSERT_STATUS:
 			ch = '=';
 			break;
 		    case MAF_MISSING_STATUS:
 			ch = 'N';
 			break;
 		    case MAF_TANDEM_STATUS:
 		    case MAF_CONTIG_STATUS:
 			ch = '-';
 			break;
 		    }
 		for(ii=lineStart; ii < lineEnd ; ii++)
 		    fputc(ch,f);
 		fprintf(f,"\n");
 		}
 	    }
 	}
 #ifdef ADDMATCHLINE
     if (lineStart == 0)
 	fprintf(f, "    %-*s %s\n", srcChars, "", summaryLine);
     else
 	fprintf(f, "%-*s %s\n", srcChars, "", summaryLine);
 #else
     fprintf(f, "\n");
 #endif
     }
 
 if (haveInserts)
     {
     fprintf(f, "<B>Inserts between block %d and %d in window</B>\n",blockNo, blockNo+1);
     for (mc = maf->components; mc != NULL; mc = mc->next)
 	{
 	char dbOnly[128], *chrom;
 	int s = mc->start + mc->size;
 	int e = s + mc->rightLen;
 	char *org;
 
 	if (mc->text == NULL)
 	    continue;
 
 	if (mc->strand == '-')
 	    reverseIntRange(&s, &e, mc->srcSize);
 
 	chrom = splitMafSrc(mc->src, dbOnly, sizeof(dbOnly), labelHash);
 
         if ((labelHash == NULL) || ((org = hashFindVal(labelHash, dbOnly)) == NULL))
             {
             if ((org = hOrganism(dbOnly)) == NULL)
                 org = dbOnly;
             }
 
 	if (mc->rightStatus == MAF_INSERT_STATUS)
 	    {
 	    char *revComp = "";
 	    if (hDbIsActive(dbOnly))
 		{
 		char strand = mc->strand;
 #ifdef REVERSESTRAND
 		if (cartCgiUsualBoolean(cart, COMPLEMENT_BASES_VAR, FALSE))
 		    strand = (strand == '+') ? '-' : '+';
 #endif
 		if (strand == '-') revComp = "&hgSeq.revComp=on";
 
 		linkToOtherBrowser(dbOnly, chrom, s, e);
 		fprintf(f,"B");
 		fprintf(f, "</A>");
 		fprintf(f, " ");
 
 		}
 	    else
 		{
 		char *hubUrl = genarkUrl(dbOnly);
 		if (hubUrl != NULL)
 		    {
 		    fprintf(f, "<A TARGET=\"_blank\" HREF=\"%s?genome=%s&hubUrl=%s&position=%s%%3A%d-%d\">B</A> ",
 			    hgTracksName(), dbOnly, cgiEncode(hubUrl), cgiEncode(chrom), s+1, e);
 		    }
 		else
 		    fprintf(f, "  ");
 		}
 
             if (hDbExists(dbOnly))
                 {
                 printf("<A TARGET=\"_blank\" HREF=\"%s?o=%d&g=getDna&i=%s&c=%s&l=%d&r=%d"
                        "&db=%s%s\">D</A> ",  hgcName(), s, cgiEncode(chrom), chrom,  s,
                        e, dbOnly,revComp);
                 }
             else
 		fprintf(f, "  ");
             fprintf(f, "%*s %dbp\n", srcChars, org,mc->rightLen);
 	    }
 	}
     fprintf(f, "\n");
     }
 freeMem(summaryLine);
 
 }
 
 static void mafLowerCase(struct mafAli *maf)
 /* Lower case letters in maf. */
 {
 struct mafComp *mc;
 for (mc = maf->components; mc != NULL; mc = mc->next)
     if (mc->size != 0)
 	tolowers(mc->text);
 }
 
