63f915b4c381054700db900e0f999c499e1054ca
braney
  Thu Dec 18 15:02:49 2014 -0800
upgrade to new version of HAL.
diff --git src/hg/hgTables/hal.c src/hg/hgTables/hal.c
index c6eb310..62bca50 100644
--- src/hg/hgTables/hal.c
+++ src/hg/hgTables/hal.c
@@ -46,42 +46,50 @@
 return NULL;
 }
 
 void doHalMaf(struct trackDb *parentTrack, char *table, struct sqlConnection *conn)
 /* Output regions as MAF.  maf tables look bed-like enough for
  * cookedBedsOnRegions to handle intersections. */
 {
 #ifdef USE_HAL
 struct region *region = NULL, *regionList = getRegions();
 struct trackDb *tdb;
 
 if ((tdb = findTrackDb(parentTrack, table)) == NULL)
     errAbort("cannot find track named %s under %s\n", table, parentTrack->table);
 char *fileName = trackDbSetting(tdb, "bigDataUrl");
 char *otherSpecies = trackDbSetting(tdb, "otherSpecies");
-int handle = halOpenLOD(fileName);
+char *errString;
+int handle = halOpenLOD(fileName, &errString);
+if (handle < 0)
+    errAbort("HAL open error: %s\n", errString);
 
-struct hal_species_t *speciesList = halGetSpecies(handle);
+struct hal_species_t *speciesList = halGetSpecies(handle, &errString);
+
+if (speciesList == NULL)
+    errAbort("HAL get species error: %s\n", errString);
 
 for(; speciesList; speciesList = speciesList->next)
     {
     if  (sameString(speciesList->name, otherSpecies))
 	break;
     }
 if (speciesList == NULL)
     errAbort("cannot find species %s in hal file %s\n",
 	otherSpecies, fileName);
 
 speciesList->next = NULL;
 
 textOpen();
 
 for (region = regionList; region != NULL; region = region->next)
     {
-    halGetMAF(stdout, handle, speciesList,
+    if (halGetMAF(stdout, handle, speciesList,
 		trackHubSkipHubName(database), region->chrom,
-		region->start, region->end, FALSE);
+		region->start, region->end, FALSE, &errString) < 0 )
+	errAbort("HAL get MAF error: %s\n", errString);
+
     }
 #else // USE_HAL
 errAbort("hgTables not compiled with HAL support.");
 #endif // USE_HAL
 }