c1e66c5c9d45f0965156318e2782714ee93b04ab
braney
  Mon Oct 19 16:08:32 2015 -0700
more work on bigMaf.  Works in hgc and hgTables now.  #15935

diff --git src/hg/hgTables/maf.c src/hg/hgTables/maf.c
index 711c2aa..42162d1 100644
--- src/hg/hgTables/maf.c
+++ src/hg/hgTables/maf.c
@@ -5,43 +5,44 @@
 
 #include "common.h"
 #include "hash.h"
 #include "linefile.h"
 #include "dystring.h"
 #include "portable.h"
 #include "obscure.h"
 #include "jksql.h"
 #include "cheapcgi.h"
 #include "cart.h"
 #include "web.h"
 #include "trackDb.h"
 #include "maf.h"
 #include "hgMaf.h"
 #include "hgTables.h"
+#include "hubConnect.h"
 
 
 boolean isMafTable(char *database, struct trackDb *track, char *table)
 /* Return TRUE if table is maf. */
 {
 if (track == NULL)
     return FALSE;
 if (isEmpty(track->type))
     return FALSE;
 
 if (sameString(track->table, table))
     {
-    if (startsWithWord("maf",track->type) || startsWithWord("wigMaf",track->type))
+    if (startsWithWord("maf",track->type) || startsWithWord("wigMaf",track->type) || startsWithWord("bigMaf",track->type))
         return TRUE;
     }
 else
     {
     struct slRef *tdbRefList = trackDbListGetRefsToDescendantLeaves(track->subtracks);
     struct slRef *tdbRef;
     for (tdbRef = tdbRefList; tdbRef != NULL; tdbRef = tdbRef->next)
         {
 	struct trackDb *childTdb = tdbRef->val;
         if(sameString(childTdb->table, table))
             {
             if (startsWithWord("maf",childTdb->type) || startsWithWord("wigMaf",childTdb->type))
                 return TRUE;
             break;
             }
@@ -75,43 +76,49 @@
 	/* this shouldn't happen */
 	printf("cannot find custom track file %s\n", mafFile);
 	return;
 	}
     }
 
 mafWriteStart(stdout, NULL);
 for (region = regionList; region != NULL; region = region->next)
     {
     struct bed *bedList = cookedBedList(conn, table, region, lm, NULL);
     struct bed *bed = NULL;
     for (bed = bedList;  bed != NULL;  bed = bed->next)
 	{
 	struct mafAli *mafList = NULL, *maf = NULL;
 	char dbChrom[64];
-	safef(dbChrom, sizeof(dbChrom), "%s.%s", database, bed->chrom);
+	safef(dbChrom, sizeof(dbChrom), "%s.%s", hubConnectSkipHubPrefix(database), bed->chrom);
 	/* For MAF, we clip to viewing window (region) instead of showing
 	 * entire items that happen to overlap the window/region, which is
 	 * what we get from cookedBedList. */
 	if (bed->chromStart < region->start)
 	    bed->chromStart = region->start;
 	if (bed->chromEnd > region->end)
 	    bed->chromEnd = region->end;
 	if (bed->chromStart >= bed->chromEnd)
 	    continue;
 	if (ct == NULL)
 	    {
-	    if (mafFile != NULL)
+            if (isBigBed(database, table, curTrack, ctLookupName))
+                {
+                char *fileName = trackDbSetting(track, "bigDataUrl");
+                struct bbiFile *bbi = bigBedFileOpen(fileName);
+                mafList = bigMafLoadInRegion(bbi, bed->chrom, bed->chromStart, bed->chromEnd);
+                }
+	    else if (mafFile != NULL)
 		mafList = mafLoadInRegion2(conn, conn, table,
 			bed->chrom, bed->chromStart, bed->chromEnd, mafFile);
 	    else
 		mafList = mafLoadInRegion(conn, table, bed->chrom,
 					  bed->chromStart, bed->chromEnd);
 	    }
 	else
 	    mafList = mafLoadInRegion2(ctConn, ctConn2, ct->dbTableName,
 		    bed->chrom, bed->chromStart, bed->chromEnd, mafFile);
 	for (maf = mafList; maf != NULL; maf = maf->next)
 	    {
 	    struct mafAli *subset = mafSubset(maf, dbChrom,
 					      bed->chromStart, bed->chromEnd);
 	    if (subset != NULL)
 		{