 #ifdef ADDEXONCAPITAL
 static boolean findAliRange(char *ali, int aliSize, int start, int end,
 	int *retStart, int *retEnd)
 /* Convert start/end in sequence coordinates to alignment
  * coordinates (that include dashes).  Return FALSE if
  * no intersection. */
 {
 int i, baseIx=0;
 char c;
 int rStart = 0, rEnd = 0;
 
 if (start >= end)
     return FALSE;
 for (i=0; i<aliSize; ++i)
     {
     c = ali[i];
     if (c != '-')
         {
 	if (baseIx == start)
 	    rStart = i;
 	++baseIx;
 	if (baseIx == end)
 	    {
 	    rEnd = i+1;
 	    break;
 	    }
 	}
     }
 if (rStart >= rEnd)
     return FALSE;
 *retStart = rStart;
 *retEnd = rEnd;
 return TRUE;
 }
 
 static void capAliTextOnTrack(struct mafAli *maf,
                               char *db, char *chrom,
                               char *track, boolean onlyCds)
 /* Capitalize exons in alignment. */
 {
 int rowOffset;
 struct sqlConnection *conn = sqlConnect(db);
 struct mafComp *selfMc = maf->components, *mc;
 int start = selfMc->start;
 int end = start + selfMc->size;
 struct sqlResult *sr = hRangeQuery(conn, track, chrom, start, end,
 		NULL, &rowOffset);
 char **row;
 
 while ((row = sqlNextRow(sr)) != NULL)
     {
     struct genePred *gp = genePredLoad(row+rowOffset);
     int i;
     for (i=0; i<gp->exonCount; ++i)
         {
 	int s = gp->exonStarts[i];
 	int e = gp->exonEnds[i];
 	if (onlyCds)
 	    {
 	    if (s < gp->cdsStart) s = gp->cdsStart;
 	    if (e > gp->cdsEnd) e = gp->cdsEnd;
 	    }
 	if (s < start) s = start;
 	if (e > end) e = end;
 	if (findAliRange(selfMc->text, maf->textSize, s-start, e-start, &s, &e))
 	    {
 	    for (mc = maf->components; mc != NULL; mc = mc->next)
 		if (mc->text)
 		    toUpperN(mc->text + s, e-s);
 	    }
 	}
     genePredFree(&gp);
     }
 sqlFreeResult(&sr);
 sqlDisconnect(&conn);
 }
 
 static void capMafOnTrack(struct mafAli *maf, char *track, boolean onlyCds)
 /* Capitalize parts of maf that correspond to exons according
  * to given gene prediction track.  */
 {
 char dbOnly[64];
 char *chrom;
 struct mafComp *mc = maf->components;
 safecpy(dbOnly, sizeof(dbOnly), mc->src);
 chrom = chopPrefix(dbOnly);
 capAliTextOnTrack(maf, dbOnly, chrom, track, onlyCds);
 }
 #endif
 
 static struct mafAli *mafOrAxtLoadInRegion2(struct sqlConnection *conn,struct sqlConnection *conn2,
                                             struct trackDb *tdb, char *chrom, int start, int end,
                                             char *axtOtherDb, char *file)
 {
 if (axtOtherDb != NULL)
     {
     struct hash *qSizeHash = hChromSizeHash(axtOtherDb);
     struct mafAli *mafList = axtLoadAsMafInRegion(conn, tdb->table,
             chrom, start, end, database, axtOtherDb, hChromSize(database, chrom), qSizeHash);
     hashFree(&qSizeHash);
     return mafList;
     }
 else
     return mafLoadInRegion2(conn, conn2, tdb->table, chrom,
 	start, end, file);
 }
 
 
 #ifdef ADDEXONCAPITAL
 static char *codeAll[] = {
 	"coding",
 	"all",
 };
 #endif
 
 static char *showAll[] = {
         "all",
         "diff",
 };
 
 static void conservationStatsLink(struct trackDb *tdb,
                                     char *label, char *table)
 /* write link that to display statistics of phastCons table */
 {
 char *chrom = cartCgiUsualString(cart, "c", "chr7");
 printf("<A HREF=\"%s&g=%s&i=%s&c=%s&l=%d&r=%d&o=%d&db=%s"
         "&parentWigMaf=%s\" TARGET=\"_blank\">%s</A>",
         hgcPathAndSettings(), table, table, chrom,
 winStart, winEnd, winStart, database, tdb->track, label);
 }
 
