b622d147b7dbac52dbf3ba26928cd18e02d42bd8
braney
  Sat Feb 26 12:34:37 2022 -0800
add support for using a bigBed as the chromAlias file

diff --git src/hg/hgTables/hic.c src/hg/hgTables/hic.c
index ab36720..cdbdb79 100644
--- src/hg/hgTables/hic.c
+++ src/hg/hgTables/hic.c
@@ -357,36 +357,35 @@
     hPrintf("<TH>%s</TH>", col->name);
     ++colIx;
     }
 hPrintf("</TR>\n");
 
 struct hicMeta *fileInfo = NULL;
 char *errMsg = hicLoadHeader(fileName, &fileInfo, database);
 
 if (errMsg != NULL)
     {
     warn("%s", errMsg);
     }
 else
     {
     /* Print sample lines. */
-    struct hash *chromAliasHash = chromAliasMakeLookupTable(database);
     char *chrName = fileInfo->chromNames[1]; // Skip 0, which is "All"
-    struct chromAlias *a = hashFindVal(chromAliasHash, chrName);
+    char *nativeChrom = chromAliasFindNative(chrName);
     char *ucscChrName = NULL;
-    if (a != NULL)
-        ucscChrName = a->chrom;
+    if (nativeChrom != NULL)
+        ucscChrName = nativeChrom;
     else
         ucscChrName = chrName;
 
     int maxRes = atoi(fileInfo->resolutions[0]);
 
     struct interact *sampleList = NULL, *sample = NULL;
     errMsg = hicLoadData(fileInfo, maxRes, "NONE", ucscChrName, 0, hChromSize(database, ucscChrName),
             ucscChrName, 0, hChromSize(database, ucscChrName), &sampleList);
     if (errMsg != NULL)
         warn("%s", errMsg);
     slSort(&sampleList, &hicCompare);
     char *row[INTERACT_NUM_COLS];
     char numBuf[HIC_NUM_BUF_SIZE];
     int count = 0;
     for (sample=sampleList; sample != NULL && count < 10; sample = sample->next, count++)