+static struct mafAli *quickLiftClickMafs(struct trackDb *tdb, char *fileName)
+/* Load MAF blocks out of the assembly the track came from and map them onto the reference.
+ * The window is on the reference, and the blocks are not, so neither the coordinates nor
+ * the connections the caller has can be used as they stand. */
+{
+char *liftDb = trackDbSetting(tdb, "quickLiftDb");
+char *table = NULL;
+quickLiftResolveTable(tdb, trackHubSkipHubName(tdb->table), &table, &liftDb);
+char *quickLiftFile = trackDbSetting(tdb, "quickLiftUrl");
+boolean isBig = sameString(tdb->type, "bigMaf");
+
+struct hash *chainHash = newHash(8);
+struct quickLiftRange *range, *rangeList = quickLiftSourceRanges(quickLiftFile, seqName,
+    winStart, winEnd, chainHash);
+struct mafAli *srcList = NULL;
+
+for (range = rangeList; range != NULL; range = range->next)
+    {
+    struct mafAli *someMafs = NULL;
+    if (isBig)
+        {
+        char *bigFile = trackDbSetting(tdb, "bigDataUrl");
+        struct bbiFile *bbi = bigBedFileOpenAlias(bigFile, chromAliasFindAliases);
+        someMafs = bigMafLoadInRegion(bbi, range->chrom, range->start, range->end);
+        bbiFileClose(&bbi);
+        }
+    else
+        {
+        struct sqlConnection *srcConn = hAllocConn(liftDb);
+        struct sqlConnection *srcConn2 = hAllocConn(liftDb);
+        someMafs = mafLoadInRegion2(srcConn, srcConn2, table, range->chrom,
+            range->start, range->end, fileName);
+        hFreeConn(&srcConn);
+        hFreeConn(&srcConn2);
+        }
+    srcList = slCat(srcList, someMafs);
+    }
+
+// the reference row has to be named the way the code below goes looking for it
+char refSrc[512];
+safef(refSrc, sizeof refSrc, "%s.%s", hubConnectSkipHubPrefix(database), seqName);
+return quickLiftMafs(chainHash, srcList, liftDb, refSrc, hChromSize(database, seqName));
+}
+
 static void mafOrAxtClick2(struct sqlConnection *conn, struct sqlConnection *conn2, struct trackDb *tdb, char *axtOtherDb, char *fileName)
 /* Display details for MAF or AXT tracks. */
 {
 if (issueBotWarning)
     {
     char *ip = getenv("REMOTE_ADDR");
     botDelayMessage(ip, botDelayMillis);
     }
 if (winEnd - winStart > 30000)
     {
     printf("Zoom so that window is 30,000 bases or less to see alignments and conservation statistics\n");
     }
 else
     {
     struct mafAli *mafList = NULL, *maf, *subList = NULL;
     int aliIx = 0, realCount = 0;
     char dbChrom[64];
     char option[128];
     char *capTrack;
     struct consWiggle *consWig, *consWiggles;
     struct hash *speciesOffHash = NULL;
     char *speciesOrder = NULL;
     char *speciesTarget = trackDbSetting(tdb, SPECIES_TARGET_VAR);
     char buffer[1024];
     int useTarg = FALSE;
     int useIrowChains = FALSE;
     struct hash *labelHash = mafGetLabelHash(tdb);
 
     safef(option, sizeof(option), "%s.%s", tdb->track, MAF_CHAIN_VAR);
     if (cartCgiUsualBoolean(cart, option, FALSE) &&
 	trackDbSetting(tdb, "irows") != NULL)
 	    useIrowChains = TRUE;
 
     safef(buffer, sizeof(buffer), "%s.vis",tdb->track);
     if (useIrowChains)
 	{
 	if (!cartVarExists(cart, buffer) && (speciesTarget != NULL))
 	    useTarg = TRUE;
 	else
 	    {
 	    char *val;
 
 	    val = cartUsualString(cart, buffer, "useCheck");
             useTarg = sameString("useTarg",val);
             }
         }
 
-    if (sameString(tdb->type, "bigMaf"))
+    if (quickLiftIsLifted(tdb))
+        mafList = quickLiftClickMafs(tdb, fileName);
+    else if (sameString(tdb->type, "bigMaf"))
         {
         char *fileName = trackDbSetting(tdb, "bigDataUrl");
         struct bbiFile *bbi =  bigBedFileOpenAlias(fileName, chromAliasFindAliases);
         mafList = bigMafLoadInRegion(bbi, seqName, winStart, winEnd);
         }
     else
         mafList = mafOrAxtLoadInRegion2(conn,conn2, tdb, seqName, winStart, winEnd,
                                         axtOtherDb, fileName);
     safef(dbChrom, sizeof(dbChrom), "%s.%s", hubConnectSkipHubPrefix(database), seqName);
 
     safef(option, sizeof(option), "%s.speciesOrder", tdb->track);
     speciesOrder = cartUsualString(cart, option, NULL);
     if (speciesOrder == NULL)
 	speciesOrder = trackDbSetting(tdb, "speciesOrder");
 
     int speciesCt = 0;
     char *species[2048];
     struct mafComp **newOrder;
     if (speciesOrder)
         {
         // chop up speciesOrder string and store it away, checking for errors along the way
         speciesCt = chopLine(cloneString(speciesOrder), species);
         newOrder = needMem((speciesCt + 1) * sizeof (struct mafComp *));
 
         int ii;
         struct hash *nameHash = newHash(5);
         for(ii=0; ii < speciesCt; ii++)
             {
             if (hashLookup(nameHash, species[ii]))
                 errAbort("speciesOrder contains %s more than once.", species[ii]);
             hashStore(nameHash, species[ii]);
             }
         }
 
     for (maf = mafList; maf != NULL; maf = maf->next)
         {
         int mcCount = 0;
         struct mafComp *mc;
         struct mafAli *subset;
         struct mafComp *nextMc;
 
         /* remove empty components and configured off components
          * from MAF, and ignore
          * the entire MAF if all components are empty
          * (solely for gap annotation) */
 
         if (!useTarg)
             {
             for (mc = maf->components->next; mc != NULL; mc = nextMc)
 		{
 		char buf[64];
                 char *organism;
 		mafSrcDb(mc->src, buf, sizeof buf);
                 organism = hOrganism(buf);
                 if (!organism)
                     organism = buf;
 		nextMc = mc->next;
 		safef(option, sizeof(option), "%s.%s", tdb->track, buf);
 		if (!cartUsualBoolean(cart, option, TRUE))
 		    {
 		    if (speciesOffHash == NULL)
 			speciesOffHash = newHash(4);
 		    hashStoreName(speciesOffHash, organism);
 		    }
 		if (!cartUsualBoolean(cart, option, TRUE))
 		    slRemoveEl(&maf->components, mc);
 		else
 		    mcCount++;
 		}
 	    }
         if (mcCount == 0)
             continue;
 
 	if (speciesCt)
 	    {
 	    struct mafComp *mcThis;
 	    int i;
 
 	    mcCount = 0;
 	    speciesCt = chopLine(cloneString(speciesOrder), species);
 	    newOrder = needMem((speciesCt + 1) * sizeof (struct mafComp *));
 	    newOrder[mcCount++] = maf->components;
 
 	    for (i = 0; i < speciesCt; i++)
 		{
 		if ((mcThis = mafMayFindCompSpecies(maf, species[i], '.')) == NULL)
 		    continue;
                 if (mcThis == maf->components)
                     errAbort("Reference species (%s) shouldn't be in speciesOrder in trackDb", species[i]);
 		newOrder[mcCount++] = mcThis;
 		}
 
 	    maf->components = NULL;
 	    for (i = 0; i < mcCount; i++)
 		{
 		newOrder[i]->next = 0;
 		slAddHead(&maf->components, newOrder[i]);
 		}
 
 	    slReverse(&maf->components);
 	    }
 	subset = mafSubsetE(maf, dbChrom, winStart, winEnd, TRUE);
 	if (subset != NULL)
 	    {
 	    /* Reformat MAF if needed so that sequence from current
 	     * database is the first component and on the
 	     * plus strand. */
 	    mafMoveComponentToTop(subset, dbChrom);
 	    if (subset->components->strand == '-')
 		mafFlipStrand(subset);
 	    subset->score = mafScoreMultiz(subset);
 	    slAddHead(&subList, subset);
 	    ++realCount;
 	    }
 	}
     slReverse(&subList);
     mafAliFreeList(&mafList);
     if (subList != NULL)
 	{
 	char *showVarName = "hgc.showMultiBase";
 	char *showVarVal = cartUsualString(cart, showVarName, "all");
 	boolean onlyDiff = sameWord(showVarVal, "diff");
 #ifdef ADDEXONCAPITAL
 	char *codeVarName = "hgc.multiCapCoding";
 	char *codeVarVal = cartUsualString(cart, codeVarName, "coding");
 	boolean onlyCds = sameWord(codeVarVal, "coding");
 #endif
         /* add links for conservation score statistics */
         consWiggles = wigMafWiggles(database, tdb);
         int wigCount = slCount(consWiggles);
         if (wigCount == 1)
             {
             conservationStatsLink(tdb, "Conservation score statistics", consWiggles->table);
             }
         else if (wigCount > 1)
             {
             /* multiple wiggles. List all that have been turned on with
              * checkboxes */
 
             /* Scan for cart variables -- do any exist, are any turned on ? */
             boolean wigSet = FALSE;
             boolean wigOn = FALSE;
             for (consWig = consWiggles; consWig != NULL;
                         consWig = consWig->next)
                 {
                 char *wigVarSuffix = NULL;
                 (void)wigMafWiggleVar(tdb->track, consWig, &wigVarSuffix);
                 if (cartVarExistsAnyLevel(cart, tdb, FALSE, wigVarSuffix))
                     {
                     wigSet = TRUE;
                     if (cartBooleanClosestToHome(cart, tdb, FALSE, wigVarSuffix))
                         wigOn = TRUE;
                     }
                 }
             /* If there are no cart vars, turn on the first (default) wig */
             if (!wigSet)
                 {
                 char *prefix = tdb->track; // use when setting things to the cart
                 if (tdbIsContainerChild(tdb))
                     prefix = tdbGetContainer(tdb)->track;
 
                 cartSetBoolean(cart, wigMafWiggleVar(prefix, consWiggles, NULL), TRUE);
                 wigOn = TRUE;
                 }
             if (wigOn)
                 {
                 boolean first = TRUE;
                 for (consWig = consWiggles; consWig != NULL;
                             consWig = consWig->next)
                     {
                     if (first)
                         {
                         printf("Conservation score statistics:");
                         first = FALSE;
                         }
                     char *wigVarSuffix = NULL;
                     (void)wigMafWiggleVar(tdb->track, consWig, &wigVarSuffix);
                     if (cartUsualBooleanClosestToHome(cart, tdb, FALSE, wigVarSuffix,FALSE))
                         {
                         printf("&nbsp;&nbsp;");
                         subChar(consWig->uiLabel, '_', ' ');
                         conservationStatsLink(tdb,
                             consWig->uiLabel, consWig->table);
                         }
                     }
                 }
             }
         puts("</P>\n");
 
         /* no alignment to display when in visibilities where only wiggle is shown */
         char *vis = cartOptionalString(cart, tdb->track);
         if (vis)
             {
             enum trackVisibility tv = hTvFromStringNoAbort(vis);
             if (tv == tvSquish || tv == tvDense)
                 return;
             }
 
 #ifdef ADDEXONCAPITAL
 	puts("<FORM ACTION=\"../cgi-bin/hgc\" NAME=\"gpForm\" METHOD=\"GET\">");
 	cartSaveSession(cart);
 	cgiContinueHiddenVar("g");
 	cgiContinueHiddenVar("c");
 	cgiContinueHiddenVar("i");
 	cgiContinueHiddenVar("o");
 	cgiContinueHiddenVar("t");
 	cgiContinueHiddenVar("l");
 	cgiContinueHiddenVar("r");
 	printf("Capitalize ");
         cgiMakeDropListFull(codeVarName, codeAll, codeAll,
 	    ArraySize(codeAll), codeVarVal, "change", autoSubmit);
 	printf("exons based on ");
         capTrack = genePredDropDown(cart, trackHash,
                                        "gpForm", "hgc.multiCapTrack");
 #endif
 	printf("show ");
         cgiMakeDropListFull(showVarName, showAll, showAll,
 	    ArraySize(showAll), showVarVal, "change", autoSubmit);
 	printf("bases");
 	printf("<BR>\n");
 	printf("</FORM>\n");
 
 #ifdef REVERSESTRAND
         /* notify if bases are complemented (hgTracks is on reverse strand) */
         if (cartCgiUsualBoolean(cart, COMPLEMENT_BASES_VAR, FALSE))
             puts("<EM>Alignment displayed on reverse strand</EM><BR>");
 #endif
 	puts("Place cursor over species for alignment detail. Click on 'B' to link to browser ");
 	puts("for aligned species, click on 'D' to get DNA for aligned species.<BR>");
 
 	printf("<TT><PRE>");
 
         /* notify if species removed from alignment */
         if (speciesOffHash) 
             {
             char *species;
             struct hashCookie hc = hashFirst(speciesOffHash);
             puts("<B>Components not displayed:</B> ");
             while ((species = hashNextName(&hc)) != NULL)
                 printf("%s ", species);
             puts("<BR>");
             }
 
 
 	for (maf = subList; maf != NULL; maf = maf->next)
 	    {
 	    mafLowerCase(maf);
 #ifdef ADDEXONCAPITAL
 	    if (capTrack != NULL)
                 capMafOnTrack(maf, capTrack, onlyCds);
 #endif
             printf("<B>Alignment block %d of %d in window, %d - %d, %d bps </B>\n",
                    ++aliIx,realCount,maf->components->start + 1,
                    maf->components->start + maf->components->size, maf->components->size);
             mafPrettyOut(stdout, maf, 70,onlyDiff, aliIx, labelHash);
             }
 	mafAliFreeList(&subList);
 	}
     else
 	{
         printf("No multiple alignment in browser window");
 	}
     printf("</PRE></TT>");
     }
 }
 
 static void mafOrAxtClick(struct sqlConnection *conn, struct trackDb *tdb, char *axtOtherDb)
 {
 struct sqlConnection *conn2 = NULL;
 if (!(isHubTrack(tdb->track) || trackHubDatabase(database)))
     conn2 = hAllocConn(database);
 // MAF file location is optionally in trackDb
 char *mafFile = hashFindVal(tdb->settingsHash, "mafFile");
 
 mafOrAxtClick2(conn, conn2, tdb, axtOtherDb, mafFile);
 
 hFreeConn(&conn2);
 }
 
 void customMafClick(struct sqlConnection *conn, struct sqlConnection *conn2,
     struct trackDb *tdb)
 {
 struct hash *settings = tdb->settingsHash;
 char *fileName;
 if ((fileName = hashFindVal(settings, "mafFile")) == NULL)
     errAbort("cannot find custom maf file setting");
 mafOrAxtClick2(conn, conn2, tdb, NULL, fileName);
 }
 
 void genericMafClick(struct sqlConnection *conn, struct trackDb *tdb,
                      char *item, int start)
 /* Display details for MAF tracks. */
 {
 mafOrAxtClick(conn, tdb, NULL);
 }
 
 void genericAxtClick(struct sqlConnection *conn, struct trackDb *tdb,
                      char *item, int start, char *otherDb)
 /* Display details for AXT tracks. */
 {
 mafOrAxtClick(conn, tdb, otherDb);
